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- PDB-7ytu: Crystal structure of vaccinia virus G3/L5 sub-complex (SeMet-labe... -

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Basic information

Entry
Database: PDB / ID: 7ytu
TitleCrystal structure of vaccinia virus G3/L5 sub-complex (SeMet-labeled, P31 space group)
Components
  • Protein G3
  • Protein L5
KeywordsVIRAL PROTEIN / the components of entry-fusion complex
Function / homology
Function and homology information


fusion of virus membrane with host plasma membrane / viral envelope / symbiont entry into host cell / virion membrane / membrane
Similarity search - Function
Poxvirus L5 / Poxvirus G3 / Poxvirus L5 protein family / Chordopoxvirus G3 protein
Similarity search - Domain/homology
Entry-fusion complex protein OPG086 / Entry-fusion complex protein OPG094
Similarity search - Component
Biological speciesVaccinia virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.504 Å
AuthorsLin, S. / Yue, D. / Lu, G.W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Emerg Microbes Infect / Year: 2023
Title: Crystal structure of vaccinia virus G3/L5 sub-complex reveals a novel fold with extended inter-molecule interactions conserved among orthopoxviruses.
Authors: Lin, S. / Yue, D. / Yang, F. / Chen, Z. / He, B. / Cao, Y. / Dong, H. / Li, J. / Zhao, Q. / Lu, G.
History
DepositionAug 16, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 8, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein G3
B: Protein L5


Theoretical massNumber of molelcules
Total (without water)19,7682
Polymers19,7682
Non-polymers00
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-19 kcal/mol
Surface area7500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.039, 54.039, 42.742
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Protein G3


Mass: 10546.639 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus (strain Western Reserve)
Strain: Western Reserve / Gene: VACWR079, G3L / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P68458
#2: Protein Protein L5 / Protein F6


Mass: 9221.222 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus (strain Western Reserve)
Strain: Western Reserve / Gene: VACWR092, L5R / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P68623
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 1.85 Å3/Da / Density % sol: 33.48 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Sodium formate (pH 7.0), 12% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97892 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97892 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 22077 / % possible obs: 99.6 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 19.46
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.611 / Mean I/σ(I) obs: 2.43 / Num. unique obs: 2153 / % possible all: 96.7

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.504→31.56 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 25.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2031 1084 4.92 %
Rwork0.1872 --
obs0.188 22050 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.504→31.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1034 0 0 115 1149
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061059
X-RAY DIFFRACTIONf_angle_d0.9551437
X-RAY DIFFRACTIONf_dihedral_angle_d17.389662
X-RAY DIFFRACTIONf_chiral_restr0.056174
X-RAY DIFFRACTIONf_plane_restr0.006180
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.504-1.5720.3051120.27112538X-RAY DIFFRACTION94
1.572-1.65490.28741680.22952580X-RAY DIFFRACTION100
1.6549-1.75850.23541500.20152644X-RAY DIFFRACTION100
1.7585-1.89430.24021700.18712568X-RAY DIFFRACTION100
1.8943-2.08490.21311350.17472661X-RAY DIFFRACTION100
2.0849-2.38650.1904980.17542675X-RAY DIFFRACTION100
2.3865-3.00640.20271300.19972642X-RAY DIFFRACTION100
3.0064-31.560.18241210.17932658X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -3.0903 Å / Origin y: -14.4565 Å / Origin z: 1.309 Å
111213212223313233
T0.1731 Å2-0.0012 Å2-0.01 Å2-0.1292 Å2-0.0077 Å2--0.1642 Å2
L2.8302 °20.2496 °2-0.5746 °2-2.5369 °2-0.7051 °2--2.017 °2
S0.0881 Å °-0.0866 Å °0.1263 Å °0.0299 Å °-0.0139 Å °0.0104 Å °-0.0469 Å °0.0012 Å °-0.0241 Å °
Refinement TLS groupSelection details: all

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