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- PDB-5szx: Epstein-Barr virus Zta DNA binding domain homodimer in complex wi... -

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Basic information

Entry
Database: PDB / ID: 5szx
TitleEpstein-Barr virus Zta DNA binding domain homodimer in complex with methylated DNA
Components
  • DNA (5'-D(*AP*AP*GP*CP*AP*CP*TP*GP*AP*GP*(5CM)P*GP*AP*TP*GP*AP*AP*G)-3')
  • DNA (5'-D(*TP*CP*TP*TP*CP*AP*TP*(5CM)P*GP*CP*TP*CP*AP*GP*TP*GP*CP*T)-3')
  • Zta transcription factor
KeywordsTRANSCRIPTION REGULATOR/DNA / Zta / Zebra / BZLF-1 / AP-1 / Epstein-Barr virus / EBV / 5-methylcytosine / 5mC / DNA methylation / transcription factor / basic leucine-zipper / bZIP / TRANSCRIPTION REGULATOR-DNA complex
Function / homology
Function and homology information


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 / host cell nucleus / chromatin / regulation of DNA-templated transcription ...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 / host cell nucleus / chromatin / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / 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 superfamily / Basic-leucine zipper domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / DNA / DNA (> 10) / Lytic switch protein BZLF1
Similarity search - Component
Biological speciesEpstein-Barr virus (Epstein-Barr virus)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.251 Å
AuthorsHong, S. / Horton, J.R. / Cheng, X.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Methyl-dependent and spatial-specific DNA recognition by the orthologous transcription factors human AP-1 and Epstein-Barr virus Zta.
Authors: Hong, S. / Wang, D. / Horton, J.R. / Zhang, X. / Speck, S.H. / Blumenthal, R.M. / Cheng, X.
History
DepositionAug 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1May 3, 2017Group: Database references
Revision 1.2Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 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(*TP*CP*TP*TP*CP*AP*TP*(5CM)P*GP*CP*TP*CP*AP*GP*TP*GP*CP*T)-3')
D: DNA (5'-D(*AP*AP*GP*CP*AP*CP*TP*GP*AP*GP*(5CM)P*GP*AP*TP*GP*AP*AP*G)-3')
A: Zta transcription factor
B: Zta transcription factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7525
Polymers25,6574
Non-polymers951
Water25214
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.549, 26.732, 99.673
Angle α, β, γ (deg.)90.00, 97.25, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-119-

DG

21B-303-

HOH

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Components

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


Mass: 5447.542 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*AP*AP*GP*CP*AP*CP*TP*GP*AP*GP*(5CM)P*GP*AP*TP*GP*AP*AP*G)-3')


Mass: 5612.684 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein Zta transcription factor / EB1 / Zebra


Mass: 7298.545 Da / Num. of mol.: 2 / Fragment: DNA binding domain (UNP residues 175-236) / Mutation: C189S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Epstein-Barr virus (Epstein-Barr virus)
Production host: Escherichia coli (E. coli) / References: UniProt: P03206
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.46 Å3/Da / Density % sol: 50.02 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.2 M NaH2PO4-H2O 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Feb 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→35 Å / Num. obs: 10789 / % possible obs: 88.7 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 16.8
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.885 / Mean I/σ(I) obs: 1.09 / % possible all: 48.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PHENIX1.9_1692model building
SERGUIdata collection
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2C9L

2c9l


Resolution: 2.251→32.959 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 39.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.284 537 5.01 %
Rwork0.2595 --
obs0.2608 10725 87.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.251→32.959 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms923 734 5 14 1676
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081761
X-RAY DIFFRACTIONf_angle_d0.8332533
X-RAY DIFFRACTIONf_dihedral_angle_d24.903707
X-RAY DIFFRACTIONf_chiral_restr0.035286
X-RAY DIFFRACTIONf_plane_restr0.009200
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2513-2.47780.3833910.36121705X-RAY DIFFRACTION59
2.4778-2.83610.37791420.34862696X-RAY DIFFRACTION94
2.8361-3.57250.32961470.30142823X-RAY DIFFRACTION97
3.5725-32.96240.24361570.22092964X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 115.0661 Å / Origin y: -0.103 Å / Origin z: -74.5322 Å
111213212223313233
T0.474 Å2-0.0357 Å20.2283 Å2-0.2989 Å20.0338 Å2--0.3931 Å2
L3.1617 °20.6525 °21.5104 °2-3.1944 °21.4667 °2--3.9493 °2
S0.2027 Å °0.0059 Å °0.2615 Å °0.5625 Å °-0.1381 Å °0.1295 Å °0.28 Å °-0.4168 Å °-0.1331 Å °
Refinement TLS groupSelection details: all

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