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- PDB-7nx5: Crystal structure of the Epstein-Barr Virus protein ZEBRA (BZLF1,... -

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Basic information

Entry
Database: PDB / ID: 7nx5
TitleCrystal structure of the Epstein-Barr Virus protein ZEBRA (BZLF1, Zta) bound to a methylated DNA duplex
Components
  • Trans-activator protein BZLF1
  • meZRE2 DNA (bottom strand)
  • meZRE2 DNA (top strand)
KeywordsVIRAL PROTEIN / DNA-binding protein / bZIP transcription factor
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 / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper domain / Basic-leucine zipper domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Lytic switch protein BZLF1
Similarity search - Component
Biological speciesEpstein-Barr virus (Epstein-Barr virus)
Human gammaherpesvirus 4 (Epstein-Barr virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBernaudat, F. / Petosa, C.
Funding support France, 2items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-10-INBS-05-02 France
Agence Nationale de la Recherche (ANR)ANR-17-EURE-0003 France
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: Structural basis of DNA methylation-dependent site selectivity of the Epstein-Barr virus lytic switch protein ZEBRA/Zta/BZLF1.
Authors: Bernaudat, F. / Gustems, M. / Gunther, J. / Oliva, M.F. / Buschle, A. / Gobel, C. / Pagniez, P. / Lupo, J. / Signor, L. / Muller, C.W. / Morand, P. / Sattler, M. / Hammerschmidt, W. / Petosa, C.
History
DepositionMar 17, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Trans-activator protein BZLF1
B: Trans-activator protein BZLF1
C: meZRE2 DNA (bottom strand)
D: meZRE2 DNA (top strand)
E: Trans-activator protein BZLF1
F: Trans-activator protein BZLF1
G: meZRE2 DNA (bottom strand)
H: meZRE2 DNA (top strand)


Theoretical massNumber of molelcules
Total (without water)53,0748
Polymers53,0748
Non-polymers00
Water1,17165
1
A: Trans-activator protein BZLF1
B: Trans-activator protein BZLF1
C: meZRE2 DNA (bottom strand)
D: meZRE2 DNA (top strand)


Theoretical massNumber of molelcules
Total (without water)26,5374
Polymers26,5374
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8570 Å2
ΔGint-47 kcal/mol
Surface area12000 Å2
MethodPISA
2
E: Trans-activator protein BZLF1
F: Trans-activator protein BZLF1
G: meZRE2 DNA (bottom strand)
H: meZRE2 DNA (top strand)


Theoretical massNumber of molelcules
Total (without water)26,5374
Polymers26,5374
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7280 Å2
ΔGint-44 kcal/mol
Surface area11480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)207.990, 26.560, 80.850
Angle α, β, γ (deg.)90.000, 103.104, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11G-107-

HOH

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Components

#1: Protein
Trans-activator protein BZLF1 / EB1 / Zebra


Mass: 7429.740 Da / Num. of mol.: 4 / Mutation: C189S
Source method: isolated from a genetically manipulated source
Details: Chains A and B form the ZEBRA homodimer in complex 1. Chains E and F form the ZEBRA homodimer in complex 2.
Source: (gene. exp.) Epstein-Barr virus (strain B95-8) (Epstein-Barr virus (strain B95-8))
Strain: B95-8 / Gene: BZLF1 / Production host: Escherichia coli (E. coli) / References: UniProt: P03206
#2: DNA chain meZRE2 DNA (bottom strand)


Mass: 5760.748 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Human gammaherpesvirus 4 (Epstein-Barr virus)
#3: DNA chain meZRE2 DNA (top strand)


Mass: 5916.876 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Human gammaherpesvirus 4 (Epstein-Barr virus)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.36 Å3/Da / Density % sol: 47.98 % / Description: Needle
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 22% polyethylene glycol (PEG) 4K, 18% PEG 400, 50 mM sodium acetate pH 4 and 20% isopropanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 27, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.5→35 Å / Num. obs: 15447 / % possible obs: 98.9 % / Redundancy: 3.632 % / Biso Wilson estimate: 42.35 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.082 / Net I/σ(I): 12.7
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 3.724 % / Mean I/σ(I) obs: 2.43 / Num. unique obs: 1710 / CC1/2: 0.767 / Rrim(I) all: 0.712 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2C9L

