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- EMDB-25104: CryoEM structure of Venezuelan Equine Encephalitis virus (VEEV) T... -

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Basic information

Entry
Database: EMDB / ID: EMD-25104
TitleCryoEM structure of Venezuelan Equine Encephalitis virus (VEEV) TC-83 strain VLP in complex with Fab hVEEV-63 (focus refine of the asymmetric unit)
Map data
Sample
  • Virus: Venezuelan equine encephalitis virus (strain TC-83)
    • Protein or peptide: Spike glycoprotein E1
    • Protein or peptide: Spike glycoprotein E2
    • Protein or peptide: Capsid proteinCapsid
    • Protein or peptide: hVEEV-63 Fab heavy chain
    • Protein or peptide: hVEEV-63 Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Function / homology
Function and homology information


togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host toll-like receptor signaling pathway / clathrin-dependent endocytosis of virus by host cell / host cell cytoplasm / symbiont-mediated suppression of host gene expression / 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 toll-like receptor signaling pathway / clathrin-dependent endocytosis of virus by host cell / host cell cytoplasm / symbiont-mediated suppression of host gene expression / 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 / 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
Similarity search - Component
Biological speciesVenezuelan equine encephalitis virus (strain TC-83) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsBinshtein E / Crowe JE
Funding support United States, 1 items
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, 2021-
Header (metadata) releaseMar 16, 2022-
Map releaseMar 16, 2022-
UpdateJul 6, 2022-
Current statusJul 6, 2022Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.06
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  • Surface view with fitted model
  • Atomic models: PDB-7sfw
  • Surface level: 0.06
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_25104.png

Downloads & links

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Map

FileDownload / File: emd_25104.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.02775 Å
Density
Contour LevelBy AUTHOR: 0.06 / Movie #1: 0.06
Minimum - Maximum-0.32327536 - 0.51456934
Average (Standard dev.)0.00024269985 (±0.015309821)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 308.325 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.027751.027751.02775
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z308.325308.325308.325
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.3230.5150.000

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Supplemental data

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Half map: #1

Fileemd_25104_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_25104_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Venezuelan equine encephalitis virus (strain TC-83)

EntireName: Venezuelan equine encephalitis virus (strain TC-83)
Components
  • Virus: Venezuelan equine encephalitis virus (strain TC-83)
    • Protein or peptide: Spike glycoprotein E1
    • Protein or peptide: Spike glycoprotein E2
    • Protein or peptide: Capsid proteinCapsid
    • Protein or peptide: hVEEV-63 Fab heavy chain
    • Protein or peptide: hVEEV-63 Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Venezuelan equine encephalitis virus (strain TC-83)

SupramoleculeName: Venezuelan equine encephalitis virus (strain TC-83) / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 / NCBI-ID: 11037
Sci species name: Venezuelan equine encephalitis virus (strain TC-83)
Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: Yes / Virus empty: Yes

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Macromolecule #1: Spike glycoprotein E1

MacromoleculeName: Spike glycoprotein E1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Venezuelan equine encephalitis virus (strain TC-83)
Strain: TC-83
Molecular weightTheoretical: 47.952066 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: YEHATTMPSQ AGISYNTIVN RAGYAPLPIS ITPTKIKLIP TVNLEYVTCH YKTGMDSPAI KCCGSQECTP TYRPDEQCKV FTGVYPFMW GGAYCFCDTE NTQVSKAYVM KSDDCLADHA EAYKAHTASV QAFLNITVGE HSIVTTVYVN GETPVNFNGV K ITAGPLST ...String:
YEHATTMPSQ AGISYNTIVN RAGYAPLPIS ITPTKIKLIP TVNLEYVTCH YKTGMDSPAI KCCGSQECTP TYRPDEQCKV FTGVYPFMW GGAYCFCDTE NTQVSKAYVM KSDDCLADHA EAYKAHTASV QAFLNITVGE HSIVTTVYVN GETPVNFNGV K ITAGPLST AWTPFDRKIV QYAGEIYNYD FPEYGAGQPG AFGDIQSRTV SSSDLYANTN LVLQRPKAGA IHVPYTQAPS GF EQWKKDK APSLKFTAPF GCEIYTNPIR AENCAVGSIP LAFDIPDALF TRVSETPTLS AAECTLNECV YSSDFGGIAT VKY SASKSG KCAVHVPSGT ATLKEAAVEL TEQGSATIHF STANIHPEFR LQICTSYVTC KGDCHPPKDH IVTHPQYHAQ TFTA AVSKT AWTWLTSLLG GSAVIIIIGL VLATIVAMYV LTNQKHN

