BMRB Entry 16109

Name: Solution Structure of human ubiquitin-like domain of Herpud2_9_85, Northeast Structural Genomics Consortium (NESG) target HT53A
Published: 2009-05-26

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PDB ID: 2kdb
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR16109
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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:

Solution Structure of human ubiquitin-like domain of Herpud2_9_85, Northeast Structural Genomics Consortium (NESG) target HT53A

Deposition date:

2009-01-06

Original release date:

2009-05-26

Authors:

Wu, Bin; Yee, Adelinda; Fares, Christophe; Lemak, Alexander; Gutmanas, Aleksandras; Doherty, Ryan; Semesi, Anthony; Dhe-Paganon, Sirano; Arrowsmith, Cheryl

Citation:

Citation: Doherty, Ryan; Wu, Bin; Fares, Christophe; Lemak, Alexander; Gutmanas, Aleksandras; Semesi, Anthony; Yee, Adelinda; Arrowsmith, Cheryl; Dhe-Paganon, Sirano. "Structure of human homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 2 (Herpud2 or Herp)" .

Assembly members:

Assembly members:
humna_ubiquitin-like_domain_of_Herp, polymer, 99 residues, 9000.604 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):
humna_ubiquitin-like_domain_of_Herp: MGSSHHHHHHSSGRENLYFQ GHPVTLIIKAPNQKYSDQTI SCFLNWTVGKLKTHLSNVYP SKPLTKDQRLVYSGRLLPDH LQLKDILRKQDEYHMVHLV

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	349
15N chemical shifts	73
1H chemical shifts	580

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	humna_ubiquitin-like_domain_of_Herp	1

Entities:

Entity 1, humna_ubiquitin-like_domain_of_Herp 99 residues - 9000.604 Da.

1

MET

GLY

SER

HIS

2

SER

GLY

ARG

GLU

ASN

LEU

TYR

PHE

GLN

3

GLY

HIS

PRO

VAL

THR

LEU

ILE

LYS

ALA

4

PRO

ASN

GLN

LYS

TYR

SER

ASP

GLN

THR

ILE

5

SER

CYS

PHE

LEU

ASN

TRP

THR

VAL

GLY

LYS

6

LEU

LYS

THR

HIS

LEU

SER

ASN

VAL

TYR

PRO

7

SER

LYS

PRO

LEU

THR

LYS

ASP

GLN

ARG

LEU

8

VAL

TYR

SER

GLY

ARG

LEU

PRO

ASP

HIS

9

LEU

GLN

LEU

LYS

ASP

ILE

LEU

ARG

LYS

GLN

10

ASP

GLU

TYR

HIS

MET

VAL

HIS

LEU

VAL

Samples:

sample_1: humna ubiquitin-like domain of Herp, [U-100% 13C; U-100% 15N], 0.5 mM; TRIS, [U-100% 2H], 10 mM; sodium chloride 300 mM; sodium azide 0.01%; benzamidine 10 mM; H2O 90%; D2O 10%

sample_2: humna ubiquitin-like domain of Herp, [U-100% 13C; U-100% 15N], 0.5 mM; TRIS, [U-100% 2H], 10 mM; sodium chloride 300 mM; sodium azide 0.01%; benzamidine 10 mM; D2O 100%

sample_3: humna ubiquitin-like domain of Herp, [U-7% 13C; U-100% 15N], 0.5 mM; TRIS, [U-100% 2H], 10 mM; sodium chloride 300 mM; sodium azide 0.01%; benzamidine 10 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 300 mM; pH: 7; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D HNCO	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D 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 NOESY	sample_2	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_3	isotropic	sample_conditions_1

Software:

MNRPipe v2.3, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

SPARKY v3.95, Goddard - data analysis, peak picking

FAWN v1.0, Lemak and Arrowsmith - backbone assignment

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

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

AutoStruct, Huang, Tejero, Powers and Montelione - NMR structure quality assessment

NMR spectrometers:

Bruker Avance 600 MHz
Bruker Avance 800 MHz
Varian INOVA 500 MHz

PDB	2KDB
DBJ	BAA95064 BAB31889 BAE22730 BAE89340 BAG38050
GB	AAH05091 AAH20264 AAH29691 AAH43693 AAH81861
REF	NP_001020159 NP_001069026 NP_001270669 NP_065611 NP_071768
SP	Q0P5H8 Q66HH4 Q9BSE4 Q9JJC9
TPG	DAA30580
AlphaFold	Q0P5H8 Q66HH4 Q9BSE4 Q9JJC9