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- PDB-8zhw: Structure of Mokola lyssavirus glycoprotein in post-fusion state -

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Basic information

Entry
Database: PDB / ID: 8zhw
TitleStructure of Mokola lyssavirus glycoprotein in post-fusion state
ComponentsGlycoprotein
KeywordsVIRAL PROTEIN / Glycoprotein / lyssavirus / membrane fusion / VIRUS
Function / homology
Function and homology information


viral envelope / virion membrane / membrane
Similarity search - Function
: / Rhabdovirus glycoprotein G PH domain / : / Rhabdovirus spike glycoprotein G central domain / Rhabdovirus glycoprotein / Rhabdovirus spike glycoprotein fusion domain
Similarity search - Domain/homology
Biological speciesLyssavirus mokola
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.199 Å
AuthorsLu, G.W. / Yang, F.L. / Lin, S. / Yang, J. / Ye, F.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Plos Pathog. / Year: 2025
Title: Structures of two lyssavirus glycoproteins trapped in pre- and post-fusion states and the implications on the spatial-temporal conformational transition along with pH-decrease.
Authors: Yang, F. / Lin, S. / Yuan, X. / Shu, S. / Yu, Y. / Yang, J. / Ye, F. / Chen, Z. / He, B. / Li, J. / Zhao, Q. / Ye, H. / Cao, Y. / Lu, G.
History
DepositionMay 11, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 5, 2025Provider: repository / Type: Initial release
Revision 1.1Aug 20, 2025Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycoprotein
B: Glycoprotein
C: Glycoprotein


Theoretical massNumber of molelcules
Total (without water)147,3453
Polymers147,3453
Non-polymers00
Water00
1
A: Glycoprotein


Theoretical massNumber of molelcules
Total (without water)49,1151
Polymers49,1151
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycoprotein


Theoretical massNumber of molelcules
Total (without water)49,1151
Polymers49,1151
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Glycoprotein


Theoretical massNumber of molelcules
Total (without water)49,1151
Polymers49,1151
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.235, 87.518, 111.189
Angle α, β, γ (deg.)90.00, 111.87, 90.00
Int Tables number3
Space group name H-MP121

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Components

#1: Protein Glycoprotein


Mass: 49114.930 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lyssavirus mokola / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: P0C572
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: 3.19 Å3/Da / Density % sol: 61.49 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 0.1M Sodium acetate trihydrate (pH 4.0), 10% w/v Polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 3.199→50 Å / Num. obs: 29464 / % possible obs: 95.2 % / Redundancy: 7.2 % / CC1/2: 0.999 / Net I/σ(I): 14.58
Reflection shellResolution: 3.199→3.31 Å / Num. unique obs: 5304 / CC1/2: 0.64

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.199→48.366 Å / SU ML: 0.49 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 35.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2877 1429 4.85 %
Rwork0.2465 --
obs0.2484 29436 95.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.199→48.366 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7217 0 0 0 7217
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047389
X-RAY DIFFRACTIONf_angle_d0.759970
X-RAY DIFFRACTIONf_dihedral_angle_d16.0724517
X-RAY DIFFRACTIONf_chiral_restr0.0481098
X-RAY DIFFRACTIONf_plane_restr0.0061256
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.199-3.31290.43371240.40152540X-RAY DIFFRACTION86
3.3129-3.44550.3871400.36182894X-RAY DIFFRACTION98
3.4455-3.60230.37121600.31572847X-RAY DIFFRACTION98
3.6023-3.79210.33261450.2862879X-RAY DIFFRACTION98
3.7921-4.02960.27521630.22252858X-RAY DIFFRACTION98
4.0296-4.34050.24741480.19862834X-RAY DIFFRACTION97
4.3405-4.7770.23081300.18412626X-RAY DIFFRACTION90
4.777-5.46740.25371440.20222822X-RAY DIFFRACTION95
5.4674-6.88520.31551460.26092892X-RAY DIFFRACTION98
6.8852-48.360.27451290.2512815X-RAY DIFFRACTION92
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)
11.322-0.2190.50240.7314-1.08255.99350.1933-0.0115-0.15250.02720.09570.05040.22630.5608-0.1711.0687-0.0303-0.12840.9022-0.04020.9705181.0112-2.6343125.5691
25.2026-0.2718-3.21991.21570.92692.3748-0.09730.51750.4136-0.0580.3288-0.01150.4197-0.3275-0.20661.3863-0.0941-0.17270.98230.17281.1134153.801826.7843135.2984
33.72461.24342.55872.97040.44583.30950.1804-0.1176-0.384-0.12550.04050.22840.39150.2023-0.05840.73020.03310.23720.85-0.00380.8375178.102-31.4383152.8981
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C

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