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- EMDB-11964: Puumala virus-like particle glycoprotein spike in complex with fa... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-11964 | |||||||||
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Title | Puumala virus-like particle glycoprotein spike in complex with fab fragment P-4G2. | |||||||||
![]() | A reconstruction of an isolated Puumala virus-like particle glycoprotein spike decorated with four 4G2 fab fragments. | |||||||||
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Function / homology | ![]() symbiont-mediated suppression of host TRAF-mediated signal transduction / host cell Golgi membrane / host cell mitochondrion / host cell surface / host cell endoplasmic reticulum membrane / virus-mediated perturbation of host defense response / virion membrane / signal transduction / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 13.4 Å | |||||||||
![]() | Rissanen I / Stass R / Huiskonen JT / Bowden TA | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 6.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19 KB 19 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 4.9 KB | Display | ![]() |
Images | ![]() | 47.8 KB | ||
Masks | ![]() | 6.9 MB | ![]() | |
Others | ![]() ![]() | 5.5 MB 5.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 452.8 KB | Display | ![]() |
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Full document | ![]() | 451.9 KB | Display | |
Data in XML | ![]() | 10.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7b09MC ![]() 6z06C ![]() 7b0aC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | A reconstruction of an isolated Puumala virus-like particle glycoprotein spike decorated with four 4G2 fab fragments. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.52 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | ![]() | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Half map (odd) used to estimate resolution by FSC.
File | emd_11964_half_map_1.map | ||||||||||||
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Annotation | Half map (odd) used to estimate resolution by FSC. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map (even) used to estimate resolution by FSC.
File | emd_11964_half_map_2.map | ||||||||||||
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Annotation | Half map (even) used to estimate resolution by FSC. | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Puumala virus - Sotkamo
Entire | Name: ![]() |
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Components |
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-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 |
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Host (natural) | Organism: ![]() |
Host system | Organism: ![]() |
-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 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 25.018047 KDa |
Recombinant expression | Organism: ![]() |
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 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 23.881582 KDa |
Recombinant expression | Organism: ![]() |
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 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 49.827898 KDa |
Recombinant expression | Organism: ![]() |
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 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 40.061566 KDa |
Recombinant expression | Organism: ![]() |
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 |
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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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![]() | subtomogram averaging |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: C-flat-2/1 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE-PROPANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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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: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |