BMRB Entry 17554

Name: solution structure of tandem UBA of USP13
Published: 2012-03-05

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PDB ID: 2lbc
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR17554
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: solution structure of tandem UBA of USP13 PubMed: 22216260

Deposition date: 2011-03-29 Original release date: 2012-03-05

Authors: Zhang, Yuhang; Zhou, Chenjie; Zhou, Ziren; Song, Aixin; Hun, Hongyu

Citation: Zhang, Yuhang; Zhou, Chenjie; Zhou, Ziren; Song, Aixin; Hu, Hongyuhu. "Domain Analysis Reveals That a Deubiquitinating Enzyme USP13 Performs Non-Activating Catalysis for Lys63-Linked Polyubiquitin" Plos One 6, e29362-e29362 (2011).

Assembly members:
tandem UBA of USP13, polymer, 126 residues, 13769.365 Da.

Natural source: Common Name: human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source: Production method: recombinant technology Host organism: Escherichia coli

Entity Sequences (FASTA):
tandem UBA of USP13: DIDESSVMQLAEMGFPLEAC RKAVYFTGNMGAEVAFNWII VHMEEPDFAEPLTMPGYGGA ASAGASVFGASGLDNQPPEE IVAIITSMGFQRNQAIQALR ATNNNLERALDWIFSHPEFE EDSDFV

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	351
15N chemical shifts	119
1H chemical shifts	702

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	tandem UBA of USP13	1

Entities:

Entity 1, tandem UBA of USP13 126 residues - 13769.365 Da.

1

ASP

ILE

ASP

GLU

SER

VAL

MET

GLN

LEU

2

ALA

GLU

MET

GLY

PHE

PRO

LEU

GLU

ALA

CYS

3

ARG

LYS

ALA

VAL

TYR

PHE

THR

GLY

ASN

MET

4

GLY

ALA

GLU

VAL

ALA

PHE

ASN

TRP

ILE

5

VAL

HIS

MET

GLU

PRO

ASP

PHE

ALA

GLU

6

PRO

LEU

THR

MET

PRO

GLY

TYR

GLY

ALA

7

ALA

SER

ALA

GLY

ALA

SER

VAL

PHE

GLY

ALA

8

SER

GLY

LEU

ASP

ASN

GLN

PRO

GLU

9

ILE

VAL

ALA

ILE

THR

SER

MET

GLY

PHE

10

GLN

ARG

ASN

GLN

ALA

ILE

GLN

ALA

LEU

ARG

11

ALA

THR

ASN

LEU

GLU

ARG

ALA

LEU

12

ASP

TRP

ILE

PHE

SER

HIS

PRO

GLU

PHE

GLU

13

GLU

ASP

SER

ASP

PHE

VAL

Samples:

sample_1: sodium phosphate 20 mM; sodium chloride 50 mM; entity, [U-100% 15N], 1 mM; H2O 90%; D2O 10%

sample_2: sodium phosphate 20 mM; sodium chloride 50 mM; entity, [U-100% 13C; U-100% 15N], 1 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 CBCA(CO)NH	sample_2	isotropic	sample_conditions_1
3D HNCACB	sample_2	isotropic	sample_conditions_1
3D C(CO)NH	sample_2	isotropic	sample_conditions_1
3D HNHA	sample_1	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:

ARIA2.0, Linge, O, . - refinement, structure solution

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

SPARKY, Goddard - chemical shift assignment, peak picking

TALOS, Cornilescu, Delaglio and Bax - data analysis

ProcheckNMR, Laskowski and MacArthur - data analysis

NMR spectrometers:

Bruker Avance 600 MHz

PDB	2LBC
DBJ	BAF83027 BAG63715
EMBL	CAL38193 CAL38270 CAL38486 CAL38655
GB	AAC63405 AAH16146 ABM83398 ABM86610 ADM34989
REF	NP_001252567 NP_003931 XP_002814369 XP_003310172 XP_003434175
SP	Q92995

Biological Magnetic Resonance Data Bank