BMRB Entry 34217

Name: Solution structure of the RING domain of the E3 ubiquitin ligase HRD1
Published: 2019-01-28

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PDB ID: 6f98
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR34217
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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: Solution structure of the RING domain of the E3 ubiquitin ligase HRD1

Deposition date: 2017-12-14 Original release date: 2019-01-28

Authors: Kniss, A.; Kazemi, S.; Lohr, F.; Guntert, P.; Dotsch, V.

Citation: Kniss, A.. "Solution structure of the RING domain of the E3 ubiquitin ligase HRD1" . ., .-..

Assembly members:
entity_1, polymer, 78 residues, 8985.388 Da.
entity_ZN, non-polymer, 65.409 Da.

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

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

Entity Sequences (FASTA):
entity_1: GAEQLQNSANDDNICIICMD ELIHSPNQQTWKNKNKKPKR LPCGHILHLSCLKNWMERSQ TCPICRLPVFDEKGNVVQ

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
spectral_peak_list

Data type	Count
13C chemical shifts	328
15N chemical shifts	73
1H chemical shifts	513

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	entity_2, 1	2
3	entity_2, 2	2

Entities:

Entity 1, entity_1 78 residues - 8985.388 Da.

1

GLY

ALA

GLU

GLN

LEU

GLN

ASN

SER

ALA

ASN

2

ASP

ASN

ILE

CYS

ILE

CYS

MET

ASP

3

GLU

LEU

ILE

HIS

SER

PRO

ASN

GLN

THR

4

TRP

LYS

ASN

LYS

ASN

LYS

PRO

LYS

ARG

5

LEU

PRO

CYS

GLY

HIS

ILE

LEU

HIS

LEU

SER

6

CYS

LEU

LYS

ASN

TRP

MET

GLU

ARG

SER

GLN

7

THR

CYS

PRO

ILE

CYS

ARG

LEU

PRO

VAL

PHE

8

ASP

GLU

LYS

GLY

ASN

VAL

GLN

Entity 2, entity_2, 1 - Zn - 65.409 Da.

1

ZN

Samples:

sample_1: E3 ubiquitin ligase Hrd1, [U-98% 13C; U-98% 15N], 0.8 mM

sample_conditions_1: ionic strength: 150 mM; pH: 7.0; pressure: 1 atm; temperature: 303 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D 1H TOCSY	sample_1	isotropic	sample_conditions_1
3D HNCACO	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HN(COCA)CB	sample_1	isotropic	sample_conditions_1
2D HCBCGCDH TOCSY	sample_1	isotropic	sample_conditions_1

Software:

SPARKY v3.13, Goddard - chemical shift assignment

CYANA v3.9, Peter Guntert - structure calculation

OPAL, Luginbuhl, Guntert, Billeter and Wuthrich - refinement

NMR spectrometers:

Bruker Avance 700 MHz
Bruker Avance 950 MHz

Download simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts