BMRB Entry 17388

Name: Solution Structure of the Zinc Finger Domain of USP13
Published: 2011-12-14

Click here to enlarge.

PDB ID: 2l80
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR17388
MolProbity Validation Chart

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
XML gzip file.
RDF gzip file.
All files associated with the entry

Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

Select model:

I am color blind

Download raw data. Direct link to this display. Help

Title:

Solution Structure of the Zinc Finger Domain of USP13

Deposition date:

2010-12-28

Original release date:

2011-12-14

Authors:

Zhang, Yuhang; Zhou, Chenjie; Zhou, Ziren; Song, Aixin; Hu, Hongyu

Citation:

Citation: Zhang, Yuhang; Song, Aixin; Zhou, Chenjie; Zhou, Ziren; Hu, Hongyu. "Biochemical Characterization of the Ubiquitin Receptors in USP13 Reveals Different Catalytic Activation of Deubiquitination from Its Analogue USP5" .

Assembly members:

Assembly members:
entity, polymer, 114 residues, 12696.393 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: pET-M

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity: VSKYANNLTQLDNGVRIPPS GWKCARCDLRENLWLNLTDG SVLCGKWFFDSSGGNGHALE HYRDMGYPLAVKLGTITPDG ADVYSFQEEEPVLDPHLAKH LAHFGIDMLHMHGT

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	408
15N chemical shifts	97
1H chemical shifts	658

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	USP13	1

Entities:

Entity 1, USP13 114 residues - 12696.393 Da.

1

VAL

SER

LYS

TYR

ALA

ASN

LEU

THR

GLN

2

LEU

ASP

ASN

GLY

VAL

ARG

ILE

PRO

SER

3

GLY

TRP

LYS

CYS

ALA

ARG

CYS

ASP

LEU

ARG

4

GLU

ASN

LEU

TRP

LEU

ASN

LEU

THR

ASP

GLY

5

SER

VAL

LEU

CYS

GLY

LYS

TRP

PHE

ASP

6

SER

GLY

ASN

GLY

HIS

ALA

LEU

GLU

7

HIS

TYR

ARG

ASP

MET

GLY

TYR

PRO

LEU

ALA

8

VAL

LYS

LEU

GLY

THR

ILE

THR

PRO

ASP

GLY

9

ALA

ASP

VAL

TYR

SER

PHE

GLN

GLU

10

PRO

VAL

LEU

ASP

PRO

HIS

LEU

ALA

LYS

HIS

11

LEU

ALA

HIS

PHE

GLY

ILE

ASP

MET

LEU

HIS

12

MET

HIS

GLY

THR

Samples:

sample_1: USP13, [U-15N], 1 mM; sodium phosphate 20 mM; sodium chloride 50 mM; H2O 90%; D2O 10%

sample_2: entity, [U-100% 13C; U-100% 15N], 1 mM; sodium phosphate 20 mM; sodium chloride 50 mM; H2O 90%; D2O 10%

sample_conditions_1: pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_2	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_2	isotropic	sample_conditions_1
3D HNHA	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_2	isotropic	sample_conditions_1
3D C(CO)NH	sample_2	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_2	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_2	isotropic	sample_conditions_1

Software:

ARIA, Linge, O'Donoghue and Nilges - refinement, structure solution

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

TALOS, Cornilescu, Delaglio and Bax - data analysis

SPARKY, Goddard - chemical shift assignment, peak picking

ProcheckNMR, Laskowski and MacArthur - data analysis

NMR spectrometers:

Bruker Avance 600 MHz

PDB	2L80
DBJ	BAF83027 BAG63715
EMBL	CAL38193 CAL38270 CAL38486 CAL38655
GB	AAC63405 AAH16146 ABM83398 ABM86610 ADM34989
REF	NP_001178195 NP_001252567 NP_003931 XP_002912504 XP_003310172
SP	E1BMF7 Q92995
TPG	DAA33286
AlphaFold	E1BMF7 Q92995