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- PDB-8zpy: Crystal structure of prefusion F of RSV -

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Basic information

Entry
Database: PDB / ID: 8zpy
TitleCrystal structure of prefusion F of RSV
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: 2.92 Å
AuthorsHuang, Q. / Lang, Q. / Han, X. / Yan, J.
Funding support China, 1items
OrganizationGrant numberCountry
Other government2022A-03-05 China
CitationJournal: To Be Published
Title: prefusion F of RSV
Authors: Huang, Q. / Lang, Q. / Han, X. / Yan, J.
History
DepositionMay 31, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 17, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)343,8746
Polymers343,8746
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, trimer of F0 protein
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26680 Å2
ΔGint-90 kcal/mol
Surface area106170 Å2
MethodPISA
2
A: Fusion glycoprotein F0,Fibritin
B: Fusion glycoprotein F0,Fibritin
E: Fusion glycoprotein F0,Fibritin


Theoretical massNumber of molelcules
Total (without water)171,9373
Polymers171,9373
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11820 Å2
ΔGint-37 kcal/mol
Surface area54700 Å2
MethodPISA
3
C: Fusion glycoprotein F0,Fibritin
D: Fusion glycoprotein F0,Fibritin
F: Fusion glycoprotein F0,Fibritin


Theoretical massNumber of molelcules
Total (without water)171,9373
Polymers171,9373
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11450 Å2
ΔGint-43 kcal/mol
Surface area54880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.329, 168.674, 189.568
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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


Mass: 57312.277 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: 3.7 Å3/Da / Density % sol: 66.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1M Sodium citrate tribasic dihydrate pH5.0+30% Jaffamine ED-2001 pH7.0

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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: 2.92→126.01 Å / Num. obs: 74733 / % possible obs: 67.25 % / Redundancy: 2 % / Biso Wilson estimate: 47.32 Å2 / CC1/2: 0.952 / Rmerge(I) obs: 0.137 / Net I/σ(I): 6.15
Reflection shellResolution: 2.922→3.026 Å / Mean I/σ(I) obs: 1.29 / Num. unique obs: 510 / CC1/2: 0.494

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.92→126.01 Å / SU ML: 0.3264 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.3847
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2549 2005 2.69 %
Rwork0.1971 72654 -
obs0.1986 74659 67.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.48 Å2
Refinement stepCycle: LAST / Resolution: 2.92→126.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20848 0 0 0 20848
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004321164
X-RAY DIFFRACTIONf_angle_d0.757928702
X-RAY DIFFRACTIONf_chiral_restr0.04653464
X-RAY DIFFRACTIONf_plane_restr0.00533620
X-RAY DIFFRACTIONf_dihedral_angle_d6.59392846
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.92-2.990.322170.3311229X-RAY DIFFRACTION3.01
2.99-3.080.2733310.3366900X-RAY DIFFRACTION11.87
3.08-3.170.3279480.29811760X-RAY DIFFRACTION23.07
3.17-3.270.3665660.29682633X-RAY DIFFRACTION34.39
3.27-3.390.343970.2833445X-RAY DIFFRACTION45.14
3.39-3.520.29331240.2514341X-RAY DIFFRACTION56.53
3.52-3.680.29861540.24045441X-RAY DIFFRACTION71.24
3.68-3.880.32382030.22437121X-RAY DIFFRACTION92.73
3.88-4.120.28442110.20677695X-RAY DIFFRACTION100
4.12-4.440.2432090.16427714X-RAY DIFFRACTION100
4.44-4.880.20832100.14457727X-RAY DIFFRACTION100
4.88-5.590.22492180.17617747X-RAY DIFFRACTION99.99
5.59-7.040.24472150.20817861X-RAY DIFFRACTION100
7.04-126.010.20162120.17538040X-RAY DIFFRACTION99.23

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