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- PDB-1b3t: EBNA-1 NUCLEAR PROTEIN/DNA COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1b3t
TitleEBNA-1 NUCLEAR PROTEIN/DNA COMPLEX
Components
  • DNA (5'-D(*GP*GP*GP*AP*AP*GP*CP*AP*TP*AP*TP*GP*CP*TP*TP*CP*CP*C)-3')
  • PROTEIN (NUCLEAR PROTEIN EBNA1)
KeywordsPROTEIN/DNA / NUCLEAR PROTEIN / PROTEIN-DNA COMPLEX / DNA-BINDING / ACTIVATOR / ORIGIN-BINDING PROTEIN
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 / endonuclease activity / DNA-binding transcription factor activity / virus-mediated perturbation of host defense response ...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 / endonuclease activity / DNA-binding transcription factor activity / virus-mediated perturbation of host defense response / host cell nucleus / positive regulation of DNA-templated transcription / DNA binding / nucleus
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 / Nuclear antigen EBNA-1
Similarity search - Component
Biological speciesHuman herpesvirus 4 (Epstein-Barr virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBochkarev, A. / Bochkareva, E. / Edwards, A. / Frappier, L.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: The 2.2 A structure of a permanganate-sensitive DNA site bound by the Epstein-Barr virus origin binding protein, EBNA1.
Authors: Bochkarev, A. / Bochkareva, E. / Frappier, L. / Edwards, A.M.
#1: Journal: Cell(Cambridge,Mass.) / Year: 1996
Title: Crystal Structure of the DNA-Binding Domain of Theepstein-Barr Virus Origin- Binding Protein, EBNA1, Boundto DNA
Authors: Bochkarev, A. / Barwell, J.A. / Pfuetzner, R.A. / Bochkareva, E. / Frappier, L. / Edwards, A.M.
#2: Journal: J.Biol.Chem. / Year: 1995
Title: Overexpression, Purification, and Crystallization of the DNA Binding and Dimerization Domains of the Epstein-Barr Virus Nuclear Antigen 1
Authors: Barwell, J.A. / Bochkarev, A. / Pfuetzner, R.A. / Tong, H. / Yang, D.S. / Frappier, L. / Edwards, A.M.
History
DepositionDec 14, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Dec 15, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 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*GP*AP*AP*GP*CP*AP*TP*AP*TP*GP*CP*TP*TP*CP*CP*C)-3')
D: DNA (5'-D(*GP*GP*GP*AP*AP*GP*CP*AP*TP*AP*TP*GP*CP*TP*TP*CP*CP*C)-3')
A: PROTEIN (NUCLEAR PROTEIN EBNA1)
B: PROTEIN (NUCLEAR PROTEIN EBNA1)


Theoretical massNumber of molelcules
Total (without water)43,0504
Polymers43,0504
Non-polymers00
Water3,279182
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.083, 64.501, 111.938
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

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


Mass: 5516.578 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein PROTEIN (NUCLEAR PROTEIN EBNA1) / EBNA-1 NUCLEAR PROTEIN


Mass: 16008.498 Da / Num. of mol.: 2
Fragment: DNA-BINDING AND DIMERIZATION DOMAIN RESIDUES 459 - 607
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 4 (Epstein-Barr virus)
Genus: Lymphocryptovirus / Strain: GD1 / Cellular location: NUCLEAR / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLUSS / References: UniProt: Q69477, UniProt: P03211*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O
Compound detailsEBNA1 ENCODED BY EBV B95-8 COMPRISES 641 AMINO ACIDS AND IS VERY STABLE DIMER BOTH IN SOLUTION AND ...EBNA1 ENCODED BY EBV B95-8 COMPRISES 641 AMINO ACIDS AND IS VERY STABLE DIMER BOTH IN SOLUTION AND WHEN BOUND TO 1 8 BP RECOGNITION SEQUENCE. DNA-BINDING AND DIMERIZATION DOMAIN HAVE BEEN LOCALIZED TO WITHIN RESIDUES 459-607. A FRAGMENT 459-607 PREVIOUSLY DETERMINED TO BE ACTIVE FOR SEQUENCE-SPECIFIC DNA BINDING. EBNA1 IS FOUND TO HAVE STRUCTURAL, BUT NOT SEQUENCE, HOMOLOGY WITH THE DNA-BINDING DOMAIN OF THE E2 PROTEIN PDB ENTRY 2BOP.

