BMRB Entry 19146

Name: Solution structure of RING domain of E3 ubiquitin ligase Doa10
Published: 2014-05-05

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PDB ID: 2m6m
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR19146
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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 RING domain of E3 ubiquitin ligase Doa10

Deposition date:

2013-04-06

Original release date:

2014-05-05

Authors:

Lim, Jongsoo; Son, Woo-Sung

Citation:

Citation: Ahn, Hee-Chul; Lim, Jongsoo; Son, Woo-Sung. "Solution structure of RING domain of E3 ubiquitin ligase Doa10" .

Assembly members:

Assembly members:
entity_1, polymer, 83 residues, 9220.431 Da.
ZINC ION, non-polymer, 65.409 Da.

Natural source:

Natural source: Common Name: baker's yeast Taxonomy ID: 4932 Superkingdom: Eukaryota Kingdom: Fungi Genus/species: Saccharomyces cerevisiae

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: VANEETDTATFNDDAPSGAT CRICRGEATEDNPLFHPCKC RGSIKYMHESCLLEWVASKN IDISKPGADVKCDICHYPIQ FKT

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	349
15N chemical shifts	83
1H chemical shifts	542

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	RING domain of E3 ubiquitin ligase Doa10	1
2	ZINC ION_1	2

Entities:

Entity 1, RING domain of E3 ubiquitin ligase Doa10 83 residues - 9220.431 Da.

1

VAL

ALA

ASN

GLU

THR

ASP

THR

ALA

THR

2

PHE

ASN

ASP

ALA

PRO

SER

GLY

ALA

THR

3

CYS

ARG

ILE

CYS

ARG

GLY

GLU

ALA

THR

GLU

4

ASP

ASN

PRO

LEU

PHE

HIS

PRO

CYS

LYS

CYS

5

ARG

GLY

SER

ILE

LYS

TYR

MET

HIS

GLU

SER

6

CYS

LEU

GLU

TRP

VAL

ALA

SER

LYS

ASN

7

ILE

ASP

ILE

SER

LYS

PRO

GLY

ALA

ASP

VAL

8

LYS

CYS

ASP

ILE

CYS

HIS

TYR

PRO

ILE

GLN

9

PHE

LYS

THR

Entity 2, ZINC ION_1 - Zn - 65.409 Da.

1

ZN

Samples:

sample_1: MES, [U-100% 13C; U-100% 15N], 0.5 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 0.05 M; pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1

Software:

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

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

NMR spectrometers:

Varian INOVA 900 MHz
Varian INOVA 600 MHz

PDB	2M6M
DBJ	GAA24084
EMBL	CAA54133 CAA86961
GB	AHY75969 AJP39437 AJR36730 AJR36925 AJR37116
REF	NP_012234
SP	P40318
TPG	DAA08517
AlphaFold	P40318