BMRB Entry 11563

Name: Refined solution structure of the first RNA recognition motif domain in CPEB3
Published: 2016-07-13

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PDB ID: 2rug
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR11563
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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:

Refined solution structure of the first RNA recognition motif domain in CPEB3

Deposition date:

2014-04-15

Original release date:

2016-07-13

Authors:

Tsuda, Kengo; Kuwasako, Kanako; Nagata, Takashi; Takahashi, Mari; Kigawa, Takanori; Kobayashi, Naohiro; Guntert, Peter; Shirouzu, Mikako; Yokoyama, Shigeyuki; Muto, Yutaka

Citation:

Citation: Tsuda, Kengo; Kuwasako, Kanako; Nagata, Takashi; Takahashi, Mari; Kigawa, Takanori; Kobayashi, Naohiro; Guntert, Peter; Shirouzu, Mikako; Yokoyama, Shigeyuki; Muto, Yutaka. "Novel RNA recognition motif domain in the cytoplasmic polyadenylation element binding protein 3" Proteins 82, 2879-2886 (2014).
PubMed: 5066254

Assembly members:

Assembly members:
The_first_RNA_recognition_motif_domain, polymer, 114 residues, 12428.944 Da.

Natural source:

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source:

Experimental source: Production method: cell free synthesis Host organism: E. coli - cell free Vector: pCR2.1

Entity Sequences (FASTA):

Entity Sequences (FASTA):
The_first_RNA_recognition_motif_domain: GSSGSSGSRKVFVGGLPPDI DEDEITASFRRFGPLVVDWP HKAESKSYFPPKGYAFLLFQ EESSVQALIDACLEEDGKLY LCVSSPTIKDKPVQIRPWNL SDSDFVMDSGPSSG

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	493
15N chemical shifts	103
1H chemical shifts	745

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	The_first_RNA_recognition_motif_domain	1

Entities:

Entity 1, The_first_RNA_recognition_motif_domain 114 residues - 12428.944 Da.

1

GLY

SER

GLY

SER

GLY

SER

ARG

LYS

2

VAL

PHE

VAL

GLY

LEU

PRO

ASP

ILE

3

ASP

GLU

ASP

GLU

ILE

THR

ALA

SER

PHE

ARG

4

ARG

PHE

GLY

PRO

LEU

VAL

ASP

TRP

PRO

5

HIS

LYS

ALA

GLU

SER

LYS

SER

TYR

PHE

PRO

6

PRO

LYS

GLY

TYR

ALA

PHE

LEU

PHE

GLN

7

GLU

SER

VAL

GLN

ALA

LEU

ILE

ASP

8

ALA

CYS

LEU

GLU

ASP

GLY

LYS

LEU

TYR

9

LEU

CYS

VAL

SER

PRO

THR

ILE

LYS

ASP

10

LYS

PRO

VAL

GLN

ILE

ARG

PRO

TRP

ASN

LEU

11

SER

ASP

SER

ASP

PHE

VAL

MET

ASP

SER

GLY

12

PRO

SER

GLY

Samples:

sample_1: The_first_RNA_recognition_motif_domain, [U-100% 13C; U-100% 15N], 1.06 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 120 mM; pH: 7.0; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1

Software:

xwinnmr v3.5, Bruker Biospin - collection

NMRPipe v20030801, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMRView v5.0.4, Johnson, One Moon Scientific - data analysis

Kujira v0.9843, Kobayashi, N - data analysis

CYANA v2.0.17, Guntert, Mumenthaler and Wuthrich - structure solution

AMBER v9, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement

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