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- PDB-6mwc: CryoEM structure of chimeric Eastern Equine Encephalitis Virus wi... -

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Basic information

Entry
Database: PDB / ID: 6mwc
TitleCryoEM structure of chimeric Eastern Equine Encephalitis Virus with Fab of EEEV-5 antibody
Components
  • E1
  • E2
  • EEEV-5 antibody heavy chain
  • EEEV-5 antibody light chain
KeywordsVIRUS/IMMUNE SYSTEM / Alphavirus / EEEV / Eastern Equine Encephalitis Virus / Sindbis / Fab / VIRUS-IMMUNE SYSTEM complex
Function / homology
Function and homology information


togavirin / T=4 icosahedral viral capsid / immunoglobulin complex / symbiont-mediated suppression of host toll-like receptor signaling pathway / adaptive immune response / host cell cytoplasm / symbiont-mediated suppression of host gene expression / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / symbiont entry into host cell ...togavirin / T=4 icosahedral viral capsid / immunoglobulin complex / symbiont-mediated suppression of host toll-like receptor signaling pathway / adaptive immune response / host cell cytoplasm / symbiont-mediated suppression of host gene expression / 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 / 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 V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin E-set / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Structural polyprotein / Structural polyprotein / Anti-human Langerin 2G3 lambda chain / Structural polyprotein
Similarity search - Component
Biological speciesEastern equine encephalitis virus
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.5 Å
AuthorsHasan, S.S. / Sun, C. / Kim, A.S. / Watanabe, Y. / Chen, C.L. / Klose, T. / Buda, G. / Crispin, M. / Diamond, M.S. / Klimstra, W.B. / Rossmann, M.G.
Funding support United States, United Kingdom, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI095366 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)2R01AI095436 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21AI117331-01 United States
Bill & Melinda Gates FoundationOPP1115782 United Kingdom
CitationJournal: Cell Rep / Year: 2018
Title: Cryo-EM Structures of Eastern Equine Encephalitis Virus Reveal Mechanisms of Virus Disassembly and Antibody Neutralization.
Authors: S Saif Hasan / Chengqun Sun / Arthur S Kim / Yasunori Watanabe / Chun-Liang Chen / Thomas Klose / Geeta Buda / Max Crispin / Michael S Diamond / William B Klimstra / Michael G Rossmann /
Abstract: Alphaviruses are enveloped pathogens that cause arthritis and encephalitis. Here, we report a 4.4-Å cryoelectron microscopy (cryo-EM) structure of eastern equine encephalitis virus (EEEV), an ...Alphaviruses are enveloped pathogens that cause arthritis and encephalitis. Here, we report a 4.4-Å cryoelectron microscopy (cryo-EM) structure of eastern equine encephalitis virus (EEEV), an alphavirus that causes fatal encephalitis in humans. Our analysis provides insights into viral entry into host cells. The envelope protein E2 showed a binding site for the cellular attachment factor heparan sulfate. The presence of a cryptic E2 glycan suggests how EEEV escapes surveillance by lectin-expressing myeloid lineage cells, which are sentinels of the immune system. A mechanism for nucleocapsid core release and disassembly upon viral entry was inferred based on pH changes and capsid dissociation from envelope proteins. The EEEV capsid structure showed a viral RNA genome binding site adjacent to a ribosome binding site for viral genome translation following genome release. Using five Fab-EEEV complexes derived from neutralizing antibodies, our investigation provides insights into EEEV host cell interactions and protective epitopes relevant to vaccine design.
History
DepositionOct 29, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 20, 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 / em_admin / 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 / _em_admin.last_update / _pdbx_entry_details.has_protein_modification / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

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  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
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Structure viewerMolecule:
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Assembly

Deposited unit
A: E1
B: E2
C: EEEV-5 antibody heavy chain
D: EEEV-5 antibody light chain
E: E1
F: E2
G: EEEV-5 antibody heavy chain
H: EEEV-5 antibody light chain
I: E1
J: E2
K: EEEV-5 antibody heavy chain
L: EEEV-5 antibody light chain
M: E1
N: E2
O: EEEV-5 antibody heavy chain
P: EEEV-5 antibody light chain