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Macromolecule #2: Spike glycoprotein E2

MacromoleculeName: Spike glycoprotein E2 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Venezuelan equine encephalitis virus (strain TC-83)
Strain: TC-83
Molecular weightTheoretical: 47.113746 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: STEELFNEYK LTRPYMARCI RCAVGSCHSP IAIEAVKSDG HDGYVRLQTS SQYGLDSSGN LKGRTMRYDM HGTIKEIPLH QVSLYTSRP CHIVDGHGYF LLARCPAGDS ITMEFKKDSV RHSCSVPYEV KFNPVGRELY THPPEHGVEQ ACQVYAHDAQ N RGAYVEMH ...String:
STEELFNEYK LTRPYMARCI RCAVGSCHSP IAIEAVKSDG HDGYVRLQTS SQYGLDSSGN LKGRTMRYDM HGTIKEIPLH QVSLYTSRP CHIVDGHGYF LLARCPAGDS ITMEFKKDSV RHSCSVPYEV KFNPVGRELY THPPEHGVEQ ACQVYAHDAQ N RGAYVEMH LPGSEVDSSL VSLSGSSVTV TPPDGTSALV ECECGGTKIS ETINKTKQFS QCTKKEQCRA YRLQNDKWVY NS DKLPKAA GATLKGKLHV PFLLADGKCT VPLAPEPMIT FGFRSVSLKL HPKNPTYLIT RQLADEPHYT HELISEPAVR NFT VTEKGW EFVWGNHPPK RFWAQETAPG NPHGLPHEVI THYYHRYPMS TILGLSICAA IATVSVAAST WLFCRSRVAC LTPY RLTPN ARIPFCLAVL CCARTARA

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Macromolecule #3: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO / EC number: togavirin
Source (natural)Organism: Venezuelan equine encephalitis virus (strain TC-83)
Strain: TC-83
Molecular weightTheoretical: 30.995879 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MFPFQPMYPM QPMPYRNPFA APRRPWFPRT DPFLAMQVQE LTRSMANLTF KQRRDAPPEG PSAKKPKKEA SQKQKGGGQG KKKKNQGKK KAKTGPPNPK AQNGNKKKTN KKPGKRQRMV MKLESDKTFP IMLEGKINGY ACVVGGKLFR PMHVEGKIDN D VLAALKTK ...String:
MFPFQPMYPM QPMPYRNPFA APRRPWFPRT DPFLAMQVQE LTRSMANLTF KQRRDAPPEG PSAKKPKKEA SQKQKGGGQG KKKKNQGKK KAKTGPPNPK AQNGNKKKTN KKPGKRQRMV MKLESDKTFP IMLEGKINGY ACVVGGKLFR PMHVEGKIDN D VLAALKTK KASKYDLEYA DVPQNMRADT FKYTHEKPQG YYSWHHGAVQ YENGRFTVPK GVGAKGDSGR PILDNQGRVV AI VLGGVNE GSRTALSVVM WNEKGVTVKY TPENCEQW

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Macromolecule #4: hVEEV-63 Fab heavy chain

MacromoleculeName: hVEEV-63 Fab heavy chain / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.403909 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLVQSGAE VKKPGASVKV SCKSSGYTFT NYIIHWVRQA PGQRLEWMGW INAGNGNTKY SQKFQGRISV TRDTSASAAY MELSSLKSE DTALYYCATL QMDYGGNGDL DYWGQGTLVT VSS

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Macromolecule #5: hVEEV-63 Fab light chain

MacromoleculeName: hVEEV-63 Fab light chain / type: protein_or_peptide / ID: 5 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.515588 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
YELTQPPSVS VSPGQTARIT CSGDALPKQY VYWYQQKPGQ APVLVIYKDS ERPSGIPERF SGSSSGTTVT LTISGVQAED DADYYCQAA DSSNTEYVFG TGTKVTVL

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 12 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293.15 K / Instrument: FEI VITROBOT MARK IV / Details: Lacey Carbon.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Detector mode: COUNTING / Digitization - Sampling interval: 14.0 µm / Number grids imaged: 1 / Number real images: 10586 / Average exposure time: 8.14 sec. / Average electron dose: 40.05 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 19000
CTF correctionSoftware - Name: RELION (ver. 3.1)
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationSoftware - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 405000
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-7sfw:
CryoEM structure of Venezuelan Equine Encephalitis virus (VEEV) TC-83 strain VLP in complex with Fab hVEEV-63 (focus refine of the asymmetric unit)

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