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

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Basic information

Entry
Database: PDB / ID: 7ytt
TitleCrystal structure of vaccinia virus G3/L5 sub-complex (SeMet-labeled, P21 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: 1.81 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 1.1Oct 9, 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
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-20 kcal/mol
Surface area8020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.277, 41.919, 53.184
Angle α, β, γ (deg.)90.000, 92.540, 90.000
Int Tables number4
Space group name H-MP1211

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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.: 62 / 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

Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 0.2 M Ammonium nitrate (pH 6.2), 20% 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: 1.8→50 Å / Num. obs: 11689 / % possible obs: 99.4 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 15.87
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.544 / Mean I/σ(I) obs: 2 / Num. unique obs: 1143 / % possible all: 98.8

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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: 1.81→29.248 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 27.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2111 592 5.07 %
Rwork0.1977 11082 -
obs0.1985 11674 98.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.48 Å2 / Biso mean: 39.9118 Å2 / Biso min: 19.54 Å2
Refinement stepCycle: final / Resolution: 1.81→29.248 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1119 0 0 62 1181
Biso mean---43.2 -
Num. residues----141
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041136
X-RAY DIFFRACTIONf_angle_d0.7441539
X-RAY DIFFRACTIONf_chiral_restr0.052185
X-RAY DIFFRACTIONf_plane_restr0.004194
X-RAY DIFFRACTIONf_dihedral_angle_d14.078714
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.81-1.99210.28421320.2185264894
1.9921-2.28030.25561260.21442810100
2.2803-2.87260.23231630.22632797100
2.8726-29.2480.18771710.1798282799
Refinement TLS params.Method: refined / Origin x: 4.3902 Å / Origin y: 1.6321 Å / Origin z: 16.1136 Å
111213212223313233
T0.1602 Å2-0.009 Å2-0.0196 Å2-0.1875 Å2-0.0086 Å2--0.18 Å2
L3.2647 °2-0.3423 °2-0.1465 °2-2.7012 °20.4115 °2--2.846 °2
S-0.0444 Å °0.0908 Å °0.1282 Å °-0.0462 Å °-0.039 Å °0.0106 Å °-0.1216 Å °-0.072 Å °0.0264 Å °
Refinement TLS groupSelection details: all

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