BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 16390

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: 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."  Not known ., .-..

Assembly members:
ubiquilin_1, polymer, 101 residues, 9053.559 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):
ubiquilin_1: MGSSHHHHHHSSGRENLYFQ GHPKIMKVTVKTPKEKEEFA VPENSSVQQFKEEISKRFKS HTDQLVLIFAGKILKDQDTL SQHGIHDGLTVHLVIKTQNR P

Data sets:
Data typeCount
13C chemical shifts328
15N chemical shifts79
1H chemical shifts545
residual dipolar couplings75

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1ubiquilin_11

Entities:

Entity 1, ubiquilin_1 101 residues - 9053.559 Da.

1   METGLYSERSERHISHISHISHISHISHIS
2   SERSERGLYARGGLUASNLEUTYRPHEGLN
3   GLYHISPROLYSILEMETLYSVALTHRVAL
4   LYSTHRPROLYSGLULYSGLUGLUPHEALA
5   VALPROGLUASNSERSERVALGLNGLNPHE
6   LYSGLUGLUILESERLYSARGPHELYSSER
7   HISTHRASPGLNLEUVALLEUILEPHEALA
8   GLYLYSILELEULYSASPGLNASPTHRLEU
9   SERGLNHISGLYILEHISASPGLYLEUTHR
10   VALHISLEUVALILELYSTHRGLNASNARG
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:

NameSampleSample stateSample conditions
3D HNCOsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D (H)CCH-TOCSYsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_1isotropicsample_conditions_1
3D 1H-13C_arom NOESYsample_1isotropicsample_conditions_1
2D 1H-15 HSQC (IPAP)sample_1anisotropicsample_conditions_1
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C Constant Time HSQCsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D HNCO (IPAP)sample_1anisotropicsample_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

Related Database Links:

PDB
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

Download simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts