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Yorodumi- EMDB-25102: CryoEM structure of Venezuelan Equine Encephalitis virus (VEEV) T... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-25102 | |||||||||
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Title | CryoEM structure of Venezuelan Equine Encephalitis virus (VEEV) TC-83 strain VLP | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | : Function and homology information | |||||||||
Biological species | Venezuelan equine encephalitis virus (strain TC-83) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.2 Å | |||||||||
Authors | Binshtein E / Crowe JE | |||||||||
Funding support | United States, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_25102.map.gz | 476.9 MB | EMDB map data format | |
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Header (meta data) | emd-25102-v30.xml emd-25102.xml | 21.6 KB 21.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_25102_fsc.xml | 18 KB | Display | FSC data file |
Images | emd_25102.png | 295.5 KB | ||
Others | emd_25102_half_map_1.map.gz emd_25102_half_map_2.map.gz | 409.7 MB 409.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-25102 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25102 | HTTPS FTP |
-Validation report
Summary document | emd_25102_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_25102_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_25102_validation.xml.gz | 25.9 KB | Display | |
Data in CIF | emd_25102_validation.cif.gz | 34.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25102 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25102 | HTTPS FTP |
-Related structure data
Related structure data | 7sfuMC 7sfvC 7sfwC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_25102.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.8065 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: #2
File | emd_25102_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_25102_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Venezuelan equine encephalitis virus (strain TC-83)
Entire | Name: Venezuelan equine encephalitis virus (strain TC-83) |
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Components |
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-Supramolecule #1: Venezuelan equine encephalitis virus (strain TC-83)
Supramolecule | Name: Venezuelan equine encephalitis virus (strain TC-83) / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 / 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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Host system | Organism: Homo sapiens (human) |
-Macromolecule #1: Spike glycoprotein E1
Macromolecule | Name: Spike glycoprotein E1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Venezuelan equine encephalitis virus (strain TC-83) Strain: TC-83 |
Molecular weight | Theoretical: 47.952066 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Macromolecule #2: Spike glycoprotein E2
Macromolecule | Name: Spike glycoprotein E2 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Venezuelan equine encephalitis virus (strain TC-83) Strain: TC-83 |
Molecular weight | Theoretical: 47.113746 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Macromolecule #3: Capsid protein
Macromolecule | Name: Capsid protein / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO / EC number: togavirin |
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Source (natural) | Organism: Venezuelan equine encephalitis virus (strain TC-83) Strain: TC-83 |
Molecular weight | Theoretical: 18.19584 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: KRQRMVMKLE SDKTFPIMLE GKINGYACVV GGKLFRPMHV EGKIDNDVLA ALKTKKASKY DLEYADVPQN MRADTFKYTH EKPQGYYSW HHGAVQYENG RFTVPKGVGA KGDSGRPILD NQGRVVAIVL GGVNEGSRTA LSVVMWNEKG VTVKYTPENC E QW |
-Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 12 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293.15 K / Instrument: FEI VITROBOT MARK IV / Details: Lacey Carbon. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film 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: 5939 / Average exposure time: 8.14 sec. / Average electron dose: 40.05 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 75000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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Output model | PDB-7sfu: |