BMRB Entry 25601

Name: Ensemble structure the closed state of Lys63-linked diubiquitin in the absence of a ligand
Published: 2015-07-13

Chem Shift validation: AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR25601

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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:

Ensemble structure the closed state of Lys63-linked diubiquitin in the absence of a ligand

Deposition date:

2015-05-10

Original release date:

2015-07-13

Authors:

Liu, Zhu; Gong, Zhou

Citation:

Citation: Liu, Zhu; Gong, Zhou; Yang, Ju; Jiang, Wen-Xue; Zhu, Wen-Kai; Guo, Da-Chuan; Zhang, Wei-Ping; Liu, Mai-Li; Tang, Chun. "Lys63-linked ubiquitin chain adopts multiple conformational states for specific target recognition" eLIFE 4, e05767-e05767 (2015).
PubMed: 26090905

Assembly members:

Assembly members:
entity_1, polymer, 76 residues, 8539.906 Da.
entity_2, polymer, 71 residues, 8035.261 Da.
entity_MTN, non-polymer, 264.385 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: pET11a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: MQIFVKTLTGKTITLEVEPS DTIECVKAKIQDKEGIPPDQ QRLIFAGCQLEDGRTLSDYN IQKESTLHLVLRLRGG
entity_2: MQIFVKTLTGKTITLEVEPS DTIENVKAKIQDKEGIPPDQ QRLIFAGKQLEDGRTLSDYN IQKESTLHLVL

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
15N chemical shifts	135
1H chemical shifts	135

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1
2	entity_2	2
3	S-[(1-OXYL-2,2,5,5-TETRAMETHYL-2,5-DIHYDRO-1H-PYRROL-3-YL)METHYL] METHANESULFONOTHIOATE_1	3
4	S-[(1-OXYL-2,2,5,5-TETRAMETHYL-2,5-DIHYDRO-1H-PYRROL-3-YL)METHYL] METHANESULFONOTHIOATE_2	3

Entities:

Entity 1, entity_1 76 residues - 8539.906 Da.

N25 and K48 mutated to C, one at a time

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

CYS

VAL

LYS

ALA

LYS

ILE

4

GLN

ASP

LYS

GLU

GLY

ILE

PRO

ASP

GLN

5

GLN

ARG

LEU

ILE

PHE

ALA

GLY

CYS

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

Entity 2, entity_2 71 residues - 8035.261 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

SER

THR

LEU

HIS

LEU

VAL

8

LEU

Entity 3, S-[(1-OXYL-2,2,5,5-TETRAMETHYL-2,5-DIHYDRO-1H-PYRROL-3-YL)METHYL] METHANESULFONOTHIOATE_1 - C10 H18 N O3 S2 - 264.385 Da.

1

MTN

Samples:

sample_1: N25C_MTS protein, [U-100% 15N], 0.5 mM; D2O, [U-99% 2H], 10 % v/v; sodium chloride 100 mM; sodium acetate 10 mM

sample_2: K48C_MTS protein, [U-100% 15N], 0.5 mM; D2O, [U-99% 2H], 10 % v/v; sodium chloride 100 mM; sodium acetate 10 mM

sample_3: N25C_MTS mixture protein, [U-100% 15N], 1 mM; D2O, [U-99% 2H], 10 % v/v; sodium chloride 100 mM; sodium acetate 10 mM

sample_4: K48C_MTS mixture protein, [U-100% 15N], 1 mM; D2O, [U-99% 2H], 10 % v/v; sodium chloride 100 mM; sodium acetate 10 mM

sample_5: 15N_distal-14N_proximal, [U-100% 15N], 0.5 mM; D2O, [U-99% 2H], 10 % v/v; sodium chloride 100 mM; sodium acetate 10 mM

sample_6: 14N_distal-15N_proximal, [U-100% 15N], 0.5 mM; D2O, [U-99% 2H], 10 % v/v; sodium chloride 100 mM; sodium acetate 10 mM

sample_conditions_1: ionic strength: 100 mM; pH: 6.0; pressure: 1 atm; temperature: 303 K

sample_conditions_2: ionic strength: 100 mM; pH: 6.0; pressure: 1 atm; temperature: 303 K

sample_conditions_3: ionic strength: 100 mM; pH: 6.0; pressure: 1 atm; temperature: 303 K

sample_conditions_4: ionic strength: 100 mM; pH: 6.0; pressure: 1 atm; temperature: 303 K

sample_conditions_5: ionic strength: 100 mM; pH: 6.0; pressure: 1 atm; temperature: 303 K

sample_conditions_6: ionic strength: 100 mM; pH: 6.0; pressure: 1 atm; temperature: 303 K

Experiments:

Name	Sample	Sample state	Sample conditions
transverse relaxation rate measurement	sample_1	isotropic	sample_conditions_1
transverse relaxation rate measurement	sample_2	isotropic	sample_conditions_2
transverse relaxation rate measurement	sample_3	isotropic	sample_conditions_3
transverse relaxation rate measurement	sample_4	isotropic	sample_conditions_4
2D 1H-15N HSQC	sample_5	isotropic	sample_conditions_5
2D 1H-15N HSQC	sample_6	isotropic	sample_conditions_6

Software:

X-PLOR_NIH, Schwieters, Kuszewski, Tjandra and Clore - structure solution

NMR spectrometers:

Bruker Avance 600 MHz
Bruker Avance 850 MHz

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