[English] 日本語
Yorodumi
- PDB-8zq7: Crystal structure of prefusion RSV F protein -

+
Open data


ID or keywords:

Loading...

-
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 / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more