BMRB Entry 16109

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):

Data sets:
Data typeCount
13C chemical shifts349
15N chemical shifts73
1H chemical shifts580

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1humna_ubiquitin-like_domain_of_Herp1

Entities:

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

1   METGLYSERSERHISHISHISHISHISHIS
2   SERSERGLYARGGLUASNLEUTYRPHEGLN
3   GLYHISPROVALTHRLEUILEILELYSALA
4   PROASNGLNLYSTYRSERASPGLNTHRILE
5   SERCYSPHELEUASNTRPTHRVALGLYLYS
6   LEULYSTHRHISLEUSERASNVALTYRPRO
7   SERLYSPROLEUTHRLYSASPGLNARGLEU
8   VALTYRSERGLYARGLEULEUPROASPHIS
9   LEUGLNLEULYSASPILELEUARGLYSGLN
10   ASPGLUTYRHISMETVALHISLEUVAL

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:

NameSampleSample stateSample conditions
3D HNCOsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D CCH-TOCSYsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_2isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_3isotropicsample_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

Related Database Links:

PDB
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 Q9JJC9 Q66HH4 Q9BSE4 Q0P5H8

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