BMRB Entry 19412

Name: K11-linked Diubiquitin average solution structure at pH 6.8, 150 mM NaCl
Published: 2013-09-03

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PDB ID: 2mbq
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR19412
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:

K11-linked Diubiquitin average solution structure at pH 6.8, 150 mM NaCl

Deposition date:

2013-08-03

Original release date:

2013-09-03

Authors:

Castaneda, Carlos; Fushman, David

Citation:

Citation: Castaneda, Carlos; Kashyap, Tanuja; Nakasone, Mark; Krueger, Susan; Fushman, David. "Unique structural, dynamical, and functional properties of K11-linked polyubiquitin chains" Structure 21, 1168-1181 (2013).
PubMed: 23823328

Assembly members:

Assembly members:
entity, polymer, 152 residues, 8576.914 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 Vector: pet3a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity: MQIFVKTLTGKTITLEVEPS DTIENVKAKIQDKEGIPPDQ QRLIFAGKQLEDGRTLSDYN IQKESTLHLVLRLRGGMQIF VKTLTGKTITLEVEPSDTIE NVKAKIQDKEGIPPDQQRLI FAGKQLEDGRTLSDYNIQKE STLHLVLRLRGG

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1
- chainB

Data type	Count
15N chemical shifts	138
1H chemical shifts	138

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	K11-linked Diubiquitin_1	1
2	K11-linked Diubiquitin_2	1

Entities:

Entity 1, K11-linked Diubiquitin_1 152 residues - 8576.914 Da.

Residues 1-76 chain A are distal Ub residues, while residues 1-76 chain B are proximal Ub residues. K11 linkage occurs between K11 of chain B and G76 of chain A.

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

SER

THR

LEU

HIS

LEU

VAL

8

LEU

ARG

LEU

ARG

GLY

MET

GLN

ILE

PHE

9

VAL

LYS

THR

LEU

THR

GLY

LYS

THR

ILE

THR

10

LEU

GLU

VAL

GLU

PRO

SER

ASP

THR

ILE

GLU

11

ASN

VAL

LYS

ALA

LYS

ILE

GLN

ASP

LYS

GLU

12

GLY

ILE

PRO

ASP

GLN

ARG

LEU

ILE

13

PHE

ALA

GLY

LYS

GLN

LEU

GLU

ASP

GLY

ARG

14

THR

LEU

SER

ASP

TYR

ASN

ILE

GLN

LYS

GLU

15

SER

THR

LEU

HIS

LEU

VAL

LEU

ARG

LEU

ARG

16

GLY

Samples:

sample_1: entity, [U-99% 15N], 75 uM; sodium phosphate 20 mM; D2O 7%; H2O 93%; sodium chloride 150 mM

sample_conditions_1: ionic strength: 150 mM; pH: 6.8; pressure: 1 atm; temperature: 296 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-15N IPAP HSQC	sample_1	anisotropic	sample_conditions_1

Software:

TOPSPIN v2.1, Bruker Biospin - collection

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

SPARKY, Goddard - chemical shift assignment

NMR spectrometers:

Bruker Avance 600 MHz

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