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BMRB: 25188

2MTV

Solution Structure of the YTH Domain of YT521-B in complex with N6-Methyladenosine containing RNA

Authors

Theler, D., Dominguez, C., Blatter, M., Boudet, J., Allain, F.H.-T.

Assembly

YTH Domain of YT521-B in complex with N6-Methyladenosine containing RNA

Entity

1. YTH Domain of YT521-B in complex with N6-Methyladenosine containing RNA, entity 1 (polymer, Thiol state: all free), 156 monomers, 17480.95 Da Detail

QTSKLKSVLQ DARFFLIKSN NHENVSLAKA KGVWSTLPVN EKKLNLAFRS ARSVILIFSV RESGKFQGFA RLSSESHHGG SPIHWVLPAG MSAKMLGGVF KIDWICRREL PFTKSAHLTN PWNEHKPVKI GRDGQEIELE CGTQLCLLFP PDESID

2. RNA (5'-R(*UP*GP*(6MA)P*CP*AP*C)-3') (polymer, Thiol state: not present), 6 monomers, 1952.189 Da Detail

UGXCAC

Total weight

19433.139 Da

Max. entity weight

17480.95 Da

Source organism

Rattus norvegicus

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete1

Sequence coverage: 95.1 %, Completeness: 89.1 %, Completeness (bb): 88.6 % Detail

Polymer type: polypeptide(L) polyribonucleotide

	Total	¹H	¹³C	¹⁵N
All	89.1 % (1732 of 1944)	89.9 % (916 of 1019)	87.1 % (661 of 759)	93.4 % (155 of 166)
Backbone	88.6 % (864 of 975)	86.4 % (298 of 345)	88.0 % (424 of 482)	95.9 % (142 of 148)
Sidechain	90.7 % (1010 of 1114)	91.7 % (618 of 674)	89.8 % (379 of 422)	72.2 % (13 of 18)
Aromatic	69.6 % (128 of 184)	77.2 % (71 of 92)	61.6 % (53 of 86)	66.7 % (4 of 6)
Methyl	98.8 % (166 of 168)	100.0 % (84 of 84)	97.6 % (82 of 84)

1. entity 1

QTSKLKSVLQ DARFFLIKSN NHENVSLAKA KGVWSTLPVN EKKLNLAFRS ARSVILIFSV RESGKFQGFA RLSSESHHGG SPIHWVLPAG MSAKMLGGVF KIDWICRREL PFTKSAHLTN PWNEHKPVKI GRDGQEIELE CGTQLCLLFP PDESID

2. RNA (5'-R(*UP*GP*(6MA)P*CP*AP*C)-3')

UGXCAC

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Concentration
1	entity_1	[U-99% 13C; U-99% 15N]	0.8 mM
2	RNA (5'-R(UPGP(6MA)PCPAPC)-3')	natural abundance	0.8 mM
3	sodium phosphate	natural abundance	25 mM
4	sodium chloride	natural abundance	25 mM
5	beta-mercaptoethanol	natural abundance	10 mM
6	D2O	natural abundance	10 %
7	H2O	natural abundance	90 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Concentration
8	entity_1	[U-99% 13C; U-99% 15N]	0.8 mM
9	RNA (5'-R(UPGP(6MA)PCPAPC)-3')	natural abundance	0.8 mM
10	sodium phosphate	natural abundance	25 mM
11	sodium chloride	natural abundance	25 mM
12	beta-mercaptoethanol	natural abundance	10 mM
13	D2O	natural abundance	100 %

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Concentration
14	entity_1	[U-99% 15N]	0.8 mM
15	RNA (5'-R(UPGP(6MA)PCPAPC)-3')	natural abundance	0.8 mM
16	sodium phosphate	natural abundance	25 mM
17	sodium chloride	natural abundance	25 mM
18	beta-mercaptoethanol	natural abundance	10 mM
19	D2O	natural abundance	100 %

Chem. Shift Complete2

Sequence coverage: 27.2 %, Completeness: 55.7 %, Completeness (bb): 56.8 % Detail

