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- PDB-6vh6: Crystal structure of Epstein-Barr Virus Nuclear Antigen-1, EBNA1,... -

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Basic information

Entry
Database: PDB / ID: 6vh6
TitleCrystal structure of Epstein-Barr Virus Nuclear Antigen-1, EBNA1, bound to fragment
ComponentsEpstein-Barr nuclear antigen 1Epstein–Barr virus nuclear antigen 1
KeywordsVIRAL PROTEIN / EBNA1 / DNA binding protein / Epstein-Barr Virus / viral protein-dna complex
Function / homology
Function and homology information


host cell PML body / symbiont-mediated suppression of host antigen processing and presentation / viral latency / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / enzyme-substrate adaptor activity / symbiont-mediated disruption of host cell PML body / regulation of DNA replication / virus-mediated perturbation of host defense response / endonuclease activity / DNA-binding transcription factor activity ...host cell PML body / symbiont-mediated suppression of host antigen processing and presentation / viral latency / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / enzyme-substrate adaptor activity / symbiont-mediated disruption of host cell PML body / regulation of DNA replication / virus-mediated perturbation of host defense response / endonuclease activity / DNA-binding transcription factor activity / positive regulation of DNA-templated transcription / DNA 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
4-hydroxy-6-methyl-2H-1-benzopyran-2-one / Epstein-Barr nuclear antigen 1
Similarity search - Component
Biological speciesEpstein-Barr virus (Epstein-Barr virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsMessick, T.E. / Lieberman, P.M.
Funding support United Kingdom, United States, 2items
OrganizationGrant numberCountry
Wellcome TrustWT096496 United Kingdom
National Institutes of Health/National Cancer Institute (NIH/NCI)5R01CA186775 United States
CitationJournal: Molecules / Year: 2020
Title: Biophysical Screens Identify Fragments That Bind to the Viral DNA-Binding Proteins EBNA1 and LANA.
Authors: Messick, T.E. / Tolvinski, L. / Zartler, E.R. / Moberg, A. / Frostell, A. / Smith, G.R. / Reitz, A.B. / Lieberman, P.M.
History
DepositionJan 9, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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

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Assembly

Deposited unit
A: Epstein-Barr nuclear antigen 1
B: Epstein-Barr nuclear antigen 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9043
Polymers30,7272
Non-polymers1761
Water8,179454
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Homo 2-mer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3810 Å2
ΔGint-22 kcal/mol
Surface area12730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.516, 68.344, 69.687
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Epstein-Barr nuclear antigen 1 / Epstein–Barr virus nuclear antigen 1 / EBV nuclear antigen 1


Mass: 15363.729 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Epstein-Barr virus (strain B95-8) (Epstein-Barr virus (strain B95-8))
Strain: B95-8 / Gene: EBNA1, BKRF1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P03211
#2: Chemical ChemComp-QX4 / 4-hydroxy-6-methyl-2H-1-benzopyran-2-one


Mass: 176.169 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 454 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.31 Å3/Da / Density % sol: 46.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 50 mM MES pH 6.5, 0-100 mM NaCl, 10 mM DTT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 19, 2015
RadiationMonochromator: Si (111) Rosenbaum-Rock double-crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 69927 / % possible obs: 99.1 % / Redundancy: 6.4 % / Biso Wilson estimate: 14.6 Å2 / Rmerge(I) obs: 0.061 / Rrim(I) all: 0.066 / Χ2: 0.882 / Net I/σ(I): 26.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) allΧ2% possible all
3.53-506.50.0533.136550.9960.0541.09396.3
2.8-3.537.20.04136.436180.9980.0440.65299.8
2.45-2.87.30.04634.835740.9970.0490.693100
2.22-2.457.30.05633.235590.9970.061.031100
2.06-2.227.30.06231.335500.9960.0661.044100
1.94-2.067.30.0728.135220.9950.0760.964100
1.84-1.947.30.0942435260.9940.1021.356100
1.76-1.847.30.10218.835240.9930.110.842100
1.7-1.767.30.12615.535060.9910.1360.873100
1.64-1.77.30.15312.735120.9880.1640.844100
1.59-1.647.20.18510.434890.9820.1990.843100
1.54-1.597.20.2278.3535010.9760.2450.815100
1.5-1.546.90.3096.5135070.9510.3341.018100
1.46-1.56.20.3344.9734910.940.3650.84100
1.43-1.465.80.4193.6334770.9030.4610.778100
1.4-1.435.40.4832.8835000.8650.5350.67699.9
1.37-1.45.10.5522.3934380.8280.6160.67499.1
1.35-1.374.40.6731.8534390.7060.7640.84199
1.32-1.353.60.6971.3633490.6140.8130.62495.8
1.3-1.323.10.81.0331900.5570.9460.64391.9

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Processing

Software
NameVersionClassification
PHENIX1.17refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1vhi

1vhi


Resolution: 1.3→21.9965 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.1608 --Random
Rwork0.15 ---
obs-62225 86.9 %-
Displacement parametersBiso mean: 23 Å2
Refinement stepCycle: LAST / Resolution: 1.3→21.9965 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2101 0 13 454 2568
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00912353
X-RAY DIFFRACTIONf_angle_d1.00743228
X-RAY DIFFRACTIONf_chiral_restr0.0737360
X-RAY DIFFRACTIONf_plane_restr0.0078431
X-RAY DIFFRACTIONf_dihedral_angle_d12.6495894

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