[English] 日本語
Yorodumi
- PDB-6oe5: Splayed open prefusion RSV F captured by CR9501 and motavizumab Fabs -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6oe5
TitleSplayed open prefusion RSV F captured by CR9501 and motavizumab Fabs
Components
  • CR9501 Fab Heavy Chain
  • CR9501 Fab Light Chain
  • Fusion glycoprotein F0,Fibritin
  • Motavizumab Fab Heavy Chain
  • Motavizumab Fab Light Chain
KeywordsViral protein/immune system / class I fusion glycoprotein / immunoglobulin / respiratory syncytial virus / trimerization / neutralizing / VIRAL PROTEIN / Viral protein-immune system complex
Function / homology
Function and homology information


symbiont-mediated induction of syncytium formation / Translation of respiratory syncytial virus mRNAs / RSV-host interactions / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / Respiratory syncytial virus (RSV) attachment and entry / host cell Golgi membrane / virion component / entry receptor-mediated virion attachment to 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 / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / Respiratory syncytial virus (RSV) attachment and entry / host cell Golgi membrane / virion component / 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 / identical protein binding / plasma membrane
Similarity search - Function
Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / Fibritin C-terminal / Fibritin C-terminal region
Similarity search - Domain/homology
Fusion glycoprotein F0 / Fibritin
Similarity search - Component
Biological speciesHuman respiratory syncytial virus A
Enterobacteria phage T4 (virus)
Mus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.1 Å
AuthorsGilman, M.S.A. / McLellan, J.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM008704 United States
CitationJournal: Nat Commun / Year: 2019
Title: Transient opening of trimeric prefusion RSV F proteins.
Authors: Gilman, M.S.A. / Furmanova-Hollenstein, P. / Pascual, G. / B van 't Wout, A. / Langedijk, J.P.M. / McLellan, J.S.
History
DepositionMar 27, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1May 22, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fusion glycoprotein F0,Fibritin
B: Motavizumab Fab Heavy Chain
C: Motavizumab Fab Light Chain
H: CR9501 Fab Heavy Chain
L: CR9501 Fab Light Chain


Theoretical massNumber of molelcules
Total (without water)156,7305
Polymers156,7305
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Each protomer is likely tethered to two identical protomers via a C-terminal trimerization domain. However, density is not visible for this domain, therefore the assembly ...Evidence: gel filtration, Each protomer is likely tethered to two identical protomers via a C-terminal trimerization domain. However, density is not visible for this domain, therefore the assembly cannot be assumed to be trimeric.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10620 Å2
ΔGint-58 kcal/mol
Surface area49660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)219.837, 219.837, 68.811
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

-
Components

#1: Protein Fusion glycoprotein F0,Fibritin / prefusion RSV F / Protein F / Collar protein / Whisker antigen control protein


Mass: 61370.312 Da / Num. of mol.: 1 / Mutation: N67I, S215P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human respiratory syncytial virus A (strain A2), (gene. exp.) Enterobacteria phage T4 (virus)
Strain: A2 / Gene: wac / Production host: Homo sapiens (human) / References: UniProt: P03420, UniProt: P10104
#2: Antibody Motavizumab Fab Heavy Chain


Mass: 24284.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Antibody Motavizumab Fab Light Chain


Mass: 23150.730 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#4: Antibody CR9501 Fab Heavy Chain


Mass: 24367.268 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#5: Antibody CR9501 Fab Light Chain


Mass: 23557.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.07 Å3/Da / Density % sol: 59.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 4.69 mg/mL prefusion F (PR-DM) + motavizumab Fab + CR9501 Fab, 30% (v/v) PEG400, 0.19 M ammonium sulfate, 3.1% (w/v) PEG8000, 0.1 M Tris pH 8.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 4.1→43.68 Å / Num. obs: 15219 / % possible obs: 99.9 % / Redundancy: 7.3 % / Biso Wilson estimate: 138.17 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.295 / Rpim(I) all: 0.116 / Rrim(I) all: 0.318 / Net I/σ(I): 5.3 / Num. measured all: 110763 / Scaling rejects: 5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
4.1-4.587.11.26742990.6070.5051.366100
9.17-43.6870.0714120.9880.0280.07698.8