Polymer type: polypeptide(L) polyribonucleotide

	Total	¹H	¹³C	¹⁵N
All	55.7 % (2164 of 3888)	56.0 % (1141 of 2038)	54.9 % (834 of 1518)	56.9 % (189 of 332)
Backbone	56.8 % (1107 of 1950)	56.7 % (391 of 690)	56.0 % (540 of 964)	59.5 % (176 of 296)
Sidechain	55.4 % (1234 of 2228)	55.6 % (750 of 1348)	55.8 % (471 of 844)	36.1 % (13 of 36)
Aromatic	43.5 % (160 of 368)	49.5 % (91 of 184)	37.8 % (65 of 172)	33.3 % (4 of 12)
Methyl	66.4 % (223 of 336)	66.7 % (112 of 168)	66.1 % (111 of 168)

1. entity 1

QTSKLKSVLQ DARFFLIKSN NHENVSLAKA KGVWSTLPVN EKKLNLAFRS ARSVILIFSV RESGKFQGFA RLSSESHHGG SPIHWVLPAG MSAKMLGGVF KIDWICRREL PFTKSAHLTN PWNEHKPVKI GRDGQEIELE CGTQLCLLFP PDESID

2. RNA (5'-R(*UP*GP*(6MA)P*CP*AP*C)-3')

UGXCAC

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Concentration
1	entity_1	[U-99% 13C; U-99% 15N]	0.8 mM
2	RNA (5'-R(UPGP(6MA)PCPAPC)-3')	natural abundance	0.8 mM
3	sodium phosphate	natural abundance	25 mM
4	sodium chloride	natural abundance	25 mM
5	beta-mercaptoethanol	natural abundance	10 mM
6	D2O	natural abundance	10 %
7	H2O	natural abundance	90 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Concentration
8	entity_1	[U-99% 13C; U-99% 15N]	0.8 mM
9	RNA (5'-R(UPGP(6MA)PCPAPC)-3')	natural abundance	0.8 mM
10	sodium phosphate	natural abundance	25 mM
11	sodium chloride	natural abundance	25 mM
12	beta-mercaptoethanol	natural abundance	10 mM
13	D2O	natural abundance	100 %

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Concentration
14	entity_1	[U-99% 15N]	0.8 mM
15	RNA (5'-R(UPGP(6MA)PCPAPC)-3')	natural abundance	0.8 mM
16	sodium phosphate	natural abundance	25 mM
17	sodium chloride	natural abundance	25 mM
18	beta-mercaptoethanol	natural abundance	10 mM
19	D2O	natural abundance	100 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.05 ppm, Outliers: 2 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.05 ppm, Outliers: 2 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.04 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.34 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2MTV, Strand ID: A Detail

Release date

2015-09-30

Citation

Solution structure of the YTH domain in complex with N6-methyladenosine RNA: a reader of methylated RNA
Theler, D., Dominguez, C., Blatter, M., Boudet, J., Allain, F.H.-T.
Nucleic Acids Res. (2014), 42, 13911-13919, PubMed 25389274 , DOI 10.1093/nar/gku1116 , Abstract

Related entities 1. YTH Domain of YT521-B in complex with N6-Methyladenosine containing RNA, entity 1, : 1 : 105 : 98 entities Detail

Experiments performed 19 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Concentration
1	entity_1	[U-99% 13C; U-99% 15N]	0.8 mM
2	RNA (5'-R(UPGP(6MA)PCPAPC)-3')	natural abundance	0.8 mM
3	sodium phosphate	natural abundance	25 mM
4	sodium chloride	natural abundance	25 mM
5	beta-mercaptoethanol	natural abundance	10 mM
6	D2O	natural abundance	10 %
7	H2O	natural abundance	90 %

2 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Concentration
1	entity_1	[U-99% 13C; U-99% 15N]	0.8 mM
2	RNA (5'-R(UPGP(6MA)PCPAPC)-3')	natural abundance	0.8 mM
3	sodium phosphate	natural abundance	25 mM
4	sodium chloride	natural abundance	25 mM
5	beta-mercaptoethanol	natural abundance	10 mM
6	D2O	natural abundance	10 %
7	H2O	natural abundance	90 %

