[English] 日本語
Yorodumi
- PDB-5any: Electron cryo-microscopy of chikungunya virus in complex with neu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5any
TitleElectron cryo-microscopy of chikungunya virus in complex with neutralizing antibody Fab CHK265
Components
  • E1
  • E2
  • FAB
  • FAB CHK265
KeywordsVIRUS / CHIKUNGUNYA VIRUS / NEUTRALIZING ANTIBODY FAB
Function / homology
Function and homology information


T=4 icosahedral viral capsid / host cell cytoplasm / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / symbiont entry into host cell / virion attachment to host cell / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity ...T=4 icosahedral viral capsid / host cell cytoplasm / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / symbiont entry into host cell / virion attachment to host cell / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / RNA binding / identical protein binding / membrane
Similarity search - Function
Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E1 glycoprotein / Alphavirus E2 glycoprotein, domain A / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein / Alphavirus core protein / Alphavirus E3 glycoprotein ...Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E1 glycoprotein / Alphavirus E2 glycoprotein, domain A / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein / Alphavirus core protein / Alphavirus E3 glycoprotein / Alphavirus E1 glycoprotein / Alphavirus core protein (CP) domain profile. / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / Immunoglobulin E-set / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Structural polyprotein
Similarity search - Component
Biological speciesCHIKUNGUNYA VIRUS
MUS MUSCULUS (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 16.9 Å
AuthorsFox, J.M. / Long, F. / Edeling, M.A. / Lin, H. / Duijl-Richter, M. / Fong, R.H. / Kahle, K.M. / Smit, J.M. / Jin, J. / Simmons, G. ...Fox, J.M. / Long, F. / Edeling, M.A. / Lin, H. / Duijl-Richter, M. / Fong, R.H. / Kahle, K.M. / Smit, J.M. / Jin, J. / Simmons, G. / Doranz, B.J. / Crowe, J.E. / Fremont, D.H. / Rossmann, M.G. / Diamond, M.S.
CitationJournal: Cell / Year: 2015
Title: Broadly Neutralizing Alphavirus Antibodies Bind an Epitope on E2 and Inhibit Entry and Egress.
Authors: Julie M Fox / Feng Long / Melissa A Edeling / Hueylie Lin / Mareike K S van Duijl-Richter / Rachel H Fong / Kristen M Kahle / Jolanda M Smit / Jing Jin / Graham Simmons / Benjamin J Doranz / ...Authors: Julie M Fox / Feng Long / Melissa A Edeling / Hueylie Lin / Mareike K S van Duijl-Richter / Rachel H Fong / Kristen M Kahle / Jolanda M Smit / Jing Jin / Graham Simmons / Benjamin J Doranz / James E Crowe / Daved H Fremont / Michael G Rossmann / Michael S Diamond /
Abstract: We screened a panel of mouse and human monoclonal antibodies (MAbs) against chikungunya virus and identified several with inhibitory activity against multiple alphaviruses. Passive transfer of ...We screened a panel of mouse and human monoclonal antibodies (MAbs) against chikungunya virus and identified several with inhibitory activity against multiple alphaviruses. Passive transfer of broadly neutralizing MAbs protected mice against infection by chikungunya, Mayaro, and O'nyong'nyong alphaviruses. Using alanine-scanning mutagenesis, loss-of-function recombinant proteins and viruses, and multiple functional assays, we determined that broadly neutralizing MAbs block multiple steps in the viral lifecycle, including entry and egress, and bind to a conserved epitope on the B domain of the E2 glycoprotein. A 16 Å resolution cryo-electron microscopy structure of a Fab fragment bound to CHIKV E2 B domain provided an explanation for its neutralizing activity. Binding to the B domain was associated with repositioning of the A domain of E2 that enabled cross-linking of neighboring spikes. Our results suggest that B domain antigenic determinants could be targeted for vaccine or antibody therapeutic development against multiple alphaviruses of global concern.
History
DepositionSep 8, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2015Group: Database references
Revision 1.2Oct 3, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id / _em_software.name
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

-
Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
  • Imaged by Jmol
  • Download
  • Biological unit as icosahedral pentamer
  • Imaged by Jmol
  • Download
  • Biological unit as icosahedral 23 hexamer
  • Imaged by Jmol
  • Download
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-3144
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-3144
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: E1
B: E2
C: E1
D: E2
E: E1
F: E2
G: E1
H: E2
I: FAB CHK265
J: FAB CHK265
K: FAB CHK265
L: FAB CHK265
M: FAB
N: FAB
O: FAB
P: FAB


Theoretical massNumber of molelcules
Total (without water)542,42116
Polymers542,42116
Non-polymers00
Water00
1
A: E1
B: E2
C: E1
D: E2
E: E1
F: E2
G: E1
H: E2
I: FAB CHK265
J: FAB CHK265
K: FAB CHK265
L: FAB CHK265
M: FAB
N: FAB
O: FAB
P: FAB
x 60


Theoretical massNumber of molelcules
Total (without water)32,545,252960
Polymers32,545,252960
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: E1
B: E2
C: E1
D: E2
E: E1
F: E2
G: E1
H: E2
I: FAB CHK265
J: FAB CHK265
K: FAB CHK265
L: FAB CHK265
M: FAB
N: FAB
O: FAB
P: FAB
x 5


  • icosahedral pentamer
  • 2.71 MDa, 80 polymers
Theoretical massNumber of molelcules
Total (without water)2,712,10480
Polymers2,712,10480
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: E1
B: E2
C: E1
D: E2
E: E1
F: E2
G: E1
H: E2
I: FAB CHK265
J: FAB CHK265
K: FAB CHK265
L: FAB CHK265
M: FAB
N: FAB
O: FAB
P: FAB
x 6


  • icosahedral 23 hexamer
  • 3.25 MDa, 96 polymers
Theoretical massNumber of molelcules
Total (without water)3,254,52596
Polymers3,254,52596
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

-
Components

#1: Protein
E1


Mass: 48776.719 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CHIKUNGUNYA VIRUS / Production host: DROSOPHILA MELANOGASTER (fruit fly) / References: UniProt: Q1H8W5
#2: Protein
E2


Mass: 39907.066 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CHIKUNGUNYA VIRUS / Production host: DROSOPHILA MELANOGASTER (fruit fly) / References: UniProt: Q1H8W5
#3: Antibody
FAB CHK265


Mass: 23743.719 Da / Num. of mol.: 4 / Fragment: HEAVY CHAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Cell line: HYBRIDOMA / Production host: MUS MUSCULUS (house mouse)
#4: Antibody
FAB


Mass: 23177.713 Da / Num. of mol.: 4 / Fragment: LIGHT CHAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Cell line: HYBRIDOMA / Production host: MUS MUSCULUS (house mouse)
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: chikungunya virus in complex with neutralizing antibody Fab CHK265
Type: COMPLEX
Buffer solutionpH: 7.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Mar 10, 2015
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 47000 X / Calibrated magnification: 78354 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 22 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Image scansNum. digital images: 500

-
Processing

EM softwareName: jspr / Category: 3D reconstruction
CTF correctionDetails: EACH PARTICLE
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: CROSS-COMMON LINES / Resolution: 16.9 Å / Num. of particles: 5828
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3144. (DEPOSITION ID: 13751)
Symmetry type: POINT
RefinementHighest resolution: 16.9 Å
Refinement stepCycle: LAST / Highest resolution: 16.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms35620 0 0 0 35620

+
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