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- PDB-7sfw: CryoEM structure of Venezuelan Equine Encephalitis virus (VEEV) T... -

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Basic information

Entry
Database: PDB / ID: 7sfw
TitleCryoEM structure of Venezuelan Equine Encephalitis virus (VEEV) TC-83 strain VLP in complex with Fab hVEEV-63 (focus refine of the asymmetric unit)
Components
  • (Spike glycoprotein ...) x 2
  • (hVEEV-63 Fab ...) x 2
  • Capsid protein
KeywordsVIRUS/IMMUNE SYSTEM / VLP / VEEV / viral protein / 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 / clathrin-dependent endocytosis of virus by host cell / host cell cytoplasm / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus ...togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host gene expression / symbiont-mediated suppression of host toll-like receptor signaling pathway / clathrin-dependent endocytosis of virus by host cell / host cell cytoplasm / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / 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
Similarity search - Component
Biological speciesVenezuelan equine encephalitis virus
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsBinshtein, E. / Crowe, J.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19 AI142790 United States
CitationJournal: J Exp Med / Year: 2022
Title: Neutralizing antibodies protect mice against Venezuelan equine encephalitis virus aerosol challenge.
Authors: Natasha M Kafai / Lauren E Williamson / Elad Binshtein / Soila Sukupolvi-Petty / Christina L Gardner / Jaclyn Liu / Samantha Mackin / Arthur S Kim / Nurgun Kose / Robert H Carnahan / Ana ...Authors: Natasha M Kafai / Lauren E Williamson / Elad Binshtein / Soila Sukupolvi-Petty / Christina L Gardner / Jaclyn Liu / Samantha Mackin / Arthur S Kim / Nurgun Kose / Robert H Carnahan / Ana Jung / Lindsay Droit / Douglas S Reed / Scott A Handley / William B Klimstra / James E Crowe / Michael S Diamond /
Abstract: Venezuelan equine encephalitis virus (VEEV) remains a risk for epidemic emergence or use as an aerosolized bioweapon. To develop possible countermeasures, we isolated VEEV-specific neutralizing ...Venezuelan equine encephalitis virus (VEEV) remains a risk for epidemic emergence or use as an aerosolized bioweapon. To develop possible countermeasures, we isolated VEEV-specific neutralizing monoclonal antibodies (mAbs) from mice and a human immunized with attenuated VEEV strains. Functional assays and epitope mapping established that potently inhibitory anti-VEEV mAbs bind distinct antigenic sites in the A or B domains of the E2 glycoprotein and block multiple steps in the viral replication cycle including attachment, fusion, and egress. A 3.2-Å cryo-electron microscopy reconstruction of VEEV virus-like particles bound by a human Fab suggests that antibody engagement of the B domain may result in cross-linking of neighboring spikes to prevent conformational requirements for viral fusion. Prophylaxis or postexposure therapy with these mAbs protected mice against lethal aerosol challenge with VEEV. Our study defines functional and structural mechanisms of mAb protection and suggests that multiple antigenic determinants on VEEV can be targeted for vaccine or antibody-based therapeutic development.
History
DepositionOct 4, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

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  • Deposited structure unit
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Assembly

Deposited unit
A: Spike glycoprotein E1
B: Spike glycoprotein E2
C: Capsid protein
D: Spike glycoprotein E1
E: Spike glycoprotein E2
F: Capsid protein
G: Spike glycoprotein E1
H: Spike glycoprotein E2
I: Capsid protein
J: Spike glycoprotein E1
K: Spike glycoprotein E2
L: Capsid protein
M: hVEEV-63 Fab heavy chain
N: hVEEV-63 Fab light chain
O: hVEEV-63 Fab heavy chain
P: hVEEV-63 Fab light chain
Q: hVEEV-63 Fab heavy chain
R: hVEEV-63 Fab light chain
S: hVEEV-63 Fab heavy chain
T: hVEEV-63 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)606,57932
Polymers603,92520
Non-polymers2,65412
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area61430 Å2
ΔGint-197 kcal/mol
Surface area215920 Å2

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Components

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Spike glycoprotein ... , 2 types, 8 molecules ADGJBEHK

#1: Protein
Spike glycoprotein E1 / E1 envelope glycoprotein


Mass: 47952.066 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Venezuelan equine encephalitis virus (strain TC-83)
Strain: TC-83 / Production host: Homo sapiens (human) / References: UniProt: P05674
#2: Protein
Spike glycoprotein E2 / E2 envelope glycoprotein


Mass: 47113.746 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Venezuelan equine encephalitis virus (strain TC-83)
Strain: TC-83 / Production host: Homo sapiens (human) / References: UniProt: P05674

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Antibody , 2 types, 8 molecules MOQSNPRT

#4: Antibody
hVEEV-63 Fab heavy chain


Mass: 13403.909 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#5: Antibody
hVEEV-63 Fab light chain


Mass: 11515.588 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Protein / Sugars , 2 types, 16 molecules CFIL

#3: Protein
Capsid protein / Coat protein / C


Mass: 30995.879 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Venezuelan equine encephalitis virus (strain TC-83)
Strain: TC-83 / Production host: Homo sapiens (human) / References: UniProt: P05674, togavirin
#6: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Details

Has ligand of interestY

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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

ComponentName: Venezuelan equine encephalitis virus (strain TC-83) / Type: VIRUS / Entity ID: #1-#5 / Source: MULTIPLE SOURCES
Molecular weightUnits: MEGADALTONS / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Venezuelan equine encephalitis virus (strain TC-83)11037
31Homo sapiens (human)9606
Source (recombinant)Organism: Homo sapiens (human)
Details of virusEmpty: YES / Enveloped: YES / Isolate: OTHER / Type: VIRUS-LIKE PARTICLE
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293.15 K / Details: Lacey Carbon

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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: OTHER
Electron lensMode: BRIGHT FIELD / Nominal magnification: 75000 X / Nominal defocus max: 1600 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 8.14 sec. / Electron dose: 40.05 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 10586
Image scansSampling size: 14 µm

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.19.1_4122refinement
PHENIX1.19.1_4122refinement
EM software
IDNameVersionCategory
1RELION3.1particle selection
2EPUimage acquisition
4RELION3.1CTF correction
7Cootmodel fitting
9PHENIXmodel refinement
10RELION3.1initial Euler assignment
11RELION3.1final Euler assignment
12RELION3.1classification
13RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 19000
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 405000 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 60.03 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003439612
ELECTRON MICROSCOPYf_angle_d0.59953924
ELECTRON MICROSCOPYf_chiral_restr0.04486007
ELECTRON MICROSCOPYf_plane_restr0.00526912
ELECTRON MICROSCOPYf_dihedral_angle_d6.49695480

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