3 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Concentration
1	entity_1	[U-99% 13C; U-99% 15N]	0.8 mM
2	RNA (5'-R(UPGP(6MA)PCPAPC)-3')	natural abundance	0.8 mM
3	sodium phosphate	natural abundance	25 mM
4	sodium chloride	natural abundance	25 mM
5	beta-mercaptoethanol	natural abundance	10 mM
6	D2O	natural abundance	10 %
7	H2O	natural abundance	90 %

4 2D 1H-1H TOCSY

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Concentration
14	entity_1	[U-99% 15N]	0.8 mM
15	RNA (5'-R(UPGP(6MA)PCPAPC)-3')	natural abundance	0.8 mM
16	sodium phosphate	natural abundance	25 mM
17	sodium chloride	natural abundance	25 mM
18	beta-mercaptoethanol	natural abundance	10 mM
19	D2O	natural abundance	100 %

5 2D 1H-1H NOESY

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Concentration
14	entity_1	[U-99% 15N]	0.8 mM
15	RNA (5'-R(UPGP(6MA)PCPAPC)-3')	natural abundance	0.8 mM
16	sodium phosphate	natural abundance	25 mM
17	sodium chloride	natural abundance	25 mM
18	beta-mercaptoethanol	natural abundance	10 mM
19	D2O	natural abundance	100 %

6 3D CBCA(CO)NH

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Concentration
1	entity_1	[U-99% 13C; U-99% 15N]	0.8 mM
2	RNA (5'-R(UPGP(6MA)PCPAPC)-3')	natural abundance	0.8 mM
3	sodium phosphate	natural abundance	25 mM
4	sodium chloride	natural abundance	25 mM
5	beta-mercaptoethanol	natural abundance	10 mM
6	D2O	natural abundance	10 %
7	H2O	natural abundance	90 %

7 3D HNCO

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Concentration
1	entity_1	[U-99% 13C; U-99% 15N]	0.8 mM
2	RNA (5'-R(UPGP(6MA)PCPAPC)-3')	natural abundance	0.8 mM
3	sodium phosphate	natural abundance	25 mM
4	sodium chloride	natural abundance	25 mM
5	beta-mercaptoethanol	natural abundance	10 mM
6	D2O	natural abundance	10 %
7	H2O	natural abundance	90 %

8 3D HNCA

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Concentration
1	entity_1	[U-99% 13C; U-99% 15N]	0.8 mM
2	RNA (5'-R(UPGP(6MA)PCPAPC)-3')	natural abundance	0.8 mM
3	sodium phosphate	natural abundance	25 mM
4	sodium chloride	natural abundance	25 mM
5	beta-mercaptoethanol	natural abundance	10 mM
6	D2O	natural abundance	10 %
7	H2O	natural abundance	90 %

9 3D HNCACB

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Concentration
1	entity_1	[U-99% 13C; U-99% 15N]	0.8 mM
2	RNA (5'-R(UPGP(6MA)PCPAPC)-3')	natural abundance	0.8 mM
3	sodium phosphate	natural abundance	25 mM
4	sodium chloride	natural abundance	25 mM
5	beta-mercaptoethanol	natural abundance	10 mM
6	D2O	natural abundance	10 %
7	H2O	natural abundance	90 %

10 3D H(CCO)NH

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Concentration
1	entity_1	[U-99% 13C; U-99% 15N]	0.8 mM
2	RNA (5'-R(UPGP(6MA)PCPAPC)-3')	natural abundance	0.8 mM
3	sodium phosphate	natural abundance	25 mM
4	sodium chloride	natural abundance	25 mM
5	beta-mercaptoethanol	natural abundance	10 mM
6	D2O	natural abundance	10 %
7	H2O	natural abundance	90 %

11 3D 1H-15N NOESY

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Concentration
1	entity_1	[U-99% 13C; U-99% 15N]	0.8 mM
2	RNA (5'-R(UPGP(6MA)PCPAPC)-3')	natural abundance	0.8 mM
3	sodium phosphate	natural abundance	25 mM
4	sodium chloride	natural abundance	25 mM
5	beta-mercaptoethanol	natural abundance	10 mM
6	D2O	natural abundance	10 %
7	H2O	natural abundance	90 %

