BMRB Entry 36430

Name: Solution structure of The first RNA binding domain of Matrin-3
Published: 2022-02-24

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PDB ID: 7fbr
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR36430
MolProbity Validation Chart

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Solution structure of The first RNA binding domain of Matrin-3

Deposition date:

2021-07-12

Original release date:

2022-02-24

Authors:

Muto, Y.; Kobayashi, N.; Yokoyama, S.; RIKEN Structural Genomics/Proteomics Initiative (RSGI), RSGI

Citation:

Citation: He, F.; Kuwasako, K.; Takizawa, M.; Takahashi, M.; Tsuda, K.; Nagata, T.; Watanabe, S.; Tanaka, A.; Kobayashi, N.; Kigawa, T.; Guntert, P.; Shirouzu, M.; Yokoyama, S.; Muto, Y.. "Solution structure of The first RNA binding domain of Matrin-3" .

Assembly members:

Assembly members:
Matrin-3, polymer, 102 residues, 11351.972 Da.

Natural source:

Natural source: Common Name: Mouse Taxonomy ID: 10090 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Mus musculus

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Cell-free gateway cloning vector N-term 8xHis eGFP pCellFree_G03

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Matrin-3: GSSGSSGQKGRVETRRVVHI MDFQRGKNLRYQLLQLVEPF GVISNHLILNKINEAFIEMA TTEDAQAAVDYYTTTPALVF GKPVRVHLSQKYKRIKSGPS SG

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	425
15N chemical shifts	89
1H chemical shifts	696

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1

Entities:

Entity 1, unit_1 102 residues - 11351.972 Da.

1

GLY

SER

GLY

SER

GLY

GLN

LYS

GLY

2

ARG

VAL

GLU

THR

ARG

VAL

HIS

ILE

3

MET

ASP

PHE

GLN

ARG

GLY

LYS

ASN

LEU

ARG

4

TYR

GLN

LEU

GLN

LEU

VAL

GLU

PRO

PHE

5

GLY

VAL

ILE

SER

ASN

HIS

LEU

ILE

LEU

ASN

6

LYS

ILE

ASN

GLU

ALA

PHE

ILE

GLU

MET

ALA

7

THR

GLU

ASP

ALA

GLN

ALA

VAL

ASP

8

TYR

THR

PRO

ALA

LEU

VAL

PHE

9

GLY

LYS

PRO

VAL

ARG

VAL

HIS

LEU

SER

GLN

10

LYS

TYR

LYS

ARG

ILE

LYS

SER

GLY

PRO

SER

11

SER

GLY

Samples:

sample_1: RNA binding protein, [U-99% 13C; U-99% 15N], 1.0 mM; Tris-Hcl, [U-100% 2H], 20 mM; NaCl 100 mM; H2O 90%; D2O, [U-2H], 10%

sample_conditions_1: ionic strength: 100 mM; pH: 7; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D_13C,15N-SEPARATED_NOESY SPECTRA	sample_1	isotropic	sample_conditions_1

Software:

Amber v12, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement

CYANA, Guntert, Mumenthaler and Wuthrich - structure calculation

KUJIRA v0.863, N. Kobayashi, T. Kigawa, S. Yokoyama - chemical shift assignment

NMRPipe v2007, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMRView v5.0.4, Johnson, One Moon Scientific - peak picking

TALOS v2007, Cornilescu, Delaglio and Bax - geometry optimization

TopSpin v2.1, Bruker Biospin - collection

NMR spectrometers:

Bruker AVANCE 800 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks