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Found 1 Document (0.694 seconds)

BMRB: 25041

2MQO

Structural Investigation of hnRNP L bound to RNA

Authors

Blatter, M., Allain, F.

Assembly

First RNA Recognition Motif Domain of hnRNP L bound to CACACA RNA

Entity

1. First RNA Recognition Motif Domain of hnRNP L bound to CACACA RNA, entity 1 (polymer, Thiol state: all free), 105 monomers, 11375.48 Da Detail

GENYDDPHKT PASPVVHIRG LIDGVVEADL VEALQEFGPI SYVVVMPKKR QALVEFEDVL GACNAVNYAA DNQIYIAGHP AFVNYSTSQK ISRPGDSDDS RSVNS

2. RNA (5'-R(*CP*AP*CP*AP*CP*A)-3') (polymer, Thiol state: not present), 6 monomers, 1921.178 Da Detail

CACACA

Total weight

13296.658 Da

Max. entity weight

11375.48 Da

Source organism

Rattus norvegicus

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete1

Sequence coverage: 94.6 %, Completeness: 79.1 %, Completeness (bb): 72.0 % Detail

Polymer type: polypeptide(L) polyribonucleotide

	Total	¹H	¹³C	¹⁵N
All	79.1 % (995 of 1258)	86.8 % (566 of 652)	65.9 % (328 of 498)	93.5 % (101 of 108)
Backbone	72.0 % (491 of 682)	80.1 % (197 of 246)	59.2 % (200 of 338)	95.9 % (94 of 98)
Sidechain	89.2 % (601 of 674)	90.9 % (369 of 406)	87.2 % (225 of 258)	70.0 % (7 of 10)
Aromatic	62.3 % (66 of 106)	77.4 % (41 of 53)	47.2 % (25 of 53)
Methyl	100.0 % (120 of 120)	100.0 % (60 of 60)	100.0 % (60 of 60)

1. entity 1

GENYDDPHKT PASPVVHIRG LIDGVVEADL VEALQEFGPI SYVVVMPKKR QALVEFEDVL GACNAVNYAA DNQIYIAGHP AFVNYSTSQK ISRPGDSDDS RSVNS

2. RNA (5'-R(*CP*AP*CP*AP*CP*A)-3')

CACACA

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310.15 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	entity_1	[U-100% 15N]	2 mM
2	RNA (5'-R(CPAPCPAPCPA)-3')	natural abundance	2 mM
3	sodium chloride	natural abundance	60 mM
4	sodium phosphate	natural abundance	40 mM
5	DTT	natural abundance	1 mM
6	D2O	natural abundance	10 %
7	H2O	natural abundance	90 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310.15 K, pH 6.5

#	Name	Isotope labeling	Concentration
8	entity_1	[U-100% 13C; U-100% 15N]	2 mM
9	RNA (5'-R(CPAPCPAPCPA)-3')	natural abundance	2 mM
10	sodium chloride	natural abundance	60 mM
11	sodium phosphate	natural abundance	40 mM
12	DTT	natural abundance	1 mM
13	D2O	natural abundance	10 %
14	H2O	natural abundance	90 %

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 310.15 K, pH 6.5

#	Name	Isotope labeling	Concentration
15	entity_1	[U-100% 15N]	2 mM
16	RNA (5'-R(CPAPCPAPCPA)-3')	natural abundance	2 mM
17	sodium chloride	natural abundance	60 mM
18	sodium phosphate	natural abundance	40 mM
19	DTT	natural abundance	1 mM
20	D2O	natural abundance	100 %

Sample #4

Solvent system 100% D2O, Pressure 1 atm, Temperature 310.15 K, pH 6.5

#	Name	Isotope labeling	Concentration
21	entity_1	[U-100% 13C; U-100% 15N]	2 mM
22	RNA (5'-R(CPAPCPAPCPA)-3')	natural abundance	2 mM
23	sodium chloride	natural abundance	60 mM
24	sodium phosphate	natural abundance	40 mM
25	DTT	natural abundance	1 mM
26	D2O	natural abundance	100 %

Chem. Shift Complete2

Sequence coverage: 20.7 %, Completeness: 47.7 %, Completeness (bb): 46.3 % Detail

Polymer type: polypeptide(L) polyribonucleotide

	Total	¹H	¹³C	¹⁵N
All	47.7 % (1199 of 2516)	51.3 % (669 of 1304)	41.6 % (414 of 996)	53.7 % (116 of 216)
Backbone	46.3 % (631 of 1364)	52.6 % (259 of 492)	38.9 % (263 of 676)	55.6 % (109 of 196)
Sidechain	50.2 % (677 of 1348)	50.5 % (410 of 812)	50.4 % (260 of 516)	35.0 % (7 of 20)
Aromatic	42.5 % (90 of 212)	50.0 % (53 of 106)	34.9 % (37 of 106)
Methyl	57.5 % (138 of 240)	58.3 % (70 of 120)	56.7 % (68 of 120)