12 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Concentration
1	entity_1	[U-99% 13C; U-99% 15N]	0.8 mM
2	RNA (5'-R(UPGP(6MA)PCPAPC)-3')	natural abundance	0.8 mM
3	sodium phosphate	natural abundance	25 mM
4	sodium chloride	natural abundance	25 mM
5	beta-mercaptoethanol	natural abundance	10 mM
6	D2O	natural abundance	10 %
7	H2O	natural abundance	90 %

13 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Concentration
1	entity_1	[U-99% 13C; U-99% 15N]	0.8 mM
2	RNA (5'-R(UPGP(6MA)PCPAPC)-3')	natural abundance	0.8 mM
3	sodium phosphate	natural abundance	25 mM
4	sodium chloride	natural abundance	25 mM
5	beta-mercaptoethanol	natural abundance	10 mM
6	D2O	natural abundance	10 %
7	H2O	natural abundance	90 %

14 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Concentration
14	entity_1	[U-99% 15N]	0.8 mM
15	RNA (5'-R(UPGP(6MA)PCPAPC)-3')	natural abundance	0.8 mM
16	sodium phosphate	natural abundance	25 mM
17	sodium chloride	natural abundance	25 mM
18	beta-mercaptoethanol	natural abundance	10 mM
19	D2O	natural abundance	100 %

15 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Concentration
14	entity_1	[U-99% 15N]	0.8 mM
15	RNA (5'-R(UPGP(6MA)PCPAPC)-3')	natural abundance	0.8 mM
16	sodium phosphate	natural abundance	25 mM
17	sodium chloride	natural abundance	25 mM
18	beta-mercaptoethanol	natural abundance	10 mM
19	D2O	natural abundance	100 %

16 3D C(CO)NH

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Concentration
1	entity_1	[U-99% 13C; U-99% 15N]	0.8 mM
2	RNA (5'-R(UPGP(6MA)PCPAPC)-3')	natural abundance	0.8 mM
3	sodium phosphate	natural abundance	25 mM
4	sodium chloride	natural abundance	25 mM
5	beta-mercaptoethanol	natural abundance	10 mM
6	D2O	natural abundance	10 %
7	H2O	natural abundance	90 %

17 2D 1H -1H NOESY 13C F1-filtered F2-filtered

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Concentration
8	entity_1	[U-99% 13C; U-99% 15N]	0.8 mM
9	RNA (5'-R(UPGP(6MA)PCPAPC)-3')	natural abundance	0.8 mM
10	sodium phosphate	natural abundance	25 mM
11	sodium chloride	natural abundance	25 mM
12	beta-mercaptoethanol	natural abundance	10 mM
13	D2O	natural abundance	100 %

18 3D 1H-13C NOESY 13C F1-edited F3-filtered

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Concentration
8	entity_1	[U-99% 13C; U-99% 15N]	0.8 mM
9	RNA (5'-R(UPGP(6MA)PCPAPC)-3')	natural abundance	0.8 mM
10	sodium phosphate	natural abundance	25 mM
11	sodium chloride	natural abundance	25 mM
12	beta-mercaptoethanol	natural abundance	10 mM
13	D2O	natural abundance	100 %

19 2D 1H -1H NOESY 13C15N F2-filtered

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Concentration
1	entity_1	[U-99% 13C; U-99% 15N]	0.8 mM
2	RNA (5'-R(UPGP(6MA)PCPAPC)-3')	natural abundance	0.8 mM
3	sodium phosphate	natural abundance	25 mM
4	sodium chloride	natural abundance	25 mM
5	beta-mercaptoethanol	natural abundance	10 mM
6	D2O	natural abundance	10 %
7	H2O	natural abundance	90 %

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25188_2mtv.nef
Input source #2: Coordindates	2mtv.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	True (see coodinates for details)
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
2:2:G:O3'	2:3:6MZ:P	unknown	unknown	n/a
2:3:6MZ:O3'	2:4:C:P	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	3	6MZ	N6-METHYLADENOSINE-5'-MONOPHOSPHATE	Assigned chemical shifts, Distance restraints, Torsion angle restraints, Coordinates

