BMRB Entry 18677

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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/BMR18677
MolProbity Validation Chart

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Title:
1H, 13C and 15N Assignments of the RING domain in ubiquitin ligase gp78
Deposition date:
2012-08-27
Original release date:
2013-08-26
Authors:
Das, Ranabir; Linag, Yuhe; Mariano, Jennifer; Li, Jess; Huang, Tao; King, Aaren; Weissman, Allan; Ji, Xinhua; Byrd, R. Andrew
Citation:

Citation: Das, Ranabir; Liang, Yu-He; Mariano, Jennifer; Li, Jess; Huang, Tao; King, Aaren; Tarasov, Sergey; Weissman, Allan; Ji, Xinhua; Byrd, R. Andrew. "Allosteric regulation of E2:E3 interactions promote a processive ubiquitination machine."  EMBO J. 32, 2504-2516 (2013).
PubMed: 23942235

Assembly members:

Assembly members:
gp78RING, polymer, 58 residues, 6473.385 Da.
ZINC ION, non-polymer, 65.409 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: pET3a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
gp78RING: AVATPEELAVNNDDCAICWD SMQAARKLPCGHLFHNSCLR SWLEQDTSCPTCRMSLNI

Data sets:
Data typeCount
13C chemical shifts232
15N chemical shifts70
1H chemical shifts352

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1RING domain in ubiquitin ligase gp781
2ZINC ION_12
3ZINC ION_22

Entities:

Entity 1, RING domain in ubiquitin ligase gp78 58 residues - 6473.385 Da.

1   ALAVALALATHRPROGLUGLULEUALAVAL
2   ASNASNASPASPCYSALAILECYSTRPASP
3   SERMETGLNALAALAARGLYSLEUPROCYS
4   GLYHISLEUPHEHISASNSERCYSLEUARG
5   SERTRPLEUGLUGLNASPTHRSERCYSPRO
6   THRCYSARGMETSERLEUASNILE

Entity 2, ZINC ION_1 - Zn - 65.409 Da.

1   ZN

Samples:

sample_1: gp78RING, [U-100% 13C; U-100% 15N], 0.7 – 1 mM; TRIS 50 mM; TCEP 2 mM; sodium azide 0,2 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 0 M; pH: 7.2; 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 CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D C(CO)NHsample_1isotropicsample_conditions_1
3D H(CCO)NHsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-15N TOCSYsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_1isotropicsample_conditions_1

Software:

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - structure solution

SPARKY, Goddard - chemical shift assignment, data analysis

NMRDraw, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMR spectrometers:

  • Varian INOVA 600 MHz
  • Varian INOVA 500 MHz

Related Database Links:

PDB
DBJ BAE01277 BAE34049 BAE41974 BAE87377 BAK63135
GB AAD56721 AAD56722 AAH17043 AAH34538 AAH40338
REF NP_001039439 NP_001135 NP_001267243 NP_035917 XP_001091030
SP Q9R049 Q9UKV5
TPG DAA20037
AlphaFold Q9R049 Q9UKV5

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