[English] 日本語
Yorodumi
- PDB-5k6f: Crystal structure of prefusion-stabilized RSV F single-chain 9-19... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5k6f
TitleCrystal structure of prefusion-stabilized RSV F single-chain 9-19 DS-Cav1 variant.
ComponentsFusion glycoprotein F0
KeywordsVIRAL PROTEIN / Respiratory Syncytial Virus / Prefusion / Vaccine / Stabilized
Function / homology
Function and homology information


positive regulation of syncytium formation by virus / Translation of respiratory syncytial virus mRNAs / RSV-host interactions / host cell Golgi membrane / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / Respiratory syncytial virus (RSV) attachment and entry / entry receptor-mediated virion attachment to host cell / symbiont entry into host cell / fusion of virus membrane with host plasma membrane ...positive regulation of syncytium formation by virus / Translation of respiratory syncytial virus mRNAs / RSV-host interactions / host cell Golgi membrane / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / Respiratory syncytial virus (RSV) attachment and entry / 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 / identical protein binding / plasma membrane
Similarity search - Function
Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0
Similarity search - Domain/homology
Fusion glycoprotein F0
Similarity search - Component
Biological speciesHuman respiratory syncytial virus A
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.59 Å
AuthorsJoyce, M.G. / Zhang, B. / Lai, Y.T. / Mascola, J.R. / Kwong, P.D.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2016
Title: Iterative structure-based improvement of a fusion-glycoprotein vaccine against RSV.
Authors: Joyce, M.G. / Zhang, B. / Ou, L. / Chen, M. / Chuang, G.Y. / Druz, A. / Kong, W.P. / Lai, Y.T. / Rundlet, E.J. / Tsybovsky, Y. / Yang, Y. / Georgiev, I.S. / Guttman, M. / Lees, C.R. / ...Authors: Joyce, M.G. / Zhang, B. / Ou, L. / Chen, M. / Chuang, G.Y. / Druz, A. / Kong, W.P. / Lai, Y.T. / Rundlet, E.J. / Tsybovsky, Y. / Yang, Y. / Georgiev, I.S. / Guttman, M. / Lees, C.R. / Pancera, M. / Sastry, M. / Soto, C. / Stewart-Jones, G.B. / Thomas, P.V. / Van Galen, J.G. / Baxa, U. / Lee, K.K. / Mascola, J.R. / Graham, B.S. / Kwong, P.D.
History
DepositionMay 24, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2016Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
F: Fusion glycoprotein F0


Theoretical massNumber of molelcules
Total (without water)49,5601
Polymers49,5601
Non-polymers00
Water1,02757
1
F: Fusion glycoprotein F0

F: Fusion glycoprotein F0

F: Fusion glycoprotein F0


Theoretical massNumber of molelcules
Total (without water)148,6813
Polymers148,6813
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area12000 Å2
ΔGint-18 kcal/mol
Surface area54370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.934, 168.934, 168.934
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132

-
Components

#1: Protein Fusion glycoprotein F0 / Protein F


Mass: 49560.414 Da / Num. of mol.: 1
Fragment: UNP residues 26-103 linked to residues 145-509 via LINKER residues GGSGGSG
Source method: isolated from a genetically manipulated source
Details: RSV F single-chain 9-19 DS-Cav1 variant
Source: (gene. exp.) Human respiratory syncytial virus A (strain A2)
Strain: A2 / Production host: Homo sapiens (human) / References: UniProt: P03420
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.11 Å3/Da / Density % sol: 70.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Na citrate pH 5.6, 15 % iso-propanol, 17 % PEG 4,000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→46.854 Å / Num. obs: 26218 / % possible obs: 100 % / Redundancy: 19.9 % / Net I/σ(I): 16.2
Reflection shellResolution: 2.55→2.64 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 1.3

-
Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.59→45.15 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2374 1260 4.82 %
Rwork0.2026 --
obs0.2043 26167 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.59→45.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3464 0 0 57 3521
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023519
X-RAY DIFFRACTIONf_angle_d0.4584773
X-RAY DIFFRACTIONf_dihedral_angle_d11.6652174
X-RAY DIFFRACTIONf_chiral_restr0.041572
X-RAY DIFFRACTIONf_plane_restr0.002601
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5901-2.69380.36811450.29852648X-RAY DIFFRACTION98
2.6938-2.81640.32671340.28562725X-RAY DIFFRACTION100
2.8164-2.96480.26311190.25672726X-RAY DIFFRACTION100
2.9648-3.15060.26221200.24022740X-RAY DIFFRACTION100
3.1506-3.39370.25981440.22362739X-RAY DIFFRACTION100
3.3937-3.73510.2591480.20842748X-RAY DIFFRACTION100
3.7351-4.27520.21621670.18612752X-RAY DIFFRACTION100
4.2752-5.38490.18421360.1612829X-RAY DIFFRACTION100
5.3849-45.15630.22931470.18783000X-RAY DIFFRACTION100
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)
10.3875-0.08380.0790.88690.00850.77510.01650.1827-0.1767-0.08730.1969-0.0790.37730.0099-0.07970.4577-0.067-0.04710.3645-0.0390.43192.8736-7.194813.3718
29.85450.14344.3443.26940.40746.38240.25280.70350.36080.0639-0.0142-0.2144-0.00870.7849-0.08460.742-0.19450.00630.628-0.16970.67464.7811-15.9732-14.1314
33.16890.731.8411.61710.20234.91020.06190.4785-0.4619-0.23840.0048-0.00790.65850.2437-0.06130.77290.0475-0.12060.5567-0.20030.67825-22.1772-2.6856
41.517-0.527-0.45313.25292.36682.1280.00330.1862-0.1668-0.2927-0.09130.3260.0219-0.20360.13220.4061-0.0312-0.09080.36210.04920.37865.3397-3.543319.1953
52.2172-1.9271-0.30783.0720.03830.2309-0.0482-0.05560.04480.27130.0127-0.12310.0175-0.00740.02530.37080-0.0080.35520.01740.34773.300115.137529.8131
66.51791.22271.06982.4432-0.48513.16860.0654-0.32550.29710.2264-0.2272-0.23750.0010.2220.15210.44890.09260.07430.2629-0.09650.33599.416823.422134.1046
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'F' and (resid 26 through 73 )
2X-RAY DIFFRACTION2chain 'F' and (resid 74 through 100 )
3X-RAY DIFFRACTION3chain 'F' and (resid 101 through 239 )
4X-RAY DIFFRACTION4chain 'F' and (resid 240 through 352 )
5X-RAY DIFFRACTION5chain 'F' and (resid 353 through 443 )
6X-RAY DIFFRACTION6chain 'F' and (resid 444 through 509 )

+
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://pdbjlvh1.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