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

---350-----360-------370-------380-------390-------400-------410-------420-------430-------440------
QTSKLKSVLQDARFFLIKSNNHENVSLAKAKGVWSTLPVNEKKLNLAFRSARSVILIFSVRESGKFQGFARLSSESHHGGSPIHWVLPAGMSAKMLGGVF
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
QTSKLKSVLQDARFFLIKSNNHENVSLAKAKGVWSTLPVNEKKLNLAFRSARSVILIFSVRESGKFQGFARLSSESHHGGSPIHWVLPAGMSAKMLGGVF
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

-450-------460-------470-------480-------490-------500--
KIDWICRRELPFTKSAHLTNPWNEHKPVKIGRDGQEIELECGTQLCLLFPPDESID
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
KIDWICRRELPFTKSAHLTNPWNEHKPVKIGRDGQEIELECGTQLCLLFPPDESID
-------110-------120-------130-------140-------150------

Entity_assembly_ID (NMR): B vs Auth_asym_ID (model): B

------
UGXCAC
||||||
UGXCAC

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	156	0	0	100.0
B	B	6	0	0	100.0

Content subtype: combined_25188_2mtv.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	2		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1723		98.7 (chain: A, length: 156)
2	Assigned chemical shifts	assigned_chem_shift_list_2	Warning	79		100.0 (chain: B, length: 6)
1	Distance restraints	DYANA/DIANA_distance_constraints_4	OK	6540 (1)	noe	98.1 (chain: A, length: 156), 66.7 (chain: B, length: 6)
2	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	140 (1)	hbond	33.3 (chain: A, length: 156)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_2	OK	237 (237)	.	92.9 (chain: A, length: 156), 50.0 (chain: B, length: 6)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 156, Sequence coverage: 98.7%
- Total number of assignments
  - ¹H chemical shifts: 917
  - ¹³C chemical shifts: 651
  - ¹⁵N chemical shifts: 155
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- Tautomeric state of HIS
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A
Saveframe: assigned_chem_shift_list_2
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: B, Chain length: 6, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 47
  - ¹³C chemical shifts: 32
- Completeness of assignments
  - Entity_assemble_ID: B
- Histogram of normalized assigned chemical shifts

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	974	917	94.1
¹³C chemical shifts	725	651	89.8
¹⁵N chemical shifts	172	155	90.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	315	298	94.6
¹³C chemical shifts	312	278	89.1
¹⁵N chemical shifts	148	140	94.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	659	619	93.9
¹³C chemical shifts	413	373	90.3
¹⁵N chemical shifts	24	15	62.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	86	86	100.0
¹³C chemical shifts	86	84	97.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	81	69	85.2
¹³C chemical shifts	77	49	63.6
¹⁵N chemical shifts	4	4	100.0

Comp_index_ID	Comp_ID
3	6MZ

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	45	37	82.2
¹³C chemical shifts	34	27	79.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	30	28	93.3
¹³C chemical shifts	25	18	72.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	15	9	60.0
¹³C chemical shifts	9	9	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	3	3	100.0
¹³C chemical shifts	3	3	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_4
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 156, Sequence coverage: 98.1%
  - Entity_assembly_ID: B, Chain length: 6, Sequence coverage: 66.7%
- Total number of restraints: 6472
- Weight of restraints: 1.0 (6472)
- Potential type of restraints: upper-bound-parabolic (6472)
- Range of distance target values: 2.23, 6.0 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map
- Saveframe: DYANA/DIANA_distance_constraints_3
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 156, Sequence coverage: 33.3%
  - Total number of restraints: 140
  - Weight of restraints: 1.0 (140)
  - Potential type of restraints: upper-bound-parabolic (140)
  - Range of distance target values: 1.9, 3.4 (Å)
  - Histogram of distance target values
  - Histogram of discrepancy in distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
      None
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 156, Sequence coverage: 92.9%
  - Entity_assembly_ID: B, Chain length: 6, Sequence coverage: 50.0%
- Total number of restraints: 237
- Total number of restraints per polymer type: 237
- Weight of restraints: 1.0 (237)
- Potential type of restraints: square-well-parabolic (237)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B

Keywords YTH, m6A

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BMRB: 25188

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Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. YTH Domain of YT521-B in complex with N6-Methyladenosine containing RNA, entity 1, : 1 : 105 : 98 entities Detail

Experiments performed 19 experiments Detail

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NMR combined restraints 6 contents Detail