[English] 日本語
Yorodumi- EMDB-11964: Puumala virus-like particle glycoprotein spike in complex with fa... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11964 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Puumala virus-like particle glycoprotein spike in complex with fab fragment P-4G2. | |||||||||
Map data | A reconstruction of an isolated Puumala virus-like particle glycoprotein spike decorated with four 4G2 fab fragments. | |||||||||
Sample |
| |||||||||
Function / homology | Function and homology information symbiont-mediated suppression of host TRAF-mediated signal transduction / host cell Golgi membrane / host cell mitochondrion / host cell surface / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host innate immune response / virus-mediated perturbation of host defense response / virion membrane / cell surface / signal transduction ...symbiont-mediated suppression of host TRAF-mediated signal transduction / host cell Golgi membrane / host cell mitochondrion / host cell surface / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host innate immune response / virus-mediated perturbation of host defense response / virion membrane / cell surface / signal transduction / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Myodes glareolus (Bank vole) / Puumala orthohantavirus / Puumala virus - Sotkamo | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 13.4 Å | |||||||||
Authors | Rissanen I / Stass R / Huiskonen JT / Bowden TA | |||||||||
Funding support | United Kingdom, 1 items
| |||||||||
Citation | Journal: Elife / Year: 2020 Title: Molecular rationale for antibody-mediated targeting of the hantavirus fusion glycoprotein. Authors: Ilona Rissanen / Robert Stass / Stefanie A Krumm / Jeffrey Seow / Ruben Jg Hulswit / Guido C Paesen / Jussi Hepojoki / Olli Vapalahti / Åke Lundkvist / Olivier Reynard / Viktor Volchkov / ...Authors: Ilona Rissanen / Robert Stass / Stefanie A Krumm / Jeffrey Seow / Ruben Jg Hulswit / Guido C Paesen / Jussi Hepojoki / Olli Vapalahti / Åke Lundkvist / Olivier Reynard / Viktor Volchkov / Katie J Doores / Juha T Huiskonen / Thomas A Bowden / Abstract: The intricate lattice of Gn and Gc glycoprotein spike complexes on the hantavirus envelope facilitates host-cell entry and is the primary target of the neutralizing antibody-mediated immune response. ...The intricate lattice of Gn and Gc glycoprotein spike complexes on the hantavirus envelope facilitates host-cell entry and is the primary target of the neutralizing antibody-mediated immune response. Through study of a neutralizing monoclonal antibody termed mAb P-4G2, which neutralizes the zoonotic pathogen Puumala virus (PUUV), we provide a molecular-level basis for antibody-mediated targeting of the hantaviral glycoprotein lattice. Crystallographic analysis demonstrates that P-4G2 binds to a multi-domain site on PUUV Gc and may preclude fusogenic rearrangements of the glycoprotein that are required for host-cell entry. Furthermore, cryo-electron microscopy of PUUV-like particles in the presence of P-4G2 reveals a lattice-independent configuration of the Gc, demonstrating that P-4G2 perturbs the (Gn-Gc) lattice. This work provides a structure-based blueprint for rationalizing antibody-mediated targeting of hantaviruses. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_11964.map.gz | 6.4 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-11964-v30.xml emd-11964.xml | 19 KB 19 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_11964_fsc.xml | 4.9 KB | Display | FSC data file |
Images | emd_11964.png | 47.8 KB | ||
Masks | emd_11964_msk_1.map | 6.9 MB | Mask map | |
Others | emd_11964_half_map_1.map.gz emd_11964_half_map_2.map.gz | 5.5 MB 5.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11964 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11964 | HTTPS FTP |
-Validation report
Summary document | emd_11964_validation.pdf.gz | 452.8 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_11964_full_validation.pdf.gz | 451.9 KB | Display | |
Data in XML | emd_11964_validation.xml.gz | 10.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11964 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11964 | HTTPS FTP |
-Related structure data
Related structure data | 7b09MC 6z06C 7b0aC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_11964.map.gz / Format: CCP4 / Size: 6.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | A reconstruction of an isolated Puumala virus-like particle glycoprotein spike decorated with four 4G2 fab fragments. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.52 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Mask #1
File | emd_11964_msk_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half map (odd) used to estimate resolution by FSC.
File | emd_11964_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half map (odd) used to estimate resolution by FSC. | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half map (even) used to estimate resolution by FSC.