1. entity 1

GENYDDPHKT PASPVVHIRG LIDGVVEADL VEALQEFGPI SYVVVMPKKR QALVEFEDVL GACNAVNYAA DNQIYIAGHP AFVNYSTSQK ISRPGDSDDS RSVNS

2. RNA (5'-R(*CP*AP*CP*AP*CP*A)-3')

CACACA

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310.15 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	entity_1	[U-100% 15N]	2 mM
2	RNA (5'-R(CPAPCPAPCPA)-3')	natural abundance	2 mM
3	sodium chloride	natural abundance	60 mM
4	sodium phosphate	natural abundance	40 mM
5	DTT	natural abundance	1 mM
6	D2O	natural abundance	10 %
7	H2O	natural abundance	90 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310.15 K, pH 6.5

#	Name	Isotope labeling	Concentration
8	entity_1	[U-100% 13C; U-100% 15N]	2 mM
9	RNA (5'-R(CPAPCPAPCPA)-3')	natural abundance	2 mM
10	sodium chloride	natural abundance	60 mM
11	sodium phosphate	natural abundance	40 mM
12	DTT	natural abundance	1 mM
13	D2O	natural abundance	10 %
14	H2O	natural abundance	90 %

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 310.15 K, pH 6.5

#	Name	Isotope labeling	Concentration
15	entity_1	[U-100% 15N]	2 mM
16	RNA (5'-R(CPAPCPAPCPA)-3')	natural abundance	2 mM
17	sodium chloride	natural abundance	60 mM
18	sodium phosphate	natural abundance	40 mM
19	DTT	natural abundance	1 mM
20	D2O	natural abundance	100 %

Sample #4

Solvent system 100% D2O, Pressure 1 atm, Temperature 310.15 K, pH 6.5

#	Name	Isotope labeling	Concentration
21	entity_1	[U-100% 13C; U-100% 15N]	2 mM
22	RNA (5'-R(CPAPCPAPCPA)-3')	natural abundance	2 mM
23	sodium chloride	natural abundance	60 mM
24	sodium phosphate	natural abundance	40 mM
25	DTT	natural abundance	1 mM
26	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: -0.21 ppm, Outliers: 1 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: -0.21 ppm, Outliers: 1 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: -0.05 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Release date

2015-12-20

Related entities 1. First RNA Recognition Motif Domain of hnRNP L bound to CACACA RNA, entity 1, : 1 : 6 : 1 : 78 entities Detail

Experiments performed 7 experiments Detail

1 3D 1H-15N NOESY

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310.15 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	entity_1	[U-100% 15N]	2 mM
2	RNA (5'-R(CPAPCPAPCPA)-3')	natural abundance	2 mM
3	sodium chloride	natural abundance	60 mM
4	sodium phosphate	natural abundance	40 mM
5	DTT	natural abundance	1 mM
6	D2O	natural abundance	10 %
7	H2O	natural abundance	90 %

2 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310.15 K, pH 6.5

#	Name	Isotope labeling	Concentration
8	entity_1	[U-100% 13C; U-100% 15N]	2 mM
9	RNA (5'-R(CPAPCPAPCPA)-3')	natural abundance	2 mM
10	sodium chloride	natural abundance	60 mM
11	sodium phosphate	natural abundance	40 mM
12	DTT	natural abundance	1 mM
13	D2O	natural abundance	10 %
14	H2O	natural abundance	90 %

3 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310.15 K, pH 6.5

#	Name	Isotope labeling	Concentration
8	entity_1	[U-100% 13C; U-100% 15N]	2 mM
9	RNA (5'-R(CPAPCPAPCPA)-3')	natural abundance	2 mM
10	sodium chloride	natural abundance	60 mM
11	sodium phosphate	natural abundance	40 mM
12	DTT	natural abundance	1 mM
13	D2O	natural abundance	10 %
14	H2O	natural abundance	90 %

4 2D 1H-1H NOESY

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 310.15 K, pH 6.5

#	Name	Isotope labeling	Concentration
15	entity_1	[U-100% 15N]	2 mM
16	RNA (5'-R(CPAPCPAPCPA)-3')	natural abundance	2 mM
17	sodium chloride	natural abundance	60 mM
18	sodium phosphate	natural abundance	40 mM
19	DTT	natural abundance	1 mM
20	D2O	natural abundance	100 %

5 2D 1H-1H TOCSY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 310.15 K, pH 6.5