2c9l


Resolution: 2.5→16 Å / SU ML: 0.4947 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 37.9689
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: The electron density is better defined for Complex 1 (chains A-D) than for Complex 2 (chain E-H). Complex 2 exhibits high B factors and two-fold disorder around the DNA pseudodyad due to a ...Details: The electron density is better defined for Complex 1 (chains A-D) than for Complex 2 (chain E-H). Complex 2 exhibits high B factors and two-fold disorder around the DNA pseudodyad due to a lack of stabilizing crystallization contacts.
RfactorNum. reflection% reflectionSelection details
Rfree0.3387 762 5.13 %RANDOM SELECTION
Rwork0.2768 14079 --
obs0.2816 14841 95.48 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.26 Å2
Refinement stepCycle: LAST / Resolution: 2.5→16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1945 1150 0 65 3160
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00993254
X-RAY DIFFRACTIONf_angle_d1.15924610
X-RAY DIFFRACTIONf_chiral_restr0.0568517
X-RAY DIFFRACTIONf_plane_restr0.0061396
X-RAY DIFFRACTIONf_dihedral_angle_d26.4531324
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.690.381340.37472713X-RAY DIFFRACTION92.68
2.69-2.960.39681600.35032728X-RAY DIFFRACTION94.44
2.96-3.390.34411560.31272790X-RAY DIFFRACTION95.93
3.39-4.250.33871540.24282862X-RAY DIFFRACTION97.2
4.25-160.3061580.23872986X-RAY DIFFRACTION97.13
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.05680014584-5.4937110273-3.276702458254.260106866593.302803702482.027319455690.4900125498060.4856126828110.604120375451-0.500125792096-0.335421492392-0.0634806705984-0.372921784353-0.145703269908-0.1206092527520.6554040968390.133407276707-0.06684526958580.39110510864-0.035711572679421.118005923130.00271245273.0661231777619.1804008191
20.2663429659750.5939497943260.480727455762.556314216170.5696247063221.14151499496-0.3787152220020.2557079400630.643528032847-1.52661759246-0.1486279118881.46346599458-1.04042006903-0.01363694769540.5118717768411.047623120639-0.1016060788735-0.4552411208841.203203112510.2907003929861.1601188128141.1502046881-20.75732162017.79470203712
39.97474311952-3.926537020820.6270289079112.385583589440.9109387319451.361940868530.61724253334-0.5296479935890.324421874704-0.909208634037-0.456838178126-1.54132103898-0.3568228227480.334266008991-0.0390177308750.5204210870830.1841217550960.1852147544860.7087294707180.3799306122731.213740049928.41171276871-0.28833718688121.4112944238
43.06922630124-0.752926606701-0.8093287369233.677317025950.1464243997682.75194579185-0.576628564167-0.0042151172274-0.621607874425-0.3447391672520.5825267043621.70842852494-0.18730447850.225902701238-0.02081461582870.4817181415670.156930557634-0.04762946760760.658725656470.4250176030210.87762461973245.4607100858-10.68912032113.987129305
56.8692153504-7.59271372645-4.779822297768.036633600084.328520556543.11952205804-0.0467047818086-0.05271620420880.20561278325-0.3535180631770.219835425788-0.097710849717-0.1338154308010.136412421741-0.0445488326410.274217980078-0.1363133434970.02101154403160.341431510624-0.09572217207110.39952463266438.1678964414-9.70493875459-19.9246360421
60.917722380521.32791986011-0.364115251572.27880505134-1.544617639673.168644491640.3662386313920.4545440235760.567329853514-2.29161152892-0.14621531575-0.486941525660.213513256222-0.322019029696-0.1623144835411.12281625304-0.03260804554170.2742166254380.2841244058290.0227144202538230.68131310440252.1902104066-33.2464911846-32.7996599146
72.36434397546-2.84641658961-1.401944594793.300209934051.329031070791.618714284390.2170196923260.255200195885-0.338720972798-0.510417740804-0.0819124669431-0.01501808860160.03741275750860.0834029821718-0.0036120762340.382820456819-0.06944013357850.0690197860750.336536839282-0.03734114197450.19924439261934.0487709428-20.035261392-21.1857243805
83.061421019211.17571042982-1.771910073457.265911212-0.5169100846188.42341495061-0.578710978510.423322799237-0.607914345483-1.230711558670.365431051706-1.666833254330.1704095769391.154808762490.1061194236941.0546342458-0.2656105109570.3109098061.019001859668-0.4618139743090.75312178434461.4573499813-20.6997364067-28.4016387192
91.0426101561330.080012334162-1.239715209794.96171287910.5198070405912.00931732649-0.0394168184950.3587492243887-0.263711404683-0.6679109237930.46110449962-1.1018159448241.42901238998-0.807007216975-0.1930193595020.7746358453880.09734132401640.10563576119130.8357179509140.2847122917781.488106230249.293652979857.5285818717524.0885072177
104.60170424851-1.859948964921.307317524793.50520137346-1.652315703312.248419580141.23740241932-0.6376117538660.2064105831410.0066134226398-0.421300802498-0.869222977169-0.371601734234-0.316312162965-0.0535424367810.3611014769570.45720484166-0.0730089725280.7285413961310.8806117157881.7479111190611.46725269489.4620176098226.9852918845
117.018610916461.068214130732.033610466878.333441864361.132613831878.135312128560.6458193439910.008718242297-0.6619102910770.608129419638-0.4032217081060.3497164822830.299216334391-0.140307626162-0.3821135284930.2183180692470.00793626547330.00171905833210.560135875875-0.07251918396730.35752874846719.1020322874-6.90137564033-14.530919023
124.401014936890.2594081147950.4879145420865.14751777846-1.559647247281.5779103792850.394316206460.875711349061-0.0679105138750.573819611269-0.6370124881050.367816722598-0.9288141301551.409608844340.2185212165210.386822801797-0.119749900774-0.04891642224710.924925076284-0.0873180190360.32162813096519.9667610167-5.03686564823-16.4319836639
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'E' and (resseq 176:221)
2X-RAY DIFFRACTION2chain 'E' and (resseq 222:236)
3X-RAY DIFFRACTION3chain 'F' and (resseq 174:198)
4X-RAY DIFFRACTION4chain 'F' and (resseq 199:235)
5X-RAY DIFFRACTION5chain 'B' and (resseq 176:218)
6X-RAY DIFFRACTION6chain 'B' and (resseq 219:236)
7X-RAY DIFFRACTION7chain 'A' and (resseq 174:221)
8X-RAY DIFFRACTION8chain 'A' and (resseq 222:235)
9X-RAY DIFFRACTION9chain 'G'
10X-RAY DIFFRACTION10chain 'H'
11X-RAY DIFFRACTION11chain 'C'
12X-RAY DIFFRACTION12chain 'D'

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