BMRBj - BMREntryMaster

Found 1 Document (1.535 seconds)

BMRB: 25499

2MZT

NMR structure of the RRM3 domain of Hrb1

Authors

Martinez-Lumbreras, S., Seraphin, B., Perez-Canadillas, J.

Assembly

RRM3 domain of Hrb1

Entity

1. RRM3 domain of Hrb1 (polymer, Thiol state: all free), 100 monomers, 11095.10 Da Detail

GSVNEEARKF TENVVGGGER NRLIYCSNLP FSTAKSDLYD LFETIGKVNN AELRYDSKGA PTGIAVVEYD NVDDADVCIE RLNNYNYGGC DLDISYAKRL

Formula weight

11095.1 Da

Source organism

Saccharomyces cerevisiae

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 86.2 %, Completeness (bb): 84.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	86.2 % (962 of 1116)	95.8 % (552 of 576)	70.4 % (304 of 432)	98.1 % (106 of 108)
Backbone	84.6 % (504 of 596)	97.6 % (202 of 207)	70.8 % (206 of 291)	98.0 % (96 of 98)
Sidechain	89.9 % (549 of 611)	94.9 % (350 of 369)	81.5 % (189 of 232)	100.0 % (10 of 10)
Aromatic	51.2 % (44 of 86)	100.0 % (43 of 43)	2.3 % (1 of 43)
Methyl	100.0 % (106 of 106)	100.0 % (53 of 53)	100.0 % (53 of 53)

1. RRM3

GSVNEEARKF TENVVGGGER NRLIYCSNLP FSTAKSDLYD LFETIGKVNN AELRYDSKGA PTGIAVVEYD NVDDADVCIE RLNNYNYGGC DLDISYAKRL

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	RRM3	[U-100% 13C; U-100% 15N]	0.8 mM
2	potassium phosphate	natural abundance	25 mM
3	sodium chloride	natural abundance	25 mM
4	DTT	natural abundance	0.1 mM
5	D2O	natural abundance	10 %
6	H2O	natural abundance	90 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
7	RRM3	[U-100% 13C; U-100% 15N]	0.8 mM
8	potassium phosphate	natural abundance	25 mM
9	sodium chloride	natural abundance	25 mM
10	DTT	natural abundance	0.1 mM
11	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: -0.16 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: -0.16 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: -0.25 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Release date

2015-11-29

Citation

Gbp2 interacts with THO/TREX through a novel type of RRM domain
Martinez-Lumbreras, S., Taverniti, V., Zorrilla, S., Seraphin, B., Perez-Canadillas, J.
Nucleic Acids Res. (2015), 44, 437-448, PubMed 26602689 , DOI 10.1093/nar/gkv1303 , Abstract

Related entities 1. RRM3 domain of Hrb1, : 1 : 2 : 88 entities Detail

Interaction partners 1. RRM3 domain of Hrb1, : 42 interactors Detail

More details for 42 interactors identified by 9 citations

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	RRM3	[U-100% 13C; U-100% 15N]	0.8 mM
2	potassium phosphate	natural abundance	25 mM
3	sodium chloride	natural abundance	25 mM
4	DTT	natural abundance	0.1 mM
5	D2O	natural abundance	10 %
6	H2O	natural abundance	90 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
7	RRM3	[U-100% 13C; U-100% 15N]	0.8 mM
8	potassium phosphate	natural abundance	25 mM
9	sodium chloride	natural abundance	25 mM
10	DTT	natural abundance	0.1 mM
11	D2O	natural abundance	100 %

3 2D 1H-1H TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	RRM3	[U-100% 13C; U-100% 15N]	0.8 mM
2	potassium phosphate	natural abundance	25 mM
3	sodium chloride	natural abundance	25 mM
4	DTT	natural abundance	0.1 mM
5	D2O	natural abundance	10 %
6	H2O	natural abundance	90 %

4 2D 1H-1H TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
7	RRM3	[U-100% 13C; U-100% 15N]	0.8 mM
8	potassium phosphate	natural abundance	25 mM
9	sodium chloride	natural abundance	25 mM
10	DTT	natural abundance	0.1 mM
11	D2O	natural abundance	100 %

5 2D 1H-1H NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	RRM3	[U-100% 13C; U-100% 15N]	0.8 mM
2	potassium phosphate	natural abundance	25 mM
3	sodium chloride	natural abundance	25 mM
4	DTT	natural abundance	0.1 mM
5	D2O	natural abundance	10 %
6	H2O	natural abundance	90 %

