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- PDB-6lqo: EBV tegument protein BBRF2/BSRF1 complex -

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Basic information

Entry
Database: PDB / ID: 6lqo
TitleEBV tegument protein BBRF2/BSRF1 complex
Components
  • Cytoplasmic envelopment protein 1
  • Tegument protein UL51 homolog
KeywordsVIRAL PROTEIN / Epstein-Barr virus (EBV)/Human herpesvirus 4 (HHV-4) / tegument protein BBEF2 (CEP1) / tegument protein BSRF1 / BBRF2-BSRF1 complex
Function / homology
Function and homology information


viral tegument / host cell Golgi apparatus
Similarity search - Function
Herpesvirus U44 / Herpes virus U44 protein / Herpesvirus UL7-like / Herpesvirus UL7 like
Similarity search - Domain/homology
ACETATE ION / Cytoplasmic envelopment protein 1 / Tegument protein UL51 homolog / Cytoplasmic envelopment protein 1
Similarity search - Component
Biological speciesHuman gammaherpesvirus 4 (Epstein-Barr virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.09112613349 Å
AuthorsHe, H.P. / Luo, M. / Cao, Y.L. / Gao, S.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2020
Title: Structure of Epstein-Barr virus tegument protein complex BBRF2-BSRF1 reveals its potential role in viral envelopment.
Authors: He, H.P. / Luo, M. / Cao, Y.L. / Lin, Y.X. / Zhang, H. / Zhang, X. / Ou, J.Y. / Yu, B. / Chen, X. / Xu, M. / Feng, L. / Zeng, M.S. / Zeng, Y.X. / Gao, S.
History
DepositionJan 14, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 21, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 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
A: Cytoplasmic envelopment protein 1
B: Cytoplasmic envelopment protein 1
C: Cytoplasmic envelopment protein 1
D: Cytoplasmic envelopment protein 1
E: Cytoplasmic envelopment protein 1
F: Cytoplasmic envelopment protein 1
H: Tegument protein UL51 homolog
I: Tegument protein UL51 homolog
J: Tegument protein UL51 homolog
K: Tegument protein UL51 homolog
L: Tegument protein UL51 homolog
M: Tegument protein UL51 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)267,84618
Polymers267,39312
Non-polymers4536
Water50428
1
A: Cytoplasmic envelopment protein 1
H: Tegument protein UL51 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6253
Polymers44,5652
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-25 kcal/mol
Surface area17400 Å2
MethodPISA
2
B: Cytoplasmic envelopment protein 1
I: Tegument protein UL51 homolog


Theoretical massNumber of molelcules
Total (without water)44,5652
Polymers44,5652
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-21 kcal/mol
Surface area16820 Å2
MethodPISA
3
C: Cytoplasmic envelopment protein 1
J: Tegument protein UL51 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7174
Polymers44,5652
Non-polymers1512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-22 kcal/mol
Surface area16980 Å2
MethodPISA
4
D: Cytoplasmic envelopment protein 1
M: Tegument protein UL51 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6583
Polymers44,5652
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-22 kcal/mol
Surface area16810 Å2
MethodPISA
5
E: Cytoplasmic envelopment protein 1
K: Tegument protein UL51 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7174
Polymers44,5652
Non-polymers1512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-28 kcal/mol
Surface area16500 Å2
MethodPISA
6
F: Cytoplasmic envelopment protein 1
L: Tegument protein UL51 homolog


Theoretical massNumber of molelcules
Total (without water)44,5652
Polymers44,5652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-19 kcal/mol
Surface area17390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.778, 161.848, 97.862
Angle α, β, γ (deg.)90.000, 100.777, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Cytoplasmic envelopment protein 1


Mass: 30289.055 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human gammaherpesvirus 4 (Epstein-Barr virus)
Strain: GD1 / Gene: BBRF2 / Production host: Escherichia coli (E. coli) / References: UniProt: K9US56, UniProt: Q3KSR8*PLUS
#2: Protein
Tegument protein UL51 homolog