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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: 2.52 Å3/Da / Density % sol: 51.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: METHOD - HANGING DROP VAPOR DIFFUSION. RESERVOIR: 100 MM MES (PH 5.6) 20% PEG 4000, 500 MM NACL, 10 MM MGCL2, 10 MM DTT PROTEIN: 10MG/ML 1MM HEPES PH 7.2 1M NACL, 10 MM DTT DRY DNA ...Details: METHOD - HANGING DROP VAPOR DIFFUSION. RESERVOIR: 100 MM MES (PH 5.6) 20% PEG 4000, 500 MM NACL, 10 MM MGCL2, 10 MM DTT PROTEIN: 10MG/ML 1MM HEPES PH 7.2 1M NACL, 10 MM DTT DRY DNA RESUSPENDED IN THE PROTEIN CONTAINING SOLUTION IN MOLAR RATIO 1.5 (DSDNA) / 1.0 (EBNA1 DIMER) DROP: 50% PROTEIN/DNA SOLUTION 50% RESERVOIR SOLUTION CRYSTALLIZATION TEMPERATURE: 4 GEDREES C, vapor diffusion - hanging drop, temperature 277K
PH range: 5.6-7.2
Components of the solutions
IDNameCrystal-IDSol-ID
1HEPES11
2NACLSodium chloride11
3DTT11
4PEG 400011
5MES11
6MGCL211
7PEG 400012
8MES12
9NACLSodium chloride12
10MGCL212
11DTT12
Crystal grow
*PLUS
pH: 7.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mg/mlEBNA1drop
21 mMHEPES1drop
31 M1dropNaCl
410 mMdithiothreitol1drop
6100 mMMES1reservoir
720 %(v/v)PEG40001reservoir
8500 mM1reservoirNaCl
910 mM1reservoirMgCl2
5dsDNA1dropa ratio of 1.5 dsDNA molecules to EBNA1 dimer
1010 mMdithiothreitol1reservoir
111

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.922
DetectorType: CUSTOM-MADE / Detector: CCD / Date: May 1, 1994
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.922 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 25865 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 4.5
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.121 / Mean I/σ(I) obs: 3.1 / % possible all: 93.2
Reflection
*PLUS
Num. measured all: 142136
Reflection shell
*PLUS
% possible obs: 74.5 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.843refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VHI

1vhi


Resolution: 2.2→6 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.268 -10 %RANDOM
Rwork0.208 ---
obs0.208 21158 98.4 %-
Refinement stepCycle: LAST / Resolution: 2.2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2250 732 0 182 3164
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.5
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2
X-RAY DIFFRACTIONx_mcangle_it2.5
X-RAY DIFFRACTIONx_scbond_it2.5
X-RAY DIFFRACTIONx_scangle_it3
LS refinement shellResolution: 2.2→2.29 Å / Total num. of bins used: 8
Rfactor% reflection
Rfree0.274 10.1 %
Rwork0.239 -
obs-97.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2DNA-RNA-MULTI-ENDO.PARAMDNA-RNA-MULTI-ENDO.TOP
X-RAY DIFFRACTION3PARAM19.SOLTOP.H2O
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 6 Å / σ(F): 2 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.5
X-RAY DIFFRACTIONx_mcbond_it2
X-RAY DIFFRACTIONx_scbond_it2.5
X-RAY DIFFRACTIONx_mcangle_it2.5
X-RAY DIFFRACTIONx_scangle_it3
LS refinement shell
*PLUS
Rfactor Rfree: 0.274 / % reflection Rfree: 10.1 % / Rfactor Rwork: 0.239

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