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- PDB-2c9n: Structure of the Epstein-Barr virus ZEBRA protein at approximatel... -

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Basic information

Entry
Database: PDB / ID: 2c9n
TitleStructure of the Epstein-Barr virus ZEBRA protein at approximately 3. 5 Angstrom resolution
Components
  • 5'-D(*CP*AP*CP*TP*GP*AP*CP*TP*CP*AP *T)-3'
  • 5'-D(*CP*AP*TP*GP*AP*GP*TP*CP*AP*GP *T)-3'
  • BZLF1 TRANS-ACTIVATOR PROTEIN
KeywordsVIRAL PROTEIN / EPSTEIN-BARR VIRUS / EBV / ZEBRA / BZLF1 / ZTA / Z / LYTIC CYCLE ACTIVATION / BZIP PROTEIN / VIRAL PROTEIN DNA-BINDING / NUCLEAR PROTEIN / TRANSCRIPTION REGULATION
Function / homology
Function and homology information


symbiont-mediated suppression of host tumor necrosis factor-mediated signaling pathway / symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / release from viral latency / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / sequence-specific DNA binding / protein dimerization activity / DNA-binding transcription factor activity / regulation of DNA-templated transcription / chromatin ...symbiont-mediated suppression of host tumor necrosis factor-mediated signaling pathway / symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / release from viral latency / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / sequence-specific DNA binding / protein dimerization activity / DNA-binding transcription factor activity / regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / host cell nucleus / DNA binding
Similarity search - Function
Trans-activator protein BZLF1, human herpesvirus 4 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper domain / Basic-leucine zipper domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Lytic switch protein BZLF1
Similarity search - Component
Biological speciesHUMAN HERPESVIRUS 4 (Epstein-Barr virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsPetosa, C. / Morand, P. / Baudin, F. / Moulin, M. / Artero, J.B. / Muller, C.W.
CitationJournal: Mol.Cell / Year: 2006
Title: Structural Basis of Lytic Cycle Activation by the Epstein-Barr Virus Zebra Protein
Authors: Petosa, C. / Morand, P. / Baudin, F. / Moulin, M. / Artero, J.B. / Muller, C.W.
History
DepositionDec 13, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-D(*CP*AP*CP*TP*GP*AP*CP*TP*CP*AP *T)-3'
B: 5'-D(*CP*AP*TP*GP*AP*GP*TP*CP*AP*GP *T)-3'
Y: BZLF1 TRANS-ACTIVATOR PROTEIN
Z: BZLF1 TRANS-ACTIVATOR PROTEIN


Theoretical massNumber of molelcules
Total (without water)21,5584
Polymers21,5584
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)185.300, 36.370, 26.470
Angle α, β, γ (deg.)90.00, 95.25, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: DNA chain 5'-D(*CP*AP*CP*TP*GP*AP*CP*TP*CP*AP *T)-3'


Mass: 3293.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) HUMAN HERPESVIRUS 4 (Epstein-Barr virus)
#2: DNA chain 5'-D(*CP*AP*TP*GP*AP*GP*TP*CP*AP*GP *T)-3'


Mass: 3373.222 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) HUMAN HERPESVIRUS 4 (Epstein-Barr virus)
#3: Protein BZLF1 TRANS-ACTIVATOR PROTEIN / EB1 / ZEBRA


Mass: 7445.806 Da / Num. of mol.: 2
Fragment: DNA-BINDING AND DIMERIZATION DOMAIN, RESIDUES 175-236
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN HERPESVIRUS 4 (Epstein-Barr virus)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P03206

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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: 2.24 Å3/Da / Density % sol: 44.74 %
Description: CRYSTALS DIFFRACT ANISOTROPICALLY. CRYSTALS DIFFRACT TO 3.7 A ALONG A-STAR AND B-STAR, AND TO BETTER THAN 3A ALONG C- STAR. WE ESTIMATE THAT THE TRUE COMPLETENESS DOES NOT EXCEED 50 ...Description: CRYSTALS DIFFRACT ANISOTROPICALLY. CRYSTALS DIFFRACT TO 3.7 A ALONG A-STAR AND B-STAR, AND TO BETTER THAN 3A ALONG C- STAR. WE ESTIMATE THAT THE TRUE COMPLETENESS DOES NOT EXCEED 50 PERCENT FOR REFLECTIONS IN THE 3.3 - 3.7 A SHELL.
Crystal growpH: 6 / Details: pH 6.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 6, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 3.3→30 Å / Num. obs: 9861 / % possible obs: 98.1 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.3
Reflection shellResolution: 3.3→3.4 Å / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 5.3

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Processing

Software
NameVersionClassification
CNS1refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2C91

2c91


Resolution: 3.3→30 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: GIVEN THE ANISOTROPY AND LOW RESOLUTION OF THE DATA, LITTLE EFFORT WAS SPENT ON PROPERLY REFINING THIS STRUCTURE. FOR A HIGH RESOLUTION STRUCTURE OF ESSENTIALLY THE SAME PROTEIN-DNA COMPLEX, ...Details: GIVEN THE ANISOTROPY AND LOW RESOLUTION OF THE DATA, LITTLE EFFORT WAS SPENT ON PROPERLY REFINING THIS STRUCTURE. FOR A HIGH RESOLUTION STRUCTURE OF ESSENTIALLY THE SAME PROTEIN-DNA COMPLEX, SEE PDB ENTRY 2C91. RESIDUES 175-177 AND 237-245 SHOW POOR DENSITY AND ARE NOT INCLUDED IN THE MODEL
RfactorNum. reflection% reflectionSelection details
Rfree0.366 159 5.3 %RANDOM
Rwork0.368 ---
obs0.368 2965 98.1 %-
Solvent computationBsol: 13.2976 Å2 / ksol: 0.316866 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.617 Å20 Å225.149 Å2
2---36.427 Å20 Å2
3---31.81 Å2
Refinement stepCycle: LAST / Resolution: 3.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms972 442 0 0 1414
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3DNA-RNA_REP.PARAMDNA-RNA.TOP

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