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- PDB-5t7x: Crystal structure of HHV-4 EBNA1 DNA binding domain (patient-deri... -

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Basic information

Entry
Database: PDB / ID: 5t7x
TitleCrystal structure of HHV-4 EBNA1 DNA binding domain (patient-derived, nasopharyngeal carcinoma) bound to DNA
Components
  • DNA (5'-D(*GP*GP*AP*TP*AP*GP*CP*CP*TP*AP*TP*GP*CP*TP*AP*CP*CP*C)-3')
  • DNA (5'-D(*GP*GP*GP*TP*AP*GP*CP*AP*TP*AP*GP*GP*CP*TP*AP*TP*CP*C)-3')
  • Epstein-Barr nuclear antigen 1
KeywordsDNA BINDING PROTEIN/DNA / Dimer / DNA / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


viral latency / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / regulation of DNA replication / endonuclease activity / symbiont-mediated suppression of host NF-kappaB cascade / DNA-binding transcription factor activity / positive regulation of DNA-templated transcription / host cell nucleus / DNA binding / identical protein binding
Similarity search - Function
Epstein Barr virus nuclear antigen-1, DNA-binding domain / Epstein Barr virus nuclear antigen-1, DNA-binding / Epstein Barr virus nuclear antigen-1, DNA-binding domain / Epstein Barr virus nuclear antigen-1, DNA-binding domain superfamily / E2/EBNA1, C-terminal / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Epstein-Barr nuclear antigen 1
Similarity search - Component
Biological speciesHuman herpesvirus 4 (Epstein-Barr virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsMalecka, K.A. / Messick, T.E. / Lieberman, P.M.
CitationJournal: Oncotarget / Year: 2017
Title: Carcinoma-risk variant of EBNA1 deregulates Epstein-Barr Virus episomal latency.
Authors: Dheekollu, J. / Malecka, K. / Wiedmer, A. / Delecluse, H.J. / Chiang, A.K. / Altieri, D.C. / Messick, T.E. / Lieberman, P.M.
History
DepositionSep 6, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: DNA (5'-D(*GP*GP*AP*TP*AP*GP*CP*CP*TP*AP*TP*GP*CP*TP*AP*CP*CP*C)-3')
D: DNA (5'-D(*GP*GP*GP*TP*AP*GP*CP*AP*TP*AP*GP*GP*CP*TP*AP*TP*CP*C)-3')
A: Epstein-Barr nuclear antigen 1
B: Epstein-Barr nuclear antigen 1


Theoretical massNumber of molelcules
Total (without water)43,6974
Polymers43,6974
Non-polymers00
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11710 Å2
ΔGint-56 kcal/mol
Surface area15780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.025, 64.904, 111.783
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: DNA chain DNA (5'-D(*GP*GP*AP*TP*AP*GP*CP*CP*TP*AP*TP*GP*CP*TP*AP*CP*CP*C)-3')


Mass: 5476.554 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Human herpesvirus 4 (strain B95-8) (Epstein-Barr virus (strain B95-8))
#2: DNA chain DNA (5'-D(*GP*GP*GP*TP*AP*GP*CP*AP*TP*AP*GP*GP*CP*TP*AP*TP*CP*C)-3')


Mass: 5556.603 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Human herpesvirus 4 (strain B95-8) (Epstein-Barr virus (strain B95-8))
#3: Protein Epstein-Barr nuclear antigen 1 / EBV nuclear antigen 1


Mass: 16332.018 Da / Num. of mol.: 2 / Fragment: UNP residues 459-507
Source method: isolated from a genetically manipulated source
Details: patient-derived, nasopharyngeal carcinoma
Source: (gene. exp.) Human herpesvirus 4 (strain B95-8) (Epstein-Barr virus (strain B95-8))
Strain: GD1 / Gene: EBNA1, BKRF1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3KSS4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 50.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2 M ammonium acetate, 0.15 M magnesium acetate tetrahydrate, 0.05 M Hepes, pH 7.0, 5% PEG 4000
Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Aug 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 19350 / % possible obs: 98.7 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.198 / Net I/σ(I): 21.9
Reflection shellRedundancy: 7.2 % / Rmerge(I) obs: 0.879 / Mean I/σ(I) obs: 7.4 / % possible all: 97.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1B3T

1b3t


Resolution: 2.35→23.373 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.79
RfactorNum. reflection% reflection
Rfree0.2329 2183 9.99 %
Rwork0.1854 --
obs0.1902 21843 62.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.35→23.373 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2272 732 0 122 3126
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053150
X-RAY DIFFRACTIONf_angle_d0.9054421
X-RAY DIFFRACTIONf_dihedral_angle_d20.0591219
X-RAY DIFFRACTIONf_chiral_restr0.036486
X-RAY DIFFRACTIONf_plane_restr0.005449
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3501-2.40120.3098480.2716453X-RAY DIFFRACTION23
2.4012-2.4570.3274680.2852565X-RAY DIFFRACTION29
2.457-2.51840.321830.2977706X-RAY DIFFRACTION36
2.5184-2.58640.3714930.2971929X-RAY DIFFRACTION46
2.5864-2.66240.2951030.3107984X-RAY DIFFRACTION51
2.6624-2.74820.34881230.30591084X-RAY DIFFRACTION54
2.7482-2.84620.29761270.31781099X-RAY DIFFRACTION56
2.8462-2.960.3441330.2841160X-RAY DIFFRACTION59
2.96-3.09440.31831370.23041267X-RAY DIFFRACTION64
3.0944-3.25710.28281510.22391332X-RAY DIFFRACTION68
3.2571-3.46060.25371590.19511425X-RAY DIFFRACTION73
3.4606-3.72680.19321840.15871627X-RAY DIFFRACTION82
3.7268-4.10.1731880.1361665X-RAY DIFFRACTION84
4.1-4.68920.16561960.12341758X-RAY DIFFRACTION89
4.6892-5.89220.17381890.12521774X-RAY DIFFRACTION89
5.8922-23.37450.20532010.13951832X-RAY DIFFRACTION93

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