Mass: 14276.442 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human gammaherpesvirus 4 (Epstein-Barr virus)
Strain: GD1 / Gene: BSRF1 / Production host: Escherichia coli (E. coli) / References: UniProt: P0CK62
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.2 Å3/Da / Density % sol: 44.21 %
Crystal growTemperature: 277.15 K / Method: evaporation
Details: 0.1 M magnesium acetate; 0.05 M MES pH 5.6; 20% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97853 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 3.09→48.07 Å / Num. obs: 42196 / % possible obs: 99.4 % / Redundancy: 3.45 % / Biso Wilson estimate: 69.6560906189 Å2 / Rsym value: 0.082 / Net I/σ(I): 13.27
Reflection shellResolution: 3.09→3.28 Å / Num. unique obs: 6720 / Rsym value: 0.495

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
REFMAC5.8.0258refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LQN

6lqn


Resolution: 3.09112613349→44.3353897675 Å / SU ML: 0.519833041801 / Cross valid method: THROUGHOUT / σ(F): 1.37306093205 / Phase error: 30.2997798242
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.26933869165 1999 4.74157356674 %RANDOM
Rwork0.21692633195 40160 --
obs0.219494301854 42159 99.4105024877 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 75.5941971662 Å2
Refinement stepCycle: LAST / Resolution: 3.09112613349→44.3353897675 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16125 0 30 28 16183
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085198228147616414
X-RAY DIFFRACTIONf_angle_d1.0950478933822166
X-RAY DIFFRACTIONf_chiral_restr0.05423393542532582
X-RAY DIFFRACTIONf_plane_restr0.006295652292782845
X-RAY DIFFRACTIONf_dihedral_angle_d18.714568833210098
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.09113-3.16840.4648802261951410.379521992372827X-RAY DIFFRACTION96.9934640523
3.1684-3.2540.404843588161410.3272084539452832X-RAY DIFFRACTION99.1661107405
3.254-3.34980.3579282053351410.2877856877822846X-RAY DIFFRACTION99.5998666222
3.3498-3.45790.3465122682951430.2733475039562863X-RAY DIFFRACTION99.7676734152
3.4579-3.58140.3322985869841440.2600043580132892X-RAY DIFFRACTION99.9341672153
3.5814-3.72470.2873916582571420.232388049532872X-RAY DIFFRACTION99.9336870027
3.7247-3.89410.3033918917491430.2210900716792869X-RAY DIFFRACTION99.9004975124
3.8941-4.09930.2603158085731440.218548706962887X-RAY DIFFRACTION99.9340586878
4.0993-4.35590.2358072881261420.1974389314112857X-RAY DIFFRACTION99.8667998668
4.3559-4.69190.2630365832221450.183119048062895X-RAY DIFFRACTION99.6394624713
4.6919-5.16340.2314470112361420.1934519342112867X-RAY DIFFRACTION99.7348359297
5.1634-5.90910.2687780952021440.2115974654892897X-RAY DIFFRACTION99.9014454665
5.9091-7.43910.2755106071161440.2137833549932891X-RAY DIFFRACTION99.8026964814
7.4391-44.33530.1817147504381430.1611263328842865X-RAY DIFFRACTION97.6940565119
Refinement TLS params.Method: refined / Origin x: 72.4896989406 Å / Origin y: 46.4760043828 Å / Origin z: 140.643197305 Å
111213212223313233
T0.239696403444 Å2-0.00276666248647 Å2-0.0311458865494 Å2-0.384191679308 Å2-0.019230166268 Å2--0.40554824475 Å2
L0.242177721693 °2-0.0150765861724 °2-0.0856274887466 °2-0.87022045044 °20.0630484459869 °2--0.568074203399 °2
S-0.0449580975678 Å °-0.0124050566712 Å °-0.0211885348036 Å °0.0818306806134 Å °0.0330081019247 Å °-0.0602983491915 Å °-0.0655787231898 Å °-0.0169055511249 Å °0.0118713353384 Å °
Refinement TLS groupSelection details: all

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