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- PDB-6jgy: Crystal structure of LASV-GP2 in a post fusion conformation -

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Basic information

Entry
Database: PDB / ID: 6jgy
TitleCrystal structure of LASV-GP2 in a post fusion conformation
ComponentsPre-glycoprotein polyprotein GP complex
KeywordsVIRAL PROTEIN / LASV / GP2
Function / homology
Function and homology information


host cell Golgi membrane / receptor-mediated endocytosis of virus by host cell / host cell endoplasmic reticulum membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / metal ion binding / membrane
Similarity search - Function
Arenavirus glycoprotein, zinc binding domain / Arenavirus glycoprotein / Arenavirus glycoprotein
Similarity search - Domain/homology
Pre-glycoprotein polyprotein GP complex / Pre-glycoprotein polyprotein GP complex
Similarity search - Component
Biological speciesLassa mammarenavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.389 Å
AuthorsZhu, Y. / Zhang, X. / Chen, B. / Ye, S. / Zhang, R.
CitationJournal: Front Microbiol / Year: 2019
Title: Crystal Structure of Refolding Fusion Core of Lassa Virus GP2 and Design of Lassa Virus Fusion Inhibitors.
Authors: Zhang, X. / Wang, C. / Chen, B. / Wang, Q. / Xu, W. / Ye, S. / Jiang, S. / Zhu, Y. / Zhang, R.
History
DepositionFeb 15, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pre-glycoprotein polyprotein GP complex


Theoretical massNumber of molelcules
Total (without water)15,1091
Polymers15,1091
Non-polymers00
Water00
1
A: Pre-glycoprotein polyprotein GP complex

A: Pre-glycoprotein polyprotein GP complex

A: Pre-glycoprotein polyprotein GP complex


Theoretical massNumber of molelcules
Total (without water)45,3283
Polymers45,3283
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-y+1,x-y-1,z1
crystal symmetry operation3_765-x+y+2,-x+1,z1
Buried area9350 Å2
ΔGint-95 kcal/mol
Surface area17970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.713, 58.713, 286.580
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Pre-glycoprotein polyprotein GP complex / GP2 / Pre-GP-C


Mass: 15109.193 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lassa mammarenavirus / Gene: GP, GPC / Production host: Escherichia coli (E. coli) / References: UniProt: Q6GWS0, UniProt: P08669*PLUS
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: 3.15 Å3/Da / Density % sol: 60.9 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.17 M Ammonium Acetate, 0.085 M Sodium Citrate:HCl, pH 5.6, 25.5% (w/v) PEG 4000, 15% (v/v) Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.389→38.037 Å / Num. obs: 2839 / % possible obs: 98.1 % / Redundancy: 6.3 % / Net I/σ(I): 19.15
Reflection shellResolution: 3.4→3.48 Å

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OMI

5omi


Resolution: 3.389→38.037 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 19.8
RfactorNum. reflection% reflection
Rfree0.2739 135 4.76 %
Rwork0.2327 --
obs0.2346 2839 97.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.389→38.037 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms873 0 0 0 873
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01890
X-RAY DIFFRACTIONf_angle_d1.2141197
X-RAY DIFFRACTIONf_dihedral_angle_d2.712542
X-RAY DIFFRACTIONf_chiral_restr0.063127
X-RAY DIFFRACTIONf_plane_restr0.006154
LS refinement shellHighest resolution: 3.389 Å
RfactorNum. reflection% reflection
Rfree0.2739 135 -
Rwork0.2327 2704 -
obs--98 %

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