[English] 日本語
Yorodumi
- PDB-3rrt: Structure of the RSV F protein in the post-fusion conformation -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3rrt
TitleStructure of the RSV F protein in the post-fusion conformation
Components(Fusion glycoprotein F0) x 2
KeywordsVIRAL PROTEIN / six-helix bundle / membrane fusion
Function / homology
Function and homology information


symbiont-mediated induction of syncytium formation / Translation of respiratory syncytial virus mRNAs / RSV-host interactions / Assembly and release of respiratory syncytial virus (RSV) virions / Maturation of hRSV A proteins / host cell Golgi membrane / 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 ...symbiont-mediated induction of syncytium formation / Translation of respiratory syncytial virus mRNAs / RSV-host interactions / Assembly and release of respiratory syncytial virus (RSV) virions / Maturation of hRSV A proteins / host cell Golgi membrane / 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
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1160 / Rhinovirus 14, subunit 4 - #50 / Rhinovirus 14, subunit 4 / Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / Other non-globular / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special
Similarity search - Domain/homology
Fusion glycoprotein F0 / Fusion glycoprotein F0
Similarity search - Component
Biological speciesHuman respiratory syncytial virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsMcLellan, J.S. / Yongping, Y. / Graham, B.S. / Kwong, P.D.
CitationJournal: J.Virol. / Year: 2011
Title: Structure of respiratory syncytial virus fusion glycoprotein in the postfusion conformation reveals preservation of neutralizing epitopes.
Authors: McLellan, J.S. / Yang, Y. / Graham, B.S. / Kwong, P.D.
History
DepositionApr 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 10, 2011Group: Database references
Revision 1.3Mar 31, 2021Group: Database references / Source and taxonomy / Category: entity_src_gen / struct_ref_seq_dif
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain / _struct_ref_seq_dif.details
Revision 1.4Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)152,5596
Polymers152,5596
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area53270 Å2
ΔGint-393 kcal/mol
Surface area52250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.024, 81.877, 271.948
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Fusion glycoprotein F0


Mass: 9529.798 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human respiratory syncytial virus / Strain: A2 / Gene: fusion (F) protein / Plasmid: paH / Cell line (production host): HEK293F / Production host: homo sapiens (human) / References: UniProt: Q84850, UniProt: P03420*PLUS
#2: Protein Fusion glycoprotein F0


Mass: 41323.137 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human respiratory syncytial virus / Strain: A2 / Gene: fusion (F) protein / Plasmid: paH / Cell line (production host): HEK293F / Production host: homo sapiens (human) / References: UniProt: Q84850, UniProt: P03420*PLUS
Has protein modificationY
Sequence details1) THE CRYSTALLIZED SEQUENCE CORRESPONDS TO A VIRAL STRAIN NOT PRESENT IN THE DATABASE UNP ENTRY ...1) THE CRYSTALLIZED SEQUENCE CORRESPONDS TO A VIRAL STRAIN NOT PRESENT IN THE DATABASE UNP ENTRY Q84850_HRSV. 2) THE FULL SEQUENCE PRESENT IN THE PLASMID WAS CLEAVED DURING EXPRESSION.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.55 %
Crystal growTemperature: 293 K / pH: 4.5
Details: 23% (w/v) PEG 3000, 0.1 M acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 10, 2011
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 26109 / % possible obs: 93.9 % / Observed criterion σ(I): 1 / Redundancy: 3.1 % / Rmerge(I) obs: 0.208 / Rsym value: 0.208 / Net I/σ(I): 6.07
Reflection shellResolution: 3.2→3.26 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 1.7 / % possible all: 82.3

-
Processing

Software
NameVersionClassification
SERGUIdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3RRR

3rrr


Resolution: 3.2→46.17 Å / SU ML: 0.37 / σ(F): 0 / Phase error: 29.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.282 1331 5.13 %
Rwork0.253 --
obs0.255 25928 91.5 %
all-28339 -
Solvent computationShrinkage radii: 0.17 Å / VDW probe radii: 0.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.74 Å2 / ksol: 0.34 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--23.3349 Å20 Å20 Å2
2--23.0759 Å20 Å2
3---0.259 Å2
Refinement stepCycle: LAST / Resolution: 3.2→46.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10064 0 0 0 10064
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810223
X-RAY DIFFRACTIONf_angle_d1.0913817
X-RAY DIFFRACTIONf_dihedral_angle_d14.3263791
X-RAY DIFFRACTIONf_chiral_restr0.0571674
X-RAY DIFFRACTIONf_plane_restr0.0041734
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1494-3.26190.394750.34721727X-RAY DIFFRACTION65
3.2619-3.39250.33371160.3092247X-RAY DIFFRACTION85
3.3925-3.54680.3361130.29652343X-RAY DIFFRACTION88
3.5468-3.73370.30351240.28032518X-RAY DIFFRACTION94
3.7337-3.96760.32361360.27162527X-RAY DIFFRACTION96
3.9676-4.27370.29521580.2272566X-RAY DIFFRACTION97
4.2737-4.70340.21671570.19232623X-RAY DIFFRACTION98
4.7034-5.38310.28631440.21712639X-RAY DIFFRACTION98
5.3831-6.77870.27461400.24162681X-RAY DIFFRACTION98
6.7787-46.17560.25541680.272726X-RAY DIFFRACTION96
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)
1-0.03530.016-0.05440.12380.07490.2127-0.0207-0.0702-0.0379-0.00090.04770.1038-0.10980.0236-0.02670.3118-0.0063-0.02220.4727-0.04620.4654-7.7972-20.966722.2837
20.02930.0522-0.10460.19410.28460.35360.0674-0.0393-0.012-0.088-0.15070.1368-0.1572-0.04690.04860.23520.0686-0.0480.12830.00930.2594-22.0307-22.214422.3986
30.0834-0.06190.05980.16620.24070.3883-0.1286-0.11340.04790.0014-0.03320.1712-0.03470.06780.13960.1423-0.06190.06120.2956-0.02970.2961-14.0705-30.639630.5954
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A or CHAIN B
2X-RAY DIFFRACTION1CHAIN A or CHAIN B
3X-RAY DIFFRACTION2CHAIN C or CHAIN D
4X-RAY DIFFRACTION2CHAIN C or CHAIN D
5X-RAY DIFFRACTION3CHAIN E or CHAIN F
6X-RAY DIFFRACTION3CHAIN E or CHAIN F

+
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