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- PDB-2c9l: Structure of the Epstein-Barr virus ZEBRA protein -

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Basic information

Entry
Database: PDB / ID: 2c9l
TitleStructure of the Epstein-Barr virus ZEBRA protein
Components
  • 5'-D(*AP*AP*GP*CP*AP*CP*TP*GP*AP*CP *TP*CP*AP*TP*GP*AP*AP*GP*T)-3'
  • 5'-D(*AP*CP*TP*TP*CP*AP*CP*TP*GP*AP *GP*TP*CP*AP*GP*TP*GP*CP*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: 2.25 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(*AP*AP*GP*CP*AP*CP*TP*GP*AP*CP *TP*CP*AP*TP*GP*AP*AP*GP*T)-3'
B: 5'-D(*AP*CP*TP*TP*CP*AP*CP*TP*GP*AP *GP*TP*CP*AP*GP*TP*GP*CP*T)-3'
Y: BZLF1 TRANS-ACTIVATOR PROTEIN
Z: BZLF1 TRANS-ACTIVATOR PROTEIN


Theoretical massNumber of molelcules
Total (without water)26,1724
Polymers26,1724
Non-polymers00
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)94.170, 26.520, 98.090
Angle α, β, γ (deg.)90.00, 103.95, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 5837.812 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) HUMAN HERPESVIRUS 4 (Epstein-Barr virus)
#2: DNA chain 5'-D(*AP*CP*TP*TP*CP*AP*CP*TP*GP*AP *GP*TP*CP*AP*GP*TP*GP*CP*T)-3'


Mass: 5506.577 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: 7413.740 Da / Num. of mol.: 2
Fragment: DNA-BINDING AND DIMERIZATION DOMAIN, RESIDUES 175-236
Mutation: YES
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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN Y, SER 186 TO ALA ENGINEERED RESIDUE IN CHAIN Z, CYS 189 TO SER ...ENGINEERED RESIDUE IN CHAIN Y, SER 186 TO ALA ENGINEERED RESIDUE IN CHAIN Z, CYS 189 TO SER ENGINEERED RESIDUE IN CHAIN Y, SER 186 TO ALA ENGINEERED RESIDUE IN CHAIN Z, CYS 189 TO SER

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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: 2.26 Å3/Da / Density % sol: 45.16 %
Crystal growpH: 7 / Details: pH 7.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.9755
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 11, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9755 Å / Relative weight: 1
ReflectionResolution: 2.25→30 Å / Num. obs: 11609 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.1
Reflection shellResolution: 2.25→2.3 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 4.4 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YSA

1ysa


Resolution: 2.25→30 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
Details: THERE IS NO SIDE CHAIN DENSITY VISIBLE FOR RESIDUES LEU175 AND GLU176 IN CHAIN Z. ONLY THE MAIN CHAIN ATOMS OF THESE RESIDUES ARE INCLUDED IN THE MODEL.
RfactorNum. reflection% reflectionSelection details
Rfree0.2644 592 5.1 %RANDOM
Rwork0.2317 ---
obs0.2317 11608 99.9 %-
Solvent computationBsol: 56.8112 Å2 / ksol: 0.335561 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.577 Å20 Å25.368 Å2
2--5.472 Å20 Å2
3----0.895 Å2
Refinement stepCycle: LAST / Resolution: 2.25→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1019 756 0 81 1856
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.2
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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