BMRB Entry 16390

Name: NMR solution structure of human ubiquitin-like domain of ubiquilin 1, Northeast Structural Genomics Consortium (NESG) target HT5A
Published: 2009-07-07

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PDB ID: 2klc
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR16390
MolProbity Validation Chart

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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

NMR solution structure of human ubiquitin-like domain of ubiquilin 1, Northeast Structural Genomics Consortium (NESG) target HT5A

Deposition date:

2009-06-30

Original release date:

2009-07-07

Authors:

Doherty, Ryan; Dhe-Paganon, Sirano; Fares, Christophe; Lemak, Sasha; Gutmanas, Aleks; Garcia, Maite; Yee, Adelinda; Montelione, Gaetano; Arrowsmith, Cheryl

Citation:

Citation: Doherty, Ryan; Dhe-Paganon, Sirano; Fares, Christophe; Lemak, Sasha; Gutmanas, Aleks; Garcia, Maite; Yee, Adelinda; Montelione, Gaetano; Arrowsmith, Cheryl. "Solution structure of ubiquitin-like domain of ubiquilin 1." .

Assembly members:

Assembly members:
ubiquilin_1, polymer, 101 residues, 9053.559 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: p15Tv lic

Entity Sequences (FASTA):

Entity Sequences (FASTA):
ubiquilin_1: MGSSHHHHHHSSGRENLYFQ GHPKIMKVTVKTPKEKEEFA VPENSSVQQFKEEISKRFKS HTDQLVLIFAGKILKDQDTL SQHGIHDGLTVHLVIKTQNR P

Data sets:

RDCs
- RDC_list_1
assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	328
15N chemical shifts	79
1H chemical shifts	545
residual dipolar couplings	75

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	ubiquilin_1	1

Entities:

Entity 1, ubiquilin_1 101 residues - 9053.559 Da.

1

MET

GLY

SER

HIS

2

SER

GLY

ARG

GLU

ASN

LEU

TYR

PHE

GLN

3

GLY

HIS

PRO

LYS

ILE

MET

LYS

VAL

THR

VAL

4

LYS

THR

PRO

LYS

GLU

LYS

GLU

PHE

ALA

5

VAL

PRO

GLU

ASN

SER

VAL

GLN

PHE

6

LYS

GLU

ILE

SER

LYS

ARG

PHE

LYS

SER

7

HIS

THR

ASP

GLN

LEU

VAL

LEU

ILE

PHE

ALA

8

GLY

LYS

ILE

LEU

LYS

ASP

GLN

ASP

THR

LEU

9

SER

GLN

HIS

GLY

ILE

HIS

ASP

GLY

LEU

THR

10

VAL

HIS

LEU

VAL

ILE

LYS

THR

GLN

ASN

ARG

11

PRO

Samples:

sample_1: ubiquilin_1, [U-13C; U-15N], 0.5 mM; TRIS 10 mM; sodium chloride (NaCl) 300 mM; sodium azide (NaN3) 0.01%; inhibitor cocktail (roche) 1 x; benzamidine 1 mM; ZnSO4 10 uM; DTT 10 mM; D20 10%; H20 90%

sample_conditions_1: ionic strength: 300 mM; pH: 7.0; pressure: 1.0 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D (H)CCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C_arom NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-15 HSQC (IPAP)	sample_1	anisotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C Constant Time HSQC	sample_1	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCO (IPAP)	sample_1	anisotropic	sample_conditions_1

Software:

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

FMC, Lemak, Steren, Llinas & Arrowsmith - chemical shift assignment

TALOS v2003.027.13.05, Cornilescu, Delaglio and Bax - data analysis

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - structure solution

CNSSOLVE v1.1, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

TOPSPIN, Bruker Biospin - collection

PSVS v1.3, Bhattacharya and Montelione - validation

SPARKY v3.106, Goddard - peak picking

NMR spectrometers:

Bruker Avance 800 MHz
Bruker Avance 600 MHz

PDB	2KLC
DBJ	BAC33666 BAG51344 BAG51350 BAI46894
EMBL	CAB66578 CAH92732
GB	AAD49751 AAG02473 AAH10066 AAH39294 AAI20032
REF	NP_001127579 NP_001155358 NP_038466 NP_444295 NP_777053
SP	Q5R684 Q9UMX0
TPG	DAA26626
AlphaFold	Q5R684 Q9UMX0