BMRB Entry 19390

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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/BMR19390
MolProbity Validation Chart

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Title:
Solution structure of the EBNA-2 N-terminal Dimerization (END) domain from the Epstein-Barr virus
Deposition date:
2013-07-26
Original release date:
2015-06-08
Authors:
Friberg, Anders; Sattler, Michael
Citation:

Citation: Friberg, Anders; Thumann, Sybille; Hennig, Janosch; Zou, Peijian; Ling, Paul; Sattler, Michael; Kempkes, Bettina. "The EBNA-2 N-Terminal Transactivation Domain Folds into a Dimeric Structure Required for Target Gene Activation"  Plos Pathog. 11, e1004910-e1004910 (2015).
PubMed: 26024477

Assembly members:

Assembly members:
END_domain, polymer, 62 residues, 6663.513 Da.

Natural source:

Natural source:   Common Name: Epstein-Barr virus   Taxonomy ID: 10377   Superkingdom: Viruses   Kingdom: not available   Genus/species: Lymphocryptovirus Human herpesvirus 4

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pET-24d

Entity Sequences (FASTA):

Entity Sequences (FASTA):
END_domain: GAMEMPTFYLALHGGQTYHL IVDTDSLGNPSLSVIPSNPY QEQLSDTPLIPLTIFVGENT GV

Data sets:
Data typeCount
13C chemical shifts211
15N chemical shifts54
1H chemical shifts421

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1END domain, chain 11
2END domain, chain 21

Entities:

Entity 1, END domain, chain 1 62 residues - 6663.513 Da.

Amino acids 1-4 represent residual non-native residues present after removal of the affinity and solubility tag.

1   GLYALAMETGLUMETPROTHRPHETYRLEU
2   ALALEUHISGLYGLYGLNTHRTYRHISLEU
3   ILEVALASPTHRASPSERLEUGLYASNPRO
4   SERLEUSERVALILEPROSERASNPROTYR
5   GLNGLUGLNLEUSERASPTHRPROLEUILE
6   PROLEUTHRILEPHEVALGLYGLUASNTHR
7   GLYVAL

Samples:

sample_1: END domain, [U-13C; U-15N], 1 mM; H2O 95%; D2O 5%; sodium phosphate 20 mM; sodium chloride 20 mM; NaN3 0.02%

sample_conditions_1: ionic strength: 20 mM; pH: 6.9; pressure: 1 atm; temperature: 323 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HNCACBsample_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 NOESY aliphaticsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_1isotropicsample_conditions_1

Software:

CYANA v3.0, Guntert, Mumenthaler and Wuthrich - structure solution

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

TOPSPIN, Bruker Biospin - collection

NMRView, Johnson, One Moon Scientific - data analysis

SPARKY, Goddard - data analysis

ARIA v2.2, Linge, O'Donoghue and Nilges - structure solution

NMR spectrometers:

  • Bruker Avance various MHz

Related Database Links:

UNP P12978
PDB
DBJ BAP94392 BAQ20285
EMBL CAA24877 CAD53395 CEP79167 CEQ32332 CEQ32414
GB AAA45903 AAY41099 AFY97831 AFY97916 AGL80643
REF YP_401644
SP P12978 Q3KSV2
AlphaFold Q777H1 P12978 Q3KSV2

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