#	Name	Isotope labeling	Concentration
15	entity_1	[U-100% 15N]	2 mM
16	RNA (5'-R(CPAPCPAPCPA)-3')	natural abundance	2 mM
17	sodium chloride	natural abundance	60 mM
18	sodium phosphate	natural abundance	40 mM
19	DTT	natural abundance	1 mM
20	D2O	natural abundance	100 %

6 3D F3-filtered-F2-edited NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 310.15 K, pH 6.5

#	Name	Isotope labeling	Concentration
21	entity_1	[U-100% 13C; U-100% 15N]	2 mM
22	RNA (5'-R(CPAPCPAPCPA)-3')	natural abundance	2 mM
23	sodium chloride	natural abundance	60 mM
24	sodium phosphate	natural abundance	40 mM
25	DTT	natural abundance	1 mM
26	D2O	natural abundance	100 %

7 2D F2-filtered NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 310.15 K, pH 6.5

#	Name	Isotope labeling	Concentration
21	entity_1	[U-100% 13C; U-100% 15N]	2 mM
22	RNA (5'-R(CPAPCPAPCPA)-3')	natural abundance	2 mM
23	sodium chloride	natural abundance	60 mM
24	sodium phosphate	natural abundance	40 mM
25	DTT	natural abundance	1 mM
26	D2O	natural abundance	100 %

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25041_2mqo.nef
Input source #2: Coordindates	2mqo.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	None
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)

None

Non-standard residues

None

Sequence alignments

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

-----90-------100-------110-------120-------130-------140-------150-------160-------170-------180---
GENYDDPHKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYSTSQKISRPGDSDDS
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GENYDDPHKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYSTSQKISRPGDSDDS
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

-----
RSVNS
|||||
RSVNS
-----

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

------
CACACA
||||||
CACACA

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	105	0	0	100.0
B	B	6	0	0	100.0

Content subtype: combined_25041_2mqo.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	988		99.0 (chain: A, length: 105)
2	Assigned chemical shifts	shifts2	OK	90		100.0 (chain: B, length: 6)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	4160 (1)	noe	99.0 (chain: A, length: 105), 100.0 (chain: B, length: 6)
2	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	128 (1)	hbond	40.0 (chain: A, length: 105)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_4	OK	152 (152)	.	87.6 (chain: A, length: 105), 100.0 (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: 105, Sequence coverage: 99.0%
- Total number of assignments
  - ¹H chemical shifts: 565
  - ¹³C chemical shifts: 321
  - ¹⁵N chemical shifts: 102
- 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: shifts2
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: B, Chain length: 6, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 48
  - ¹³C chemical shifts: 42
- 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	598	565	94.5
¹³C chemical shifts	456	321	70.4
¹⁵N chemical shifts	112	102	91.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	210	196	93.3
¹³C chemical shifts	210	96	45.7
¹⁵N chemical shifts	98	94	95.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	388	369	95.1
¹³C chemical shifts	246	225	91.5
¹⁵N chemical shifts	14	8	57.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	61	61	100.0
¹³C chemical shifts	61	61	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	41	41	100.0
¹³C chemical shifts	41	25	61.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	54	48	88.9
¹³C chemical shifts	42	42	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	36	36	100.0
¹³C chemical shifts	30	30	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	18	12	66.7
¹³C chemical shifts	12	12	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	6	6	100.0
¹³C chemical shifts	6	6	100.0

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 105, Sequence coverage: 99.0%
  - Entity_assembly_ID: B, Chain length: 6, Sequence coverage: 100.0%
- Total number of restraints: 4116
- Weight of restraints: 1.0 (4116)
- Potential type of restraints: upper-bound-parabolic (4116)
- Range of distance target values: 2.8, 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: 105, Sequence coverage: 40.0%
  - Total number of restraints: 128
  - Weight of restraints: 1.0 (128)
  - Potential type of restraints: upper-bound-parabolic (128)
  - Range of distance target values: 1.8, 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_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 105, Sequence coverage: 87.6%
  - Entity_assembly_ID: B, Chain length: 6, Sequence coverage: 100.0%
- Total number of restraints: 152
- Total number of restraints per polymer type: 152
- Weight of restraints: 1.0 (152)
- Potential type of restraints: square-well-parabolic (152)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B

Keywords Protein/RNA Complex, RRM

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Found 1 Document (0.694 seconds)

BMRB: 25041

Sample #1

Sample #2

Sample #3

Sample #4

Sample #1

Sample #2

Sample #3

Sample #4

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. First RNA Recognition Motif Domain of hnRNP L bound to CACACA RNA, entity 1, : 1 : 6 : 1 : 78 entities Detail

Experiments performed 7 experiments Detail

Instrument

Sample

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Sample

Instrument

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NMR combined restraints 6 contents Detail