BMRB Entry 30340

Name: Structures of REV1 UBM2 domain complex with ubiquitin and with the first small-molecule that inhibits the REV1 UBM2-ubiquitin interaction
Published: 2018-06-21

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PDB ID: 6axd
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30340
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:

Structures of REV1 UBM2 domain complex with ubiquitin and with the first small-molecule that inhibits the REV1 UBM2-ubiquitin interaction

Deposition date:

2017-09-06

Original release date:

2018-06-21

Authors:

Fujii, N.; Vanarotti, M.

Citation:

Citation: Vanarotti, Murugendra; Grace, Christy; Miller, Darcie; Actis, Marcelo; Inoue, Akira; Evison, Benjamin; Vaithiyalingam, Sivaraja; Singh, Aman; McDonald, Ezelle; Fujii, Naoaki. "Structures of REV1 UBM2 Domain Complex with Ubiquitin and with a Small-Molecule that Inhibits the REV1 UBM2-Ubiquitin Interaction" J. Mol. Biol. 430, 2857-2872 (2018).
PubMed: 29864443

Assembly members:

Assembly members:
entity_1, polymer, 72 residues, 7813.632 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: recombinant technology Host organism: Escherichia coli-Pichia pastoris shuttle vector pPpARG4

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: MGSSHHHHHHHHLNGSSLVP RGSIKSSGLESNSDAGINLI ALPAFSQVDPEVFAALPAEL QRELKAAYDQRQ

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	58
15N chemical shifts	55
1H chemical shifts	99

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1

Entities:

Entity 1, entity_1 72 residues - 7813.632 Da.

1

MET

GLY

SER

HIS

2

HIS

LEU

ASN

GLY

SER

LEU

VAL

PRO

3

ARG

GLY

SER

ILE

LYS

SER

GLY

LEU

GLU

4

SER

ASN

SER

ASP

ALA

GLY

ILE

ASN

LEU

ILE

5

ALA

LEU

PRO

ALA

PHE

SER

GLN

VAL

ASP

PRO

6

GLU

VAL

PHE

ALA

LEU

PRO

ALA

GLU

LEU

7

GLN

ARG

GLU

LEU

LYS

ALA

TYR

ASP

GLN

8

ARG

GLN

Samples:

sample_1: REV1 UBM2, [U-13C; U-15N], 0.5 mM

sample_2: REV1 UBM2, [U-99% 15N], 0.5 mM

sample_conditions_1: ionic strength: 0.5 mM; pH: 7.0; pressure: 1 mbar; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_2	anisotropic	sample_conditions_1
3D HNCA	sample_1	anisotropic	sample_conditions_1
3D HNCACB	sample_1	anisotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	anisotropic	sample_conditions_1
3D 1H-15N NOESY	sample_2	anisotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	anisotropic	sample_conditions_1

Software:

CARA, Keller and Wuthrich - peak picking, refinement

CYANA, Guntert, Mumenthaler and Wuthrich - refinement, structure calculation

TOPSPIN, Bruker Biospin - data analysis

NMR spectrometers:

Bruker Avance 600 MHz
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