BMRB Entry 36759

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR36759
MolProbity Validation Chart

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
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Title:
Encounter complex structure of E2N and Ubiquitin
Deposition date:
2025-05-09
Original release date:
2026-02-12
Authors:
Gong, Z.; Liu, M.; Zhang, X.; He, L.; Zhao, Q.; Zhang, L.; Zhang, B.
Citation:

Citation: Gong, Z.; Zhang, B.; He, X.; Zhong, B.; Zhu, Y.; Tan, K.; Liu, Z.; Chen, J.; Liang, Z.; Zhang, X.; He, L.; Zhang, Y.; Zhang, L.; Liu, M.; Zhao, Q.. "X-GAME: An Integrative Framework for Deciphering Protein-Protein Interactions in Living Cells"  .

Assembly members:

Assembly members:
Ubiquitin-conjugating enzyme E2 N, polymer, 150 residues, 16944.533 Da.
Ubiquitin, polymer, 76 residues, 8576.831 Da.
(5~{S},16~{S})-16-[2-[2,5-bis(oxidanylidene)pyrrolidin-1-yl]ethylamino]-2,11,12,17-tetraoxa-5,8-diaza-1$l^{4}-manganatricyclo[6.3.3.3^{1,5}]heptadecane-3,10,13-trione, non-polymer, 469.305 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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Ubiquitin-conjugating enzyme E2 N: GLPRRIIKETQRLLAEPVPG IKAEPDESNARYFHVVIAGP QDSPFEGGTFKLELFLPEEY PMAAPKVRFMTKIYHPNVDK LGRICLDILKDKWSPALQIR TVLLSIQALLSAPNPDDPLA CDVAEQWKTNEAQAIETARA WTRLYAMNNI
Ubiquitin: MQIFVKTLTGKTITLEVEPS DTIENVKAKIQDKEGIPPDQ QRLIFAGKQLEDGRTLSDYN IQKESTLHLVLRLRGG

Data sets:
Data typeCount
13C chemical shifts214
15N chemical shifts70
1H chemical shifts70

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11
2entity_22
3entity_A1EQF3

Entities:

Entity 1, entity_1 150 residues - 16944.533 Da.

1   GLYLEUPROARGARGILEILELYSGLUTHR
2   GLNARGLEULEUALAGLUPROVALPROGLY
3   ILELYSALAGLUPROASPGLUSERASNALA
4   ARGTYRPHEHISVALVALILEALAGLYPRO
5   GLNASPSERPROPHEGLUGLYGLYTHRPHE
6   LYSLEUGLULEUPHELEUPROGLUGLUTYR
7   PROMETALAALAPROLYSVALARGPHEMET
8   THRLYSILETYRHISPROASNVALASPLYS
9   LEUGLYARGILECYSLEUASPILELEULYS
10   ASPLYSTRPSERPROALALEUGLNILEARG
11   THRVALLEULEUSERILEGLNALALEULEU
12   SERALAPROASNPROASPASPPROLEUALA
13   CYSASPVALALAGLUGLNTRPLYSTHRASN
14   GLUALAGLNALAILEGLUTHRALAARGALA
15   TRPTHRARGLEUTYRALAMETASNASNILE

Entity 2, entity_2 76 residues - 8576.831 Da.

1   METGLNILEPHEVALLYSTHRLEUTHRGLY
2   LYSTHRILETHRLEUGLUVALGLUPROSER
3   ASPTHRILEGLUASNVALLYSALALYSILE
4   GLNASPLYSGLUGLYILEPROPROASPGLN
5   GLNARGLEUILEPHEALAGLYLYSGLNLEU
6   GLUASPGLYARGTHRLEUSERASPTYRASN
7   ILEGLNLYSGLUSERTHRLEUHISLEUVAL
8   LEUARGLEUARGGLYGLY

Entity 3, entity_A1EQF - C16 H22 Mn N4 O9 - 469.305 Da.

1   A1EQF

Samples:

sample_1: E2N 0.2 mM; Ubi, [U-15N], 0.6 mM; HEPES 20 mM; D2O, [U-2H], 10%; H2O 90%

sample_conditions_1: ionic strength: 0.02 M; pH: 7.5; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D PREsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D iHNCAsample_1isotropicsample_conditions_1
3D iHN(CA)CBsample_1isotropicsample_conditions_1

Software:

NMRPipe v2010, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - peak picking

Amber, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement

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

NMR spectrometers:

  • Bruker AVANCE 800 MHz

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