-
Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
Aimless0.5.26data scaling
PDB_EXTRACT3.24data extraction
iMOSFLM7.2.1data reduction
PHASER2.5.7phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.1→43.677 Å / SU ML: 0.66 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.86
RfactorNum. reflection% reflection
Rfree0.3057 748 4.92 %
Rwork0.2616 --
obs0.2637 15196 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 308.45 Å2 / Biso mean: 174.2892 Å2 / Biso min: 106.9 Å2
Refinement stepCycle: final / Resolution: 4.1→43.677 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8527 0 0 0 8527
Num. residues----1113
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038716
X-RAY DIFFRACTIONf_angle_d0.50111864
X-RAY DIFFRACTIONf_chiral_restr0.0421386
X-RAY DIFFRACTIONf_plane_restr0.0051486
X-RAY DIFFRACTIONf_dihedral_angle_d3.965214
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
4.1005-4.41680.38111640.320228403004
4.4168-4.86080.31911380.282428813019
4.8608-5.56290.33341530.264228452998
5.5629-7.0040.29941490.300229143063
7.004-43.67960.27041440.22229683112
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)
16.1919-3.2477-2.12663.73872.181-1.137-0.1606-0.2728-0.05640.42390.4031-0.40290.5184-0.2328-0.24871.77350.0019-0.12531.48990.10180.8575158.43771.3646-46.7085
21.49850.1997-0.06923.02232.93060.8390.6122-0.4385-0.47190.8618-0.52030.14480.23390.13170.01081.7745-0.19630.05961.28060.1991.0729152.05464.4141-48.282
3-0.60830.6218-0.45885.84650.5662-0.80390.39410.0153-0.3034-0.4001-0.2322-1.15920.1749-0.1962-0.1771.86430.14-0.15921.5820.03611.2228168.176441.9669-49.183
45.1959-0.44843.58455.15531.59031.6064-0.98381.07941.9008-0.45490.46990.1019-0.3831-0.38930.41741.6598-0.2262-0.08771.64010.28821.2902146.268855.0409-81.0124
56.6595-1.36854.08646.9771-1.11921.4676-1.00390.50571.292-1.22020.34651.6693-1.26130.7450.48581.9581-0.5952-0.45111.86260.48991.9805126.793740.1921-97.8413
61.44123.47171.69829.66072.73343.2263-0.12540.6125-0.3646-0.20190.4063-0.42570.17130.5842-0.26091.814-0.04640.03271.63140.15661.9816153.962134.1345-77.2564
75.3302-0.9326.94696.80753.37168.89080.96721.3089-0.5846-3.06920.20620.6974-0.0510.3473-0.9882.6303-0.26470.01862.2796-0.02651.4382134.523929.6603-108.6626
85.47954.30513.34343.3925-0.33347.5032-0.8152-0.30760.66491.38351.23710.46760.1113-0.0014-0.60441.58320.04130.17351.3027-0.0851.1347159.7776102.609-33.153
90.3071.87471.40653.25531.0392.36850.258-0.64680.34030.4749-0.27540.7835-0.1706-0.74520.07421.4925-0.05590.40971.4851-0.09581.4565147.7972123.0109-38.939
108.7554-3.97055.22726.3628-6.95095.4599-0.2023-0.1272-0.25120.20120.36090.4877-0.2757-0.2562-0.08511.4543-0.05080.09271.1656-0.22630.7488150.631999.6283-54.4444
117.0438-1.00232.19184.61785.81378.7284-0.5542-0.13420.4036-0.35130.09030.0771-0.5227-0.34270.35281.82560.19270.04251.21780.29691.2775145.1497136.617-53.9878
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 44:191)A44 - 191
2X-RAY DIFFRACTION2(chain A and resid 192:295)A192 - 295
3X-RAY DIFFRACTION3(chain A and resid 296:462)A296 - 462
4X-RAY DIFFRACTION4(chain B and resid 1:124)B1 - 124
5X-RAY DIFFRACTION5(chain B and resid 125:213)B125 - 213
6X-RAY DIFFRACTION6(chain C and resid 1:106)C1 - 106
7X-RAY DIFFRACTION7(chain C and resid 107:212)C107 - 212
8X-RAY DIFFRACTION8(chain H and resid 2:80)H2 - 80
9X-RAY DIFFRACTION9(chain H and resid 81:214)H81 - 214
10X-RAY DIFFRACTION10(chain L and resid 1:104)L1 - 104
11X-RAY DIFFRACTION11(chain L and resid 105:212)L105 - 212

+
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