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- PDB-8zq7: Crystal structure of prefusion RSV F protein -

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Basic information

Entry
Database: PDB / ID: 8zq7
TitleCrystal structure of prefusion RSV F protein
ComponentsFusion glycoprotein F0,Fibritin
KeywordsVIRAL PROTEIN / RSV
Function / homology
Function and homology information


symbiont-mediated induction of syncytium formation / host cell Golgi membrane / entry receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / viral envelope / symbiont entry into host cell / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / Fibritin C-terminal / Fibritin C-terminal region
Similarity search - Domain/homology
Fibritin / Fusion glycoprotein F0
Similarity search - Component
Biological specieshuman respiratory syncytial virus
Enterobacteria phage T6 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.77 Å
AuthorsHuang, Q. / Lang, Q. / Han, X. / Yan, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: preF8P of RSV glycoprotein F0
Authors: Huang, Q. / Lang, Q. / Han, X. / Yan, J.
History
DepositionJun 1, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fusion glycoprotein F0,Fibritin
B: Fusion glycoprotein F0,Fibritin
C: Fusion glycoprotein F0,Fibritin
D: Fusion glycoprotein F0,Fibritin
E: Fusion glycoprotein F0,Fibritin
F: Fusion glycoprotein F0,Fibritin


Theoretical massNumber of molelcules
Total (without water)343,7726
Polymers343,7726
Non-polymers00
Water00
1
A: Fusion glycoprotein F0,Fibritin
C: Fusion glycoprotein F0,Fibritin
F: Fusion glycoprotein F0,Fibritin


Theoretical massNumber of molelcules
Total (without water)171,8863
Polymers171,8863
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12760 Å2
ΔGint-52 kcal/mol
Surface area55100 Å2
MethodPISA
2
B: Fusion glycoprotein F0,Fibritin
D: Fusion glycoprotein F0,Fibritin
E: Fusion glycoprotein F0,Fibritin


Theoretical massNumber of molelcules
Total (without water)171,8863
Polymers171,8863
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12570 Å2
ΔGint-55 kcal/mol
Surface area54660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.423, 168.696, 190.683
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#1: Protein
Fusion glycoprotein F0,Fibritin / F2 / Phage neck whiskers protein


Mass: 57295.293 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) human respiratory syncytial virus, (gene. exp.) Enterobacteria phage T6 (virus)
Gene: wac, EcT6_00157 / Production host: Homo sapiens (human) / References: UniProt: P12568, UniProt: A0A346FJN8
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: 3.71 Å3/Da / Density % sol: 66.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 8% Tacsimate pH6.0+20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 5, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.77→126.35 Å / Num. obs: 99576 / % possible obs: 76.68 % / Redundancy: 2 % / Biso Wilson estimate: 60.82 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.08525 / Net I/σ(I): 7.94
Reflection shellResolution: 2.77→2.87 Å / Rmerge(I) obs: 0.6812 / Num. unique obs: 899 / CC1/2: 0.291

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.77→126.35 Å / SU ML: 0.2941 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.8089
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2419 2010 2.02 %
Rwork0.2069 97470 -
obs0.2076 99480 76.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.15 Å2
Refinement stepCycle: LAST / Resolution: 2.77→126.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21095 0 0 0 21095
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004421426
X-RAY DIFFRACTIONf_angle_d0.859529062
X-RAY DIFFRACTIONf_chiral_restr0.05193493
X-RAY DIFFRACTIONf_plane_restr0.00553674
X-RAY DIFFRACTIONf_dihedral_angle_d16.29037968
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.77-2.840.366790.3208535X-RAY DIFFRACTION5.95
2.84-2.920.3913290.34221160X-RAY DIFFRACTION13.01
2.92-30.3074450.32672093X-RAY DIFFRACTION23.34
3-3.10.3189820.31624002X-RAY DIFFRACTION44.36
3.1-3.210.3681590.29717656X-RAY DIFFRACTION85.19
3.21-3.340.33881880.27598905X-RAY DIFFRACTION99.06
3.34-3.490.31171810.25759047X-RAY DIFFRACTION99.92
3.49-3.680.27371790.2359033X-RAY DIFFRACTION99.99
3.68-3.910.25851900.2159070X-RAY DIFFRACTION99.99
3.91-4.210.24171850.19319074X-RAY DIFFRACTION100
4.21-4.630.19241840.16089104X-RAY DIFFRACTION100
4.63-5.30.20081910.16359138X-RAY DIFFRACTION100
5.3-6.680.24661890.20649198X-RAY DIFFRACTION100
6.68-126.350.17941990.17969455X-RAY DIFFRACTION99.35

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