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- PDB-8zq6: preF6P of RSV glycoprotein -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8zq6
TitlepreF6P of RSV glycoprotein
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 speciesRespiratory syncytial virus
Enterobacteria phage T6 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.77 Å
AuthorsHan, X. / Lang, Q. / Huang, Q. / Yan, J.
Funding support China, 1items
OrganizationGrant numberCountry
Other government2022A-03-05 China
CitationJournal: To Be Published
Title: preF6P of RSV glycoprotein
Authors: Huang, Q. / Lang, Q. / Han, X. / Yan, J.
History
DepositionJun 1, 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)343,8086
Polymers343,8086
Non-polymers00
Water00
1
A: Fusion glycoprotein F0,Fibritin
B: Fusion glycoprotein F0,Fibritin
F: Fusion glycoprotein F0,Fibritin


Theoretical massNumber of molelcules
Total (without water)171,9043
Polymers171,9043
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11340 Å2
ΔGint-43 kcal/mol
Surface area55750 Å2
MethodPISA
2
C: Fusion glycoprotein F0,Fibritin
D: Fusion glycoprotein F0,Fibritin
E: Fusion glycoprotein F0,Fibritin


Theoretical massNumber of molelcules
Total (without water)171,9043
Polymers171,9043
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11080 Å2
ΔGint-54 kcal/mol
Surface area55820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.155, 170.076, 190.883
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
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 / Phage neck whiskers protein


Mass: 57301.301 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Respiratory syncytial virus, (gene. exp.) Enterobacteria phage T6 (virus)
Gene: wac, EcT6_00157 / Production host: Homo sapiens (human) / References: UniProt: C3UPB8, 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: 3.74 Å3/Da / Density % sol: 67.09 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1M Sodium citrate tribasic dihydrate pH5.5, 24% 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: 2.77→26.94 Å / Num. obs: 131462 / % possible obs: 86.94 % / Redundancy: 13.5 % / Biso Wilson estimate: 44.7 Å2 / CC1/2: 0.997 / CC star: 0.999 / Net I/σ(I): 11.83
Reflection shellResolution: 2.77→2.87 Å / Mean I/σ(I) obs: 0.82 / Num. unique obs: 1517 / CC1/2: 0.286 / % possible all: 11.66

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.77→26.94 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2366 1995 1.74 %
Rwork0.1978 --
obs0.1985 114487 86.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.77→26.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20971 0 0 0 20971
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00321291
X-RAY DIFFRACTIONf_angle_d0.60928873
X-RAY DIFFRACTIONf_dihedral_angle_d5.5662862
X-RAY DIFFRACTIONf_chiral_restr0.0443489
X-RAY DIFFRACTIONf_plane_restr0.0043635
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.77-2.840.565680.3294489X-RAY DIFFRACTION5
2.84-2.910.3286540.31543175X-RAY DIFFRACTION35
2.91-30.34161230.31516802X-RAY DIFFRACTION74
3-3.090.34991630.29968954X-RAY DIFFRACTION97
3.09-3.20.31621630.27459206X-RAY DIFFRACTION100
3.2-3.330.31821630.25269189X-RAY DIFFRACTION100
3.33-3.480.26531600.21749208X-RAY DIFFRACTION100
3.48-3.670.26491720.19769238X-RAY DIFFRACTION100
3.67-3.90.19811600.18959272X-RAY DIFFRACTION100
3.9-4.20.22481620.16949258X-RAY DIFFRACTION100
4.2-4.620.17461600.13939302X-RAY DIFFRACTION100
4.62-5.280.17571720.1459345X-RAY DIFFRACTION100
5.28-6.640.24141670.19669398X-RAY DIFFRACTION100
6.64-26.940.19681680.17939656X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 20.0627 Å / Origin y: 11.6203 Å / Origin z: 72.2801 Å
111213212223313233
T0.1313 Å20.0406 Å2-0.0136 Å2-0.1448 Å2-0.0509 Å2--0.173 Å2
L0.2238 °20.1327 °2-0.2239 °2-0.2302 °2-0.2735 °2--0.5586 °2
S0.0095 Å °-0.0062 Å °-0.0037 Å °0.0185 Å °-0.0099 Å °-0.0173 Å °-0.0562 Å °0.0232 Å °-0.0117 Å °
Refinement TLS groupSelection details: all

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