BMRB Entry 11529

Name: Solution structure of a regulatory domain of meiosis inhibitor
Published: 2014-07-14

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PDB ID: 2rt9
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR11529
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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 a regulatory domain of meiosis inhibitor

Deposition date:

2013-07-04

Original release date:

2014-07-14

Authors:

Shoji, S; Muto, Y; Ikeda, M; He, F; Tsuda, K; Ohsawa, N; Akasaka, R; Terada, T; Wakiyama, M; Shirouzu, M; Yokoyama, S

Citation:

Citation: Shoji, S.; Muto, Y.; Ikeda, M.; He, F.; Tsuda, K.; Ohsawa, N.; Akasaka, R.; Terada, T.; Wakiyama, M.; Shirouzu, M.; Yokoyama, S.. "The zinc-binding region (ZBR) fragment of Emi2 can inhibit APC/C by targeting its association with the coactivator Cdc20 and UBE2C-mediated ubiquitylation" FEBS OPEN BIO. 4, 689-703 (2014).
PubMed: 25161877

Assembly members:

Assembly members:
entity_1, polymer, 59 residues, 5830.834 Da.
ZINC ION, non-polymer, 65.409 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: cell free synthesis Host organism: E. coli - cell free Vector: PCR2.1

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GSSGSSGTDEALKPCPRCQS PAKYQPHKKRGLCSRLACGF DFCVLCLCAYHGSEDCRRG

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	225
15N chemical shifts	50
1H chemical shifts	341

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1
2	ZINC ION_1	2
3	ZINC ION_2	2

Entities:

Entity 1, entity_1 59 residues - 5830.834 Da.

The first 7 residues (GSSGSSG) are cloning artifacts.

1

GLY

SER

GLY

SER

GLY

THR

ASP

GLU

2

ALA

LEU

LYS

PRO

CYS

PRO

ARG

CYS

GLN

SER

3

PRO

ALA

LYS

TYR

GLN

PRO

HIS

LYS

ARG

4

GLY

LEU

CYS

SER

ARG

LEU

ALA

CYS

GLY

PHE

5

ASP

PHE

CYS

VAL

LEU

CYS

LEU

CYS

ALA

TYR

6

HIS

GLY

SER

GLU

ASP

CYS

ARG

GLY

Entity 2, ZINC ION_1 - Zn - 65.409 Da.

1

ZN

Samples:

sample_1: entity_1, [U-100% 13C; U-100% 15N], 0.47 mM; H2O 90%; D2O 10%; dTris-HCl, [U-2H], 20 mM; NaCl 100 mM; d-DTT, [U-2H], 1 mM; ZnCl2 50 uM; NaN3 0.02%

sample_conditions_1: ionic strength: 120 mM; pH: 6.5; 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

Software:

TOPSPIN, Bruker Biospin - collection

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

NMRView, Johnson, One Moon Scientific - data analysis

Kujira, Kobayashi, N - data analysis

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

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

NMR spectrometers:

Bruker Avance 800 MHz

PDB	2RT9
DBJ	BAC26733
GB	AAH26503 AAH82107 AAH98484 EDL08829 EDM16401
REF	NP_001012117 NP_001074722 XP_006241597 XP_006520259 XP_006520260
SP	Q66H04 Q8CDI2
AlphaFold	Q66H04 Q8CDI2