File | emd_11964_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half map (even) used to estimate resolution by FSC. | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Puumala virus - Sotkamo
Entire | Name: Puumala virus - Sotkamo |
---|---|
Components |
|
-Supramolecule #1: Puumala virus - Sotkamo
Supramolecule | Name: Puumala virus - Sotkamo / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 / NCBI-ID: 11606 / Sci species name: Puumala virus - Sotkamo / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: Yes |
---|---|
Host (natural) | Organism: Myodes glareolus (Bank vole) |
Host system | Organism: Homo sapiens (human) |
-Macromolecule #1: Heavy chain of fab fragment P-4G2
Macromolecule | Name: Heavy chain of fab fragment P-4G2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Myodes glareolus (Bank vole) |
Molecular weight | Theoretical: 25.018047 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: TGQVQMKESG GGLVQPGKSL KLSCAASGFT FSDFWMSWVR QPSGKGLEWV ARINTNGDTT HYTDDMKGRF TISRDNAKTT LYLEMSPLK SEDTAMYYCT RDRLGPFDYW GQGTTVTVSS ATTKGPSVYP LAPGSAAQTN SMVTLGCLVK GYFPEPVTVT W NSGSLSSG ...String: TGQVQMKESG GGLVQPGKSL KLSCAASGFT FSDFWMSWVR QPSGKGLEWV ARINTNGDTT HYTDDMKGRF TISRDNAKTT LYLEMSPLK SEDTAMYYCT RDRLGPFDYW GQGTTVTVSS ATTKGPSVYP LAPGSAAQTN SMVTLGCLVK GYFPEPVTVT W NSGSLSSG VHTFPAVLQS DLYTLSSSVT VPSSTWPSQT VTCNVAHPAS STKVDKKIVP RDCGGTKHHH HHH |
-Macromolecule #2: Light chain of fab fragment P-4G2
Macromolecule | Name: Light chain of fab fragment P-4G2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Myodes glareolus (Bank vole) |
Molecular weight | Theoretical: 23.881582 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: TGDIVMTQSP AFPPVSLGDT VTITCQASQS VYKNLAWYQQ KPGKSPRLLI FGMSSLADGV PSRFSASGSD KQYSLKIRGL QPEDAAIYY CQQHYIAPYT FGAGTRLEIK RTDAAPTVSI FPPSSEQLTS GGASVVCFLN NFYPKDINVK WKIDGSERQN G VLNSWTDQ ...String: TGDIVMTQSP AFPPVSLGDT VTITCQASQS VYKNLAWYQQ KPGKSPRLLI FGMSSLADGV PSRFSASGSD KQYSLKIRGL QPEDAAIYY CQQHYIAPYT FGAGTRLEIK RTDAAPTVSI FPPSSEQLTS GGASVVCFLN NFYPKDINVK WKIDGSERQN G VLNSWTDQ DSKDSTYSMS STLTLTKDEY ERHNSYTCEA THKTSTSPIV KSFNRNEC |
-Macromolecule #3: Envelope polyprotein
Macromolecule | Name: Envelope polyprotein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Puumala orthohantavirus |
Molecular weight | Theoretical: 49.827898 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: GPGETQNLNS GWTDTAHGSG IIPMRTDLEL DFSLPSSASY TYRRQLQNPA NEQEKIPFHL QISKQVIHAE IQHLGHWMDG TFNLKTAFH CYGSCEKYAY PWQTAGCFIE KDYEYESGWG CNPPDCPGVG TGCTACGVYL DKLKSVGKAF KIVSLRYTRK A CIQLGTEQ ...String: GPGETQNLNS GWTDTAHGSG IIPMRTDLEL DFSLPSSASY TYRRQLQNPA NEQEKIPFHL QISKQVIHAE IQHLGHWMDG TFNLKTAFH CYGSCEKYAY PWQTAGCFIE KDYEYESGWG CNPPDCPGVG TGCTACGVYL DKLKSVGKAF KIVSLRYTRK A CIQLGTEQ TCKSVDSNDC LVTTSVKVCL IGTVSKFQPS DTLLFLGPLE QGGLIFKQWC TTTCQFGDPG DIMSTPVGMK CP ELNGSFR KKCAFATTPV CQFDGNTLSG YKRMIATKDS FQSFNVTEPH ISASSLEWID PDSSLRDHIN VIVGRDLSFQ DLS ETPCQV DLATTSIDGA WGSGVGFNLV CSVSLTECST FLTSIKACDS AMCYGSTTAN LLRGQNTVHI VGKGGHSGSK FMCC HDTKC SSTGLVAAAP HLDRVTGYNQ ADSDKIFDDG APECGISCWF TKSGEGTETS QVAPA |
-Macromolecule #4: Envelope polyprotein
Macromolecule | Name: Envelope polyprotein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Puumala orthohantavirus |
Molecular weight | Theoretical: 40.061566 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: ETGELKIECP HTIGLGQGLV IGSVELPPVP LTQVESLKLE SSCNFDLHTS TSSQQPFTKW TWEMKSDLAE NTQASSTSFQ TKSSEINLR GLCLVPPLVI ETAARTRKTI ACFDLSCNQT ACQPTVFLIG PIQTCITTKS CLLGLGDQRI QVNYEKTYCV S GQLVEGVC ...String: ETGELKIECP HTIGLGQGLV IGSVELPPVP LTQVESLKLE SSCNFDLHTS TSSQQPFTKW TWEMKSDLAE NTQASSTSFQ TKSSEINLR GLCLVPPLVI ETAARTRKTI ACFDLSCNQT ACQPTVFLIG PIQTCITTKS CLLGLGDQRI QVNYEKTYCV S GQLVEGVC FNPVHTMALS QPSHTYDIVT VMVRCFLIAK KVSTGDSMKL EKSFETLVQK TSCTGNGFQG YYICLVGSSS EP LYIPTLD DYRSAEVLSR MAFAPHGEDH DVEKNAISAM RIIGKVTGKA PSTESSDTIQ GVAFSGNPLY TSTGVLTAKD DPV YIWAPG IIMEGNHSVC DKKTLPLTWT GFIPLPGEIE KTGTKHHHHH H |
-Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 1 / Formula: NAG |
---|---|
Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | subtomogram averaging |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
---|---|
Grid | Model: C-flat-2/1 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 4.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |