[English] 日本語
Yorodumi
- PDB-7cvz: Cryo-EM structure of Chikungunya virus in complex with Fab fragme... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7cvz
TitleCryo-EM structure of Chikungunya virus in complex with Fab fragments of mAb CHK-263
Components
  • Capsid protein
  • E1 glycoprotein
  • E2 glycoprotein
  • Fab heavy chain
  • Fab light chain
KeywordsVIRUS/IMMUNE SYSTEM / virus / Fab / complex / VIRUS-IMMUNE SYSTEM complex
Function / homology
Function and homology information


togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / symbiont entry into host cell / viral translational frameshifting / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / host cell nucleus / virion attachment to host cell ...togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / symbiont entry into host cell / viral translational frameshifting / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / host cell nucleus / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / RNA binding / membrane / plasma membrane / cytoplasm
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 / Structural polyprotein
Similarity search - Component
Biological speciesChikungunya virus
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.7 Å
AuthorsZhou, Q.F. / Fox, J.M. / Earnest, J.T. / Ng, T.S. / Kim, A.S. / Fibriansah, G. / Kostyuchenko, V.A. / Shu, B. / Diamond, M.S. / Lok, S.M.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Other government Singapore
CitationJournal: Proc Natl Acad Sci U S A / Year: 2020
Title: Structural basis of Chikungunya virus inhibition by monoclonal antibodies.
Authors: Qun Fei Zhou / Julie M Fox / James T Earnest / Thiam-Seng Ng / Arthur S Kim / Guntur Fibriansah / Victor A Kostyuchenko / Jian Shi / Bo Shu / Michael S Diamond / Shee-Mei Lok /
Abstract: Chikungunya virus (CHIKV) is an emerging viral pathogen that causes both acute and chronic debilitating arthritis. Here, we describe the functional and structural basis as to how two anti-CHIKV ...Chikungunya virus (CHIKV) is an emerging viral pathogen that causes both acute and chronic debilitating arthritis. Here, we describe the functional and structural basis as to how two anti-CHIKV monoclonal antibodies, CHK-124 and CHK-263, potently inhibit CHIKV infection in vitro and in vivo. Our in vitro studies show that CHK-124 and CHK-263 block CHIKV at multiple stages of viral infection. CHK-124 aggregates virus particles and blocks attachment. Also, due to antibody-induced virus aggregation, fusion with endosomes and egress are inhibited. CHK-263 neutralizes CHIKV infection mainly by blocking virus attachment and fusion. To determine the structural basis of neutralization, we generated cryogenic electron microscopy reconstructions of Fab:CHIKV complexes at 4- to 5-Å resolution. CHK-124 binds to the E2 domain B and overlaps with the Mxra8 receptor-binding site. CHK-263 blocks fusion by binding an epitope that spans across E1 and E2 and locks the heterodimer together, likely preventing structural rearrangements required for fusion. These results provide structural insight as to how neutralizing antibody engagement of CHIKV inhibits different stages of the viral life cycle, which could inform vaccine and therapeutic design.
History
DepositionAug 27, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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-30477
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-30477
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
D: E1 glycoprotein
E: E2 glycoprotein
F: Capsid protein
O: Fab heavy chain
P: Fab light chain
G: E1 glycoprotein
H: E2 glycoprotein
J: E1 glycoprotein
K: E2 glycoprotein
L: Capsid protein
I: Capsid protein
Q: Fab heavy chain
R: Fab light chain
A: E1 glycoprotein
B: E2 glycoprotein
C: Capsid protein


Theoretical massNumber of molelcules
Total (without water)535,85316
Polymers535,85316
Non-polymers00
Water00
1
D: E1 glycoprotein
E: E2 glycoprotein
F: Capsid protein
O: Fab heavy chain
P: Fab light chain
G: E1 glycoprotein
H: E2 glycoprotein
J: E1 glycoprotein
K: E2 glycoprotein
L: Capsid protein
I: Capsid protein
Q: Fab heavy chain
R: Fab light chain
A: E1 glycoprotein
B: E2 glycoprotein
C: Capsid protein
x 60


Theoretical massNumber of molelcules
Total (without water)32,151,192960
Polymers32,151,192960
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
D: E1 glycoprotein
E: E2 glycoprotein
F: Capsid protein
O: Fab heavy chain
P: Fab light chain
G: E1 glycoprotein
H: E2 glycoprotein
J: E1 glycoprotein
K: E2 glycoprotein
L: Capsid protein
I: Capsid protein
Q: Fab heavy chain
R: Fab light chain
A: E1 glycoprotein
B: E2 glycoprotein
C: Capsid protein
x 5


  • icosahedral pentamer
  • 2.68 MDa, 80 polymers
Theoretical massNumber of molelcules
Total (without water)2,679,26680
Polymers2,679,26680
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
D: E1 glycoprotein
E: E2 glycoprotein
F: Capsid protein
O: Fab heavy chain
P: Fab light chain
G: E1 glycoprotein
H: E2 glycoprotein
J: E1 glycoprotein
K: E2 glycoprotein
L: Capsid protein
I: Capsid protein
Q: Fab heavy chain
R: Fab light chain
A: E1 glycoprotein
B: E2 glycoprotein
C: Capsid protein
x 6


  • icosahedral 23 hexamer
  • 3.22 MDa, 96 polymers
Theoretical massNumber of molelcules
Total (without water)3,215,11996
Polymers3,215,11996
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

-
Components

#1: Protein
E1 glycoprotein / Coordinate model: Cα atoms only


Mass: 47503.016 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Chikungunya virus / References: UniProt: Q8JUX5*PLUS
#2: Protein
E2 glycoprotein / Coordinate model: Cα atoms only


Mass: 46904.559 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Chikungunya virus / References: UniProt: Q8JUX5*PLUS, togavirin
#3: Protein
Capsid protein / Togavirin / Coordinate model: Cα atoms only


Mass: 16428.607 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Chikungunya virus
References: UniProt: A0A6B9KBE1, UniProt: Q8JUX5*PLUS, togavirin
#4: Antibody Fab heavy chain / Coordinate model: Cα atoms only


Mass: 22872.670 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#5: Antibody Fab light chain / Coordinate model: Cα atoms only


Mass: 23381.570 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

-
Experimental details

-
Experiment

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

-
Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Chikungunya virus in complex with Fab fragments of mAb CHK-263COMPLEXall0MULTIPLE SOURCES
2Chikungunya virusORGANELLE OR CELLULAR COMPONENT#1-#31NATURAL
3CHK-263 FabORGANELLE OR CELLULAR COMPONENT#4-#51NATURAL
Molecular weight
IDEntity assembly-IDExperimental value
11NO
21NO
31NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Chikungunya virus37124
33Mus musculus (house mouse)10090
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 20 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

-
Processing

SoftwareName: PHENIX / Version: 1.18_3845: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 164158 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00241841
ELECTRON MICROSCOPYf_angle_d0.61956978
ELECTRON MICROSCOPYf_dihedral_angle_d10.3635725
ELECTRON MICROSCOPYf_chiral_restr0.0456407
ELECTRON MICROSCOPYf_plane_restr0.0047325

+
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