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Found 1 Document (1.953 seconds)

BMRB: 25496

2MZQ

NMR structure of the RRM3 domain of Gbp2

Authors

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

Assembly

RRM3 domain of Gbp2

Entity

1. RRM3 domain of Gbp2 (polymer, Thiol state: all free), 101 monomers, 11085.12 Da Detail

GSHIDETAAK FTEGVNPGGD RNCFIYCSNL PFSTARSDLF DLFGPIGKIN NAELKPQENG QPTGVAVVEY ENLVDADFCI QKLNNYNYGG CSLQISYARR D

Formula weight

11085.12 Da

Source organism

Saccharomyces cerevisiae

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 91.2 %, Completeness (bb): 96.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	91.2 % (1038 of 1138)	94.7 % (559 of 590)	84.7 % (371 of 438)	98.2 % (108 of 110)
Backbone	96.3 % (574 of 596)	97.6 % (202 of 207)	94.9 % (278 of 293)	97.9 % (94 of 96)
Sidechain	87.7 % (555 of 633)	93.2 % (357 of 383)	78.0 % (184 of 236)	100.0 % (14 of 14)
Aromatic	46.2 % (48 of 104)	92.3 % (48 of 52)	0.0 % (0 of 52)
Methyl	100.0 % (94 of 94)	100.0 % (47 of 47)	100.0 % (47 of 47)

1. RRM3

GSHIDETAAK FTEGVNPGGD RNCFIYCSNL PFSTARSDLF DLFGPIGKIN NAELKPQENG QPTGVAVVEY ENLVDADFCI QKLNNYNYGG CSLQISYARR D

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: -0.06 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: -0.06 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: 0.27 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2MZQ, 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: 25497 released on 2015-11-29
    Title NMR structure of the RRM1 domain of Hrb1
  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. RRM3 domain of Gbp2, : 1 : 2 : 91 entities Detail

Interaction partners 1. RRM3 domain of Gbp2, : 64 interactors Detail

More details for 64 interactors identified by 12 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 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 %

4 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 %

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	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 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 %

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	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 CBCA(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 %

9 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 %

10 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 %

11 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 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_25496_2mzq.nef
Input source #2: Coordindates	2mzq.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

---330-----340-------350-------360-------370-------380-------390-------400-------410-------420------
GSHIDETAAKFTEGVNPGGDRNCFIYCSNLPFSTARSDLFDLFGPIGKINNAELKPQENGQPTGVAVVEYENLVDADFCIQKLNNYNYGGCSLQISYARR
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSHIDETAAKFTEGVNPGGDRNCFIYCSNLPFSTARSDLFDLFGPIGKINNAELKPQENGQPTGVAVVEYENLVDADFCIQKLNNYNYGGCSLQISYARR
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

-
D
|
D
-

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	101	0	0	100.0

Content subtype: combined_25496_2mzq.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1050		100.0 (chain: A, length: 101)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	3754 (1)	noe	98.0 (chain: A, length: 101)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 101, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 569
  - ¹³C chemical shifts: 369
  - ¹⁵N chemical shifts: 112
- 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)
347	ARG	HH11	6.821
347	ARG	HH21	6.821
347	ARG	NH1	70.689
347	ARG	NH2	72.146
353	CYS	HG	1.433
360	THR	HG1	6.13
389	THR	HG1	5.321
396	TYR	HH	7.75
405	CYS	HG	1.836
422	SER	HG	5.465

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	590	561	95.1
¹³C chemical shifts	438	369	84.2
¹⁵N chemical shifts	114	110	96.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	207	203	98.1
¹³C chemical shifts	202	185	91.6
¹⁵N chemical shifts	96	92	95.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	383	358	93.5
¹³C chemical shifts	236	184	78.0
¹⁵N chemical shifts	18	18	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	47	47	100.0
¹³C chemical shifts	47	47	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	52	48	92.3
¹³C chemical shifts	52	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: 101, Sequence coverage: 98.0%
- Total number of restraints: 3734
- Weight of restraints: 1.0 (3734)
- Potential type of restraints: upper-bound-parabolic (3734)
- Range of distance target values: 2.18, 6.03 (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 Gbp2, RNA binding domain, RRM, THO/TREX

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Found 1 Document (1.953 seconds)

BMRB: 25496

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. RRM3 domain of Gbp2, : 1 : 2 : 91 entities Detail

Interaction partners 1. RRM3 domain of Gbp2, : 64 interactors Detail

Experiments performed 11 experiments Detail

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NMR combined restraints 3 contents Detail