BMRB Entry 36081

Name: Retracted state of S65-phosphorylated ubiquitin
Published: 2017-11-17

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PDB ID: 5xk4
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR36081
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:

Retracted state of S65-phosphorylated ubiquitin

Deposition date:

2017-05-05

Original release date:

2017-11-17

Authors:

Dong, X.; Gong, Z.; Qin, L.; Ran, M.; Zhang, C.; Liu, K.; Liu, Z.; Zhang, W.; Tang, C.

Citation:

Citation: Dong, X.; Gong, Z.; Lu, Y.; Liu, K.; Qin, L.; Ran, M.; Zhang, C.; Liu, Z.; Zhang, W.; Tang, C.. "Ubiquitin S65 phosphorylation engenders a pH-sensitive conformational switch" Proc. Natl. Acad. Sci. U.S.A. 114, 6770-6775 (2017).
PubMed: 28611216

Assembly members:

Assembly members:
Polyubiquitin-B, polymer, 76 residues, 8656.811 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 K-12

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Polyubiquitin-B: MQIFVKTLTGKTITLEVEPS DTIENVKAKIQDKEGIPPDQ QRLIFAGKQLEDGRTLSDYN IQKEXTLHLVLRLRGG

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	282
15N chemical shifts	65
1H chemical shifts	384

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 76 residues - 8656.811 Da.

1

MET

GLN

ILE

PHE

VAL

LYS

THR

LEU

THR

GLY

2

LYS

THR

ILE

THR

LEU

GLU

VAL

GLU

PRO

SER

3

ASP

THR

ILE

GLU

ASN

VAL

LYS

ALA

LYS

ILE

4

GLN

ASP

LYS

GLU

GLY

ILE

PRO

ASP

GLN

5

GLN

ARG

LEU

ILE

PHE

ALA

GLY

LYS

GLN

LEU

6

GLU

ASP

GLY

ARG

THR

LEU

SER

ASP

TYR

ASN

7

ILE

GLN

LYS

GLU

SEP

THR

LEU

HIS

LEU

VAL

8

LEU

ARG

LEU

ARG

GLY

Samples:

sample_1: phosphorylated ubiquitin, [U-98% 13C; U-98% 15N], 0.8 mM; HEPES 20 mM; NaCl 150 mM; H2O 90%; D2O, [U-2H], 10%

sample_conditions_1: ionic strength: 150 mM; pH: 7.4; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1

Software:

CcpNMR, CCPN - chemical shift assignment, peak picking

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure calculation

NMR spectrometers:

Bruker AvanceIII 600 MHz
Bruker AvanceIII 850 MHz

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