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- PDB-7vcl: structure of viral protein BKRF4 in complex with H2A-H2B -

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Basic information

Entry
Database: PDB / ID: 7vcl
Titlestructure of viral protein BKRF4 in complex with H2A-H2B
Components
  • Tegument protein BKRF4
  • histone H2A-H2B
KeywordsNUCLEAR PROTEIN / H2A-H2B / H3-H4 / histone / Viral protein / nucleosome
Function / homology: / Epstein-Barr virus BKRF4 histone binding protein / viral tegument / histone binding / host cell perinuclear region of cytoplasm / host cell nucleus / Tegument protein BKRF4
Function and homology information
Biological speciesHomo sapiens (human)
Epstein-Barr virus (Epstein-Barr virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsLiu, Y.R.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Mol.Biol. / Year: 2022
Title: Epstein-Barr Virus Tegument Protein BKRF4 is a Histone Chaperone.
Authors: Liu, Y. / Li, Y. / Bao, H. / Liu, Y. / Chen, L. / Huang, H.
History
DepositionSep 3, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Nov 29, 2023Group: 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: histone H2A-H2B
B: Tegument protein BKRF4


Theoretical massNumber of molelcules
Total (without water)29,8172
Polymers29,8172
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint-4 kcal/mol
Surface area12410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.474, 78.040, 105.845
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein histone H2A-H2B


Mass: 22162.729 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Protein Tegument protein BKRF4


Mass: 7654.257 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Epstein-Barr virus (strain GD1) (Epstein-Barr virus)
Strain: GD1 / Gene: BKRF4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3KSS1

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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: 2.23 Å3/Da / Density % sol: 44.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M sodium chloride; 0.1 M HEPES pH 7.5; 35% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 4730 / % possible obs: 99.1 % / Redundancy: 11.6 % / Biso Wilson estimate: 61.08 Å2 / Rmerge(I) obs: 0.171 / Rpim(I) all: 0.051 / Rrim(I) all: 0.179 / Χ2: 0.994 / Net I/σ(I): 3.2 / Num. measured all: 54863
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.2-3.269.20.7472080.5030.2490.790.82792
3.26-3.319.30.7392230.7150.2450.7810.79894.5
3.31-3.38100.732280.7310.2340.7690.85797.9
3.38-3.45100.5972320.9090.1930.6290.86599.1
3.45-3.5210.80.6962360.7880.220.7310.94699.6
3.52-3.610.40.5892260.8550.190.620.89499.6
3.6-3.6910.80.4982450.9320.1570.5230.971100
3.69-3.7911.30.4512260.9210.1390.4731.014100
3.79-3.9112.50.3852420.9660.1120.4021.074100
3.91-4.0313.20.3182230.9740.090.331.077100
4.03-4.1812.80.3142360.970.090.3271.09100
4.18-4.3413.20.2732390.9850.0780.2841.069100
4.34-4.54130.2092330.9930.0590.2171.141100
4.54-4.7812.80.2012420.990.0580.2091.193100
4.78-5.0812.20.1842380.990.0540.1921.13100
5.08-5.4711.70.172410.9920.0510.1771.041100
5.47-6.0212.40.1792480.990.0530.1871.017100
6.02-6.8912.90.1352410.9960.0390.1410.951100
6.89-8.6712.30.0882470.9980.0260.0920.945100
8.67-5010.70.0592760.9990.0180.0620.74299.6

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.10-2155refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6K01

6k01


Resolution: 3.2→24.853 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.42 / Phase error: 26.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2775 386 9.61 %
Rwork0.2294 3629 -
obs0.2339 4015 86.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.53 Å2 / Biso mean: 45.9416 Å2 / Biso min: 27.9 Å2
Refinement stepCycle: final / Resolution: 3.2→24.853 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1452 0 0 0 1452
Num. residues----185
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031475
X-RAY DIFFRACTIONf_angle_d0.5581987
X-RAY DIFFRACTIONf_chiral_restr0.037225
X-RAY DIFFRACTIONf_plane_restr0.004254
X-RAY DIFFRACTIONf_dihedral_angle_d20.367906
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.2004-3.66230.3133950.271385963
3.6623-4.60930.2951440.2257133497
4.6093-24.850.25061470.2183143699
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)
10.39080.1650.52440.6861-0.84433.61170.0448-0.14410.19420.0982-0.0424-0.123-0.3568-0.28120.08860.32490.0372-0.00990.3512-0.05290.471930.879696.423816.7308
20.3467-0.6236-0.29971.1360.34973.1350.3360.2474-0.50190.05370.20630.10650.762-0.4344-0.56170.7445-0.2754-0.0210.913-0.26011.085821.681884.740433.6124
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 6 through 186)A6 - 186
2X-RAY DIFFRACTION2(chain 'B' and resid 81 through 88)B81 - 88

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