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- PDB-7cw3: Cryo-EM structure of Chikungunya virus in complex with mAb CHK-26... -

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Basic information

Entry
Database: PDB / ID: 7cw3
TitleCryo-EM structure of Chikungunya virus in complex with mAb CHK-263 IgG (subregion around icosahedral 2-fold vertex)
Components
  • Capsid protein
  • E1 glycoprotein
  • E2 glycoprotein
  • Fab heavy chain
  • Fab light chain
KeywordsVIRUS/IMMUNE SYSTEM / virus / IgG / localized reconstruction / 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 / viral translational frameshifting / symbiont entry into host cell / 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 / viral translational frameshifting / symbiont entry into host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / host cell nucleus / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / RNA 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 / Structural polyprotein
Similarity search - Component
Biological speciesChikungunya virus
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 9.4 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 / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 13, 2024Group: Data collection / Source and taxonomy / Structure summary
Category: em_admin / em_entity_assembly_naturalsource / pdbx_entry_details
Item: _em_admin.last_update / _em_entity_assembly_naturalsource.entity_assembly_id / _em_entity_assembly_naturalsource.id

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Structure visualization

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  • Deposited structure unit
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  • EMDB-30480
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Structure viewerMolecule:
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Assembly

Deposited unit
A: E1 glycoprotein
B: E2 glycoprotein
C: E1 glycoprotein
D: E2 glycoprotein
G: E1 glycoprotein
H: E2 glycoprotein
E: E1 glycoprotein
F: E2 glycoprotein
q: Fab heavy chain
r: Fab light chain
K: E1 glycoprotein
L: E2 glycoprotein
I: E1 glycoprotein
J: E2 glycoprotein
i: E1 glycoprotein
j: E2 glycoprotein
g: E1 glycoprotein
h: E2 glycoprotein
e: E1 glycoprotein
f: E2 glycoprotein
s: Capsid protein
k: Fab heavy chain
l: Fab light chain
W: E1 glycoprotein
X: E2 glycoprotein
U: E1 glycoprotein
V: E2 glycoprotein
Y: E1 glycoprotein
Z: E2 glycoprotein
S: E1 glycoprotein
T: E2 glycoprotein
m: Fab heavy chain
n: Fab light chain
c: E1 glycoprotein
d: E2 glycoprotein
a: E1 glycoprotein
b: E2 glycoprotein
Q: E1 glycoprotein
R: E2 glycoprotein
O: E1 glycoprotein
P: E2 glycoprotein
M: E1 glycoprotein
N: E2 glycoprotein
t: Capsid protein
o: Fab heavy chain
p: Fab light chain


Theoretical massNumber of molelcules
Total (without water)1,917,21146
Polymers1,917,21146
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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


Mass: 47503.016 Da / Num. of mol.: 18 / 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.: 18 / Source method: isolated from a natural source / Source: (natural) Chikungunya virus / References: UniProt: Q8JUX5*PLUS, togavirin
#3: Antibody
Fab heavy chain / Coordinate model: Cα atoms only


Mass: 22872.670 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#4: Antibody
Fab light chain / Coordinate model: Cα atoms only


Mass: 23381.570 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#5: Protein Capsid protein / Togavirin / Coordinate model: Cα atoms only


Mass: 16428.607 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chikungunya virus
References: UniProt: A0A6B9KBE1, UniProt: Q8JUX5*PLUS, togavirin
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Subregions around the icosahedral 2-fold vertex of Chikungunya virus in complexed with CHK-263 IgGCOMPLEXall0MULTIPLE SOURCES
2Chikungunya virusCOMPLEX#1-#2, #51NATURAL
3Fab region of CHK-263 IgGCOMPLEX#3-#41NATURAL
Molecular weight
IDEntity assembly-IDExperimental value
11NO
21NO
31NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Chikungunya virus37124
32Mus musculus (house mouse)10090
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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 / Cs: 2.7 mm
Image recordingElectron dose: 20 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 9.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 14693 / Symmetry type: POINT

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