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- PDB-6mwx: CryoEM structure of Chimeric Eastern Equine Encephalitis Virus wi... -

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Basic information

Entry
Database: PDB / ID: 6mwx
TitleCryoEM structure of Chimeric Eastern Equine Encephalitis Virus with Fab of EEEV-69 Antibody
Components
  • E1
  • E2
  • EEEV-69 antibody heavy chain
  • EEEV-69 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 / symbiont-mediated suppression of host gene expression / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / 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 gene expression / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / 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 / 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 V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / : / Immunoglobulin E-set / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Immunoglobulin-like fold
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: 8.2 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 30, 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 1.3Oct 16, 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_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-69 antibody heavy chain
D: EEEV-69 antibody light chain
E: E1
F: E2
G: EEEV-69 antibody heavy chain
H: EEEV-69 antibody light chain
I: E1
J: E2
K: EEEV-69 antibody heavy chain
L: EEEV-69 antibody light chain
M: E1
N: E2
O: EEEV-69 antibody heavy chain
P: EEEV-69 antibody light chain


Theoretical massNumber of molelcules
Total (without water)567,62616
Polymers567,62616
Non-polymers00
Water00
1
A: E1
B: E2
C: EEEV-69 antibody heavy chain
D: EEEV-69 antibody light chain
E: E1
F: E2
G: EEEV-69 antibody heavy chain
H: EEEV-69 antibody light chain
I: E1
J: E2
K: EEEV-69 antibody heavy chain
L: EEEV-69 antibody light chain
M: E1
N: E2
O: EEEV-69 antibody heavy chain
P: EEEV-69 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-69 antibody heavy chain
D: EEEV-69 antibody light chain
E: E1
F: E2
G: EEEV-69 antibody heavy chain
H: EEEV-69 antibody light chain
I: E1
J: E2
K: EEEV-69 antibody heavy chain
L: EEEV-69 antibody light chain
M: E1
N: E2
O: EEEV-69 antibody heavy chain
P: EEEV-69 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-69 antibody heavy chain
D: EEEV-69 antibody light chain
E: E1
F: E2
G: EEEV-69 antibody heavy chain
H: EEEV-69 antibody light chain
I: E1
J: E2
K: EEEV-69 antibody heavy chain
L: EEEV-69 antibody light chain
M: E1
N: E2
O: EEEV-69 antibody heavy chain
P: EEEV-69 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-69 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-69 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

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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-69 Fab complexCOMPLEXPurified from infected BHK-15 cellsall0MULTIPLE SOURCES
2Eastern equine encephalitis virusCOMPLEX#1-#21NATURAL
3EEEV-69 FabCOMPLEX#3-#41NATURAL
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Eastern equine encephalitis virus11021
23Mus musculus (house mouse)10090
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: 8.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 5964 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT

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