BMRB Entry 34351

Name: Solution NMR ensemble for human ubiquitin at 298K compiled using the CoMAND method
Published: 2019-10-03

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PDB ID: 6qf8
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR34351
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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 NMR ensemble for human ubiquitin at 298K compiled using the CoMAND method

Deposition date:

2019-01-09

Original release date:

2019-10-03

Authors:

ElGamacy, M.; Truffault, V.; Zhu, H.; Coles, M.

Citation:

Citation: ElGamacy, M.; Riss, M.; Zhu, H.; Truffault, V.; Coles, M.. "Mapping Local Conformational Landscapes of Proteins in Solution." Structure 27, 853-865 (2019).
PubMed: 30930065

Assembly members:

Assembly members:
entity_1, polymer, 79 residues, 8836.156 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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: AMGMQIFVKTLTGKTITLEV EPSDTIENVKAKIQDKEGIP PDQQRLIFAGKQLEDGRTLS DYNIQKESTLHLVLRLRGG

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	325
15N chemical shifts	79
1H chemical shifts	324

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 79 residues - 8836.156 Da.

1

ALA

MET

GLY

MET

GLN

ILE

PHE

VAL

LYS

THR

2

LEU

THR

GLY

LYS

THR

ILE

THR

LEU

GLU

VAL

3

GLU

PRO

SER

ASP

THR

ILE

GLU

ASN

VAL

LYS

4

ALA

LYS

ILE

GLN

ASP

LYS

GLU

GLY

ILE

PRO

5

PRO

ASP

GLN

ARG

LEU

ILE

PHE

ALA

GLY

6

LYS

GLN

LEU

GLU

ASP

GLY

ARG

THR

LEU

SER

7

ASP

TYR

ASN

ILE

GLN

LYS

GLU

SER

THR

LEU

8

HIS

LEU

VAL

LEU

ARG

LEU

ARG

GLY

Samples:

sample_1: human ubiquitin, [U-99% 13C; U-99% 15N], 1.0 mM; sodium phosphate 40 mM

sample_conditions_1: ionic strength: 100 mM; pH: 5.8; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D CNH-NOESY	sample_1	isotropic	sample_conditions_1
3D C(CO)NH	sample_1	isotropic	sample_conditions_1

Software:

TopSpin, Bruker Biospin - collection

Sparky, Goddard - chemical shift assignment

Rosetta v3.6, Das & Baker - structure calculation

NAMD 2.12, University of Illinois - refinement

SHINE, Riss & Coles - refinement

CoMAND, in house - refinement

NMR spectrometers:

Bruker AvanceIII 800 MHz
Bruker AvanceIII 600 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks