BMRB Entry 17554

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR17554
MolProbity Validation Chart

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Title:
solution structure of tandem UBA of USP13
Deposition date:
2011-03-29
Original release date:
2012-03-05
Authors:
Zhang, Yuhang; Zhou, Chenjie; Zhou, Ziren; Song, Aixin; Hun, Hongyu
Citation:

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).
PubMed: 22216260

Assembly members:

Assembly members:
tandem UBA of USP13, polymer, 126 residues, 13769.365 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: pET-32M

Entity Sequences (FASTA):

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

Data sets:
Data typeCount
13C chemical shifts351
15N chemical shifts119
1H chemical shifts702

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1tandem UBA of USP131

Entities:

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

1   ASPILEASPGLUSERSERVALMETGLNLEU
2   ALAGLUMETGLYPHEPROLEUGLUALACYS
3   ARGLYSALAVALTYRPHETHRGLYASNMET
4   GLYALAGLUVALALAPHEASNTRPILEILE
5   VALHISMETGLUGLUPROASPPHEALAGLU
6   PROLEUTHRMETPROGLYTYRGLYGLYALA
7   ALASERALAGLYALASERVALPHEGLYALA
8   SERGLYLEUASPASNGLNPROPROGLUGLU
9   ILEVALALAILEILETHRSERMETGLYPHE
10   GLNARGASNGLNALAILEGLNALALEUARG
11   ALATHRASNASNASNLEUGLUARGALALEU
12   ASPTRPILEPHESERHISPROGLUPHEGLU
13   GLUASPSERASPPHEVAL

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:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_2isotropicsample_conditions_1
3D HNCACBsample_2isotropicsample_conditions_1
3D C(CO)NHsample_2isotropicsample_conditions_1
3D HNHAsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_2isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_2isotropicsample_conditions_1

Software:

ARIA2.0, Linge, O'Donoghue and Nilges - 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

Related Database Links:

PDB
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
AlphaFold Q92995

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