6 2D 1H-1H NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
7	RRM3	[U-100% 13C; U-100% 15N]	0.8 mM
8	potassium phosphate	natural abundance	25 mM
9	sodium chloride	natural abundance	25 mM
10	DTT	natural abundance	0.1 mM
11	D2O	natural abundance	100 %

7 3D HNCO

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	RRM3	[U-100% 13C; U-100% 15N]	0.8 mM
2	potassium phosphate	natural abundance	25 mM
3	sodium chloride	natural abundance	25 mM
4	DTT	natural abundance	0.1 mM
5	D2O	natural abundance	10 %
6	H2O	natural abundance	90 %

8 3D HNCA

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	RRM3	[U-100% 13C; U-100% 15N]	0.8 mM
2	potassium phosphate	natural abundance	25 mM
3	sodium chloride	natural abundance	25 mM
4	DTT	natural abundance	0.1 mM
5	D2O	natural abundance	10 %
6	H2O	natural abundance	90 %

9 3D HNCACB

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	RRM3	[U-100% 13C; U-100% 15N]	0.8 mM
2	potassium phosphate	natural abundance	25 mM
3	sodium chloride	natural abundance	25 mM
4	DTT	natural abundance	0.1 mM
5	D2O	natural abundance	10 %
6	H2O	natural abundance	90 %

10 3D HBHA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	RRM3	[U-100% 13C; U-100% 15N]	0.8 mM
2	potassium phosphate	natural abundance	25 mM
3	sodium chloride	natural abundance	25 mM
4	DTT	natural abundance	0.1 mM
5	D2O	natural abundance	10 %
6	H2O	natural abundance	90 %

11 3D HCCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
7	RRM3	[U-100% 13C; U-100% 15N]	0.8 mM
8	potassium phosphate	natural abundance	25 mM
9	sodium chloride	natural abundance	25 mM
10	DTT	natural abundance	0.1 mM
11	D2O	natural abundance	100 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_25499_2mzt.nef
Input source #2: Coordindates	2mzt.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

---360-------370-------380-------390-------400-------410-------420-------430-------440-------450----
GSVNEEARKFTENVVGGGERNRLIYCSNLPFSTAKSDLYDLFETIGKVNNAELRYDSKGAPTGIAVVEYDNVDDADVCIERLNNYNYGGCDLDISYAKRL
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSVNEEARKFTENVVGGGERNRLIYCSNLPFSTAKSDLYDLFETIGKVNNAELRYDSKGAPTGIAVVEYDNVDDADVCIERLNNYNYGGCDLDISYAKRL
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	100	0	0	100.0

Content subtype: combined_25499_2mzt.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	960		100.0 (chain: A, length: 100)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	3720 (1)	noe	99.0 (chain: A, length: 100)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 100, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 559
  - ¹³C chemical shifts: 288
  - ¹⁵N chemical shifts: 113
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
374	ARG	HH11	7.023
374	ARG	HH12	6.913
374	ARG	NH1	69.345
380	CYS	HG	1.541
387	THR	HG1	6.179
398	THR	HG1	5.433
416	THR	HG1	4.803
432	CYS	HG	2.089
449	SER	HG	6.257

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	576	551	95.7
¹³C chemical shifts	432	288	66.7
¹⁵N chemical shifts	114	112	98.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	207	204	98.6
¹³C chemical shifts	200	100	50.0
¹⁵N chemical shifts	98	96	98.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	369	347	94.0
¹³C chemical shifts	232	188	81.0
¹⁵N chemical shifts	16	16	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	53	53	100.0
¹³C chemical shifts	53	53	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	43	43	100.0
¹³C chemical shifts	43	0	0.0

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 100, Sequence coverage: 99.0%
- Total number of restraints: 3708
- Weight of restraints: 1.0 (3708)
- Potential type of restraints: upper-bound-parabolic (3708)
- Range of distance target values: 2.21, 6.0 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Keywords Hrb1, RNA binding domain, RRM, THO/TREX

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Found 1 Document (1.535 seconds)

BMRB: 25499

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. RRM3 domain of Hrb1, : 1 : 2 : 88 entities Detail

Interaction partners 1. RRM3 domain of Hrb1, : 42 interactors Detail

Experiments performed 11 experiments Detail

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NMR combined restraints 3 contents Detail