BMRBj - BMREntryMaster

Found 1 Document (1.138 seconds)

BMRB: 25498

2MZS

NMR structure of the RRM2 domain of Hrb1

Authors

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

Assembly

RRM2 domain of Hrb1

Entity

1. RRM2 domain of Hrb1 (polymer, Thiol state: all free), 99 monomers, 10689.53 Da Detail

GSEVIVKNLP ASVNWQALKD IFKECGNVAH ADVELDGDGV STGSGTVSFY DIKDLHRAIE KYNGYSIEGN VLDVKSKESV HNHSDGDDVD IPMDDSPVN

Formula weight

10689.53 Da

Source organism

Saccharomyces cerevisiae

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 99.0 %, Completeness: 95.5 %, Completeness (bb): 96.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	95.5 % (1029 of 1077)	94.7 % (523 of 552)	96.0 % (403 of 420)	98.1 % (103 of 105)
Backbone	96.6 % (568 of 588)	97.1 % (198 of 204)	95.8 % (276 of 288)	97.9 % (94 of 96)
Sidechain	95.0 % (550 of 579)	93.4 % (325 of 348)	97.3 % (216 of 222)	100.0 % (9 of 9)
Aromatic	97.2 % (70 of 72)	100.0 % (36 of 36)	94.3 % (33 of 35)	100.0 % (1 of 1)
Methyl	100.0 % (106 of 106)	100.0 % (53 of 53)	100.0 % (53 of 53)

1. RRM2

GSEVIVKNLP ASVNWQALKD IFKECGNVAH ADVELDGDGV STGSGTVSFY DIKDLHRAIE KYNGYSIEGN VLDVKSKESV HNHSDGDDVD IPMDDSPVN

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	RRM2	[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	RRM2	[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: -0.13 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: -0.13 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: 0.01 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: 0.15 ppm, Outliers: 7 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2MZS, 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: 25497 released on 2015-11-29
    Title NMR structure of the RRM1 domain of Hrb1
  BMRB: 25499 released on 2015-11-29
    Title NMR structure of the RRM3 domain of Hrb1

Related entities 1. RRM2 domain of Hrb1, : 1 : 2 : 68 entities Detail

Interaction partners 1. RRM2 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	RRM2	[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	RRM2	[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	RRM2	[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	RRM2	[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 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	RRM2	[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 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	RRM2	[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	RRM2	[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	RRM2	[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_25498_2mzs.nef
Input source #2: Coordindates	2mzs.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

260-----270-------280-------290-------300-------310-------320-------330-------340-------350--------
GSEVIVKNLPASVNWQALKDIFKECGNVAHADVELDGDGVSTGSGTVSFYDIKDLHRAIEKYNGYSIEGNVLDVKSKESVHNHSDGDDVDIPMDDSPVN
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSEVIVKNLPASVNWQALKDIFKECGNVAHADVELDGDGVSTGSGTVSFYDIKDLHRAIEKYNGYSIEGNVLDVKSKESVHNHSDGDDVDIPMDDSPVN
--------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	99	0	0	100.0

Content subtype: combined_25498_2mzs.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1038		99.0 (chain: A, length: 99)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	1048 (1)	noe	87.9 (chain: A, length: 99)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 99, Sequence coverage: 99.0%
- Total number of assignments
  - ¹³C chemical shifts: 409
  - ¹H chemical shifts: 527
  - 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	420	409	97.4
¹H chemical shifts	552	527	95.5
¹⁵N chemical shifts	106	102	96.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	198	189	95.5
¹H chemical shifts	204	198	97.1
¹⁵N chemical shifts	96	92	95.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	222	220	99.1
¹H chemical shifts	348	329	94.5
¹⁵N chemical shifts	10	10	100.0

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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	35	33	94.3
¹H chemical shifts	36	36	100.0
¹⁵N chemical shifts	1	1	100.0

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 99, Sequence coverage: 87.9%
- Total number of restraints: 1048
- Weight of restraints: 1.0 (1048)
- Potential type of restraints: upper-bound-parabolic (1048)
- Range of distance target values: 2.32, 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 (1.138 seconds)

BMRB: 25498

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. RRM2 domain of Hrb1, : 1 : 2 : 68 entities Detail

Interaction partners 1. RRM2 domain of Hrb1, : 42 interactors Detail

Experiments performed 8 experiments Detail

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Sample

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NMR combined restraints 3 contents Detail