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Found 1 Document (1.234 seconds)

BMRB: 25497

2MZR

NMR structure of the RRM1 domain of Hrb1

Authors

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

Assembly

RRM1 domain of Hrb1

Entity

1. RRM1 domain of Hrb1 (polymer, Thiol state: not present), 95 monomers, 10919.81 Da Detail

GSARELDSTY EEKVNRNYSN SIFVGNLTYD STPEDLTEFF SQIGKVVRAD IITSRGHHRG MGTVEFTNSD DVDRAIRQYD GAFFMDRKIF VRQDN

Formula weight

10919.81 Da

Source organism

Saccharomyces cerevisiae

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.9 %, Completeness: 87.6 %, Completeness (bb): 89.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	87.6 % (957 of 1092)	86.2 % (488 of 566)	88.9 % (376 of 423)	90.3 % (93 of 103)
Backbone	89.6 % (509 of 568)	88.8 % (174 of 196)	90.3 % (251 of 278)	89.4 % (84 of 94)
Sidechain	86.6 % (530 of 612)	84.9 % (314 of 370)	88.8 % (207 of 233)	100.0 % (9 of 9)
Aromatic	80.0 % (88 of 110)	87.3 % (48 of 55)	72.7 % (40 of 55)
Methyl	100.0 % (86 of 86)	100.0 % (43 of 43)	100.0 % (43 of 43)

1. RRM1

GSARELDSTY EEKVNRNYSN SIFVGNLTYD STPEDLTEFF SQIGKVVRAD IITSRGHHRG MGTVEFTNSD DVDRAIRQYD GAFFMDRKIF VRQDN

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	RRM1	[U-100% 13C; U-100% 15N]	0.2 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	RRM1	[U-100% 13C; U-100% 15N]	0.2 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: 0.0 ppm, Outliers: 3 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: 0.0 ppm, Outliers: 3 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: 0.0 ppm, Outliers: 2 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: 0.11 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2MZR, 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

Entries sharing articles BMRB: 3 entries Detail

  BMRB: 25496 released on 2015-11-29
    Title NMR structure of the RRM3 domain of Gbp2
  BMRB: 25498 released on 2015-11-29
    Title NMR structure of the RRM2 domain of Hrb1
  BMRB: 25499 released on 2015-11-29
    Title NMR structure of the RRM3 domain of Hrb1

Related entities 1. RRM1 domain of Hrb1, : 1 : 2 : 121 entities Detail

Interaction partners 1. RRM1 domain of Hrb1, : 42 interactors Detail

More details for 42 interactors identified by 9 citations

Experiments performed 8 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	RRM1	[U-100% 13C; U-100% 15N]	0.2 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	RRM1	[U-100% 13C; U-100% 15N]	0.2 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	RRM1	[U-100% 13C; U-100% 15N]	0.2 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 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	RRM1	[U-100% 13C; U-100% 15N]	0.2 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 %

5 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	RRM1	[U-100% 13C; U-100% 15N]	0.2 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 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	RRM1	[U-100% 13C; U-100% 15N]	0.2 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 %

7 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	RRM1	[U-100% 13C; U-100% 15N]	0.2 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 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	RRM1	[U-100% 13C; U-100% 15N]	0.2 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_25497_2mzr.nef
Input source #2: Coordindates	2mzr.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

------150-------160-------170-------180-------190-------200-------210-------220-------230------
GSARELDSTYEEKVNRNYSNSIFVGNLTYDSTPEDLTEFFSQIGKVVRADIITSRGHHRGMGTVEFTNSDDVDRAIRQYDGAFFMDRKIFVRQDN
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSARELDSTYEEKVNRNYSNSIFVGNLTYDSTPEDLTEFFSQIGKVVRADIITSRGHHRGMGTVEFTNSDDVDRAIRQYDGAFFMDRKIFVRQDN
--------10--------20--------30--------40--------50--------60--------70--------80--------90-----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	95	0	0	100.0

Content subtype: combined_25497_2mzr.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	946		95.8 (chain: A, length: 95)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	1148 (1)	noe	78.9 (chain: A, length: 95)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 95, Sequence coverage: 95.8%
- Total number of assignments
  - ¹H chemical shifts: 486
  - ¹³C chemical shifts: 371
  - ¹⁵N chemical shifts: 89
- Completeness of assignments
  - Entity_assemble_ID: A
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	566	486	85.9
¹³C chemical shifts	423	371	87.7
¹⁵N chemical shifts	112	89	79.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	196	172	87.8
¹³C chemical shifts	190	162	85.3
¹⁵N chemical shifts	94	80	85.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	370	314	84.9
¹³C chemical shifts	233	209	89.7
¹⁵N chemical shifts	18	9	50.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	45	45	100.0
¹³C chemical shifts	45	45	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	55	48	87.3
¹³C chemical shifts	55	40	72.7

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 95, Sequence coverage: 78.9%
- Total number of restraints: 1148
- Weight of restraints: 1.0 (1148)
- Potential type of restraints: upper-bound-parabolic (1148)
- Range of distance target values: 2.24, 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 (1.234 seconds)

BMRB: 25497

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Entries sharing articles BMRB: 3 entries Detail

Related entities 1. RRM1 domain of Hrb1, : 1 : 2 : 121 entities Detail

Interaction partners 1. RRM1 domain of Hrb1, : 42 interactors Detail

Experiments performed 8 experiments Detail

Instrument

Sample

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Sample

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Sample

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Sample

NMR combined restraints 3 contents Detail