Theoretical massNumber of molelcules
Total (without water)567,62616
Polymers567,62616
Non-polymers00
Water00
1
A: E1
B: E2
C: EEEV-5 antibody heavy chain
D: EEEV-5 antibody light chain
E: E1
F: E2
G: EEEV-5 antibody heavy chain
H: EEEV-5 antibody light chain
I: E1
J: E2
K: EEEV-5 antibody heavy chain
L: EEEV-5 antibody light chain
M: E1
N: E2
O: EEEV-5 antibody heavy chain
P: EEEV-5 antibody light chain
x 60


Theoretical massNumber of molelcules
Total (without water)34,057,566960
Polymers34,057,566960
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: EEEV-5 antibody heavy chain
D: EEEV-5 antibody light chain
E: E1
F: E2
G: EEEV-5 antibody heavy chain
H: EEEV-5 antibody light chain
I: E1
J: E2
K: EEEV-5 antibody heavy chain
L: EEEV-5 antibody light chain
M: E1
N: E2
O: EEEV-5 antibody heavy chain
P: EEEV-5 antibody light chain
x 5


  • icosahedral pentamer
  • 2.84 MDa, 80 polymers
Theoretical massNumber of molelcules
Total (without water)2,838,13180
Polymers2,838,13180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: E1
B: E2
C: EEEV-5 antibody heavy chain
D: EEEV-5 antibody light chain
E: E1
F: E2
G: EEEV-5 antibody heavy chain
H: EEEV-5 antibody light chain
I: E1
J: E2
K: EEEV-5 antibody heavy chain
L: EEEV-5 antibody light chain
M: E1
N: E2
O: EEEV-5 antibody heavy chain
P: EEEV-5 antibody light chain
x 6


  • icosahedral 23 hexamer
  • 3.41 MDa, 96 polymers
Theoretical massNumber of molelcules
Total (without water)3,405,75796
Polymers3,405,75796
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))

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Components

#1: Protein
E1


Mass: 47938.141 Da / Num. of mol.: 4 / Fragment: ectodomain (UNP residues 802-1242)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eastern equine encephalitis virus / Cell (production host): BHK-15 / Production host: Mesocricetus auratus (golden hamster) / References: UniProt: E9KXM2, UniProt: Q4QXJ7*PLUS
#2: Protein
E2


Mass: 47046.953 Da / Num. of mol.: 4 / Fragment: ectodomain (UNP residues 325-744)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eastern equine encephalitis virus / Cell (production host): BHK-15 / Production host: Mesocricetus auratus (golden hamster) / References: UniProt: E9KXL2, UniProt: Q4QXJ7*PLUS
#3: Antibody
EEEV-5 antibody heavy chain


Mass: 23743.719 Da / Num. of mol.: 4 / Fragment: Fab / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#4: Antibody
EEEV-5 antibody light chain


Mass: 23177.713 Da / Num. of mol.: 4 / Fragment: Fab / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: G0YP42
Has protein modificationY
Sequence detailsThe antibody heavy chain and light chain amino acid sequences in this model are Fab CHK265 (from ...The antibody heavy chain and light chain amino acid sequences in this model are Fab CHK265 (from PDB entry 5ANY) and do not correspond to the amino acid sequences of the antibody heavy chain and light chains present in the sample.

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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
IDNameTypeDetailsEntity IDParent-IDSource
1Eastern equine encephalitis virus / EEEV-5 Fab complexCOMPLEXPurified from infected BHK-15 cellsall0MULTIPLE SOURCES
2Eastern equine encephalitis virusCOMPLEXall1RECOMBINANT
3EEEV-5 FabCOMPLEX#3-#41NATURAL
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Eastern equine encephalitis virus11021
23Mus musculus (house mouse)10090
Source (recombinant)Organism: Mesocricetus auratus (golden hamster) / Cell: BHK-15
Details of virusEmpty: NO / Enveloped: YES / Isolate: OTHER / Type: VIRION
Buffer solutionpH: 7.5
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: HELIUM / Humidity: 80 % / Chamber temperature: 295 K

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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
Image recordingElectron dose: 31 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 7.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 6583 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT

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