BMRB Entry 16789

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR16789
MolProbity Validation Chart

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Title:
Solution NMR structure of human ubiquitin specific protease Usp7 UBL domain (residues 537-664). NESG target hr4395c/ SGC-Toronto
Deposition date:
2010-03-25
Original release date:
2010-09-24
Authors:
Bezsonova, Irina; Lemak, Alexander; Avvakumov, George; Bezsonova, Irina; Dhe-Paganon, Sirano; Arrowsmith, Cheryl
Citation:

Citation: Bezsonova, Irina; Avvakumov, George; Dhe-Paganon, Sirano; Arrowsmith, Cheryl. "solution structure of the ubiquitin specific protease Usp7 ubiquitin-like domain"  .

Assembly members:

Assembly members:
usp7-ubl1, polymer, 130 residues, 15040.011 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: pET28a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
usp7-ubl1: GSPQQLVERLQEEKRIEAQK RKERQEAHLYMQVQIVAEDQ FCGHQGNDMYDEEKVKYTVF KVLKNSSLAEFVQSLSQTMG FPQDQIRLWPMQARSNGTKR PAMLDNEADGNKTMIELSDN ENPWTIFLET

Data sets:
Data typeCount
13C chemical shifts524
15N chemical shifts123
1H chemical shifts866

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1usp7-ubl11

Entities:

Entity 1, usp7-ubl1 130 residues - 15040.011 Da.

residues 1-2 are non-native. Residues 3-130 correspond to residues 537-664 in the full length Usp7.

1   GLYSERPROGLNGLNLEUVALGLUARGLEU
2   GLNGLUGLULYSARGILEGLUALAGLNLYS
3   ARGLYSGLUARGGLNGLUALAHISLEUTYR
4   METGLNVALGLNILEVALALAGLUASPGLN
5   PHECYSGLYHISGLNGLYASNASPMETTYR
6   ASPGLUGLULYSVALLYSTYRTHRVALPHE
7   LYSVALLEULYSASNSERSERLEUALAGLU
8   PHEVALGLNSERLEUSERGLNTHRMETGLY
9   PHEPROGLNASPGLNILEARGLEUTRPPRO
10   METGLNALAARGSERASNGLYTHRLYSARG
11   PROALAMETLEUASPASNGLUALAASPGLY
12   ASNLYSTHRMETILEGLULEUSERASPASN
13   GLUASNPROTRPTHRILEPHELEUGLUTHR

Samples:

sample_1: entity, [U-100% 13C; U-100% 15N], 0.8-1.2 mM; sodium phosphate, pH 7.0 20 mM; sodium chloride 250 mM; DTT 2 mM; PMSF 0.5 mM; benzamidine 1 mM; TCEP 1 mM

sample_conditions_1: ionic strength: 250 mM; pH: 7.0; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_1isotropicsample_conditions_1
3D aromatic 1H-13C NOESYsample_1isotropicsample_conditions_1

Software:

NMRPipe v2.3, Frank Delaglio - processing

ABACUS, A. Lemak - chemical shift assignment

CYANA v2.1, Peter Guntert - structure solution

SPARKY, T. D. Goddard and D. G. Kneller - data analysis

NMR spectrometers:

  • Bruker Avance 800 MHz
  • Bruker Avance 600 MHz

Related Database Links:

PDB
DBJ BAH13721 BAH13801 BAH13841 BAH14812
EMBL CAA96580
GB AAI00667 AAI66012 AAI66690 AAQ12339 AAQ74887
REF NP_001003918 NP_001019961 NP_001129152 NP_001273386 NP_001273387
SP Q4VSI4 Q6A4J8 Q6U7I1 Q93009
AlphaFold Q4VSI4 Q6A4J8 Q6U7I1 Q93009

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