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- EMDB-11966: Puumala virus-like particle glycoprotein lattice. -

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Basic information

Entry
Database: EMDB / ID: EMD-11966
TitlePuumala virus-like particle glycoprotein lattice.
Map dataA reconstruction of a Puumala virus-like particle glycoprotein spike.
SamplePuumala virus - Sotkamo != Puumala orthohantavirus

Puumala virus - Sotkamo

  • Virus: Puumala orthohantavirus
    • Protein or peptide: Envelope polyprotein
  • Protein or peptide: Envelope polyprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
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
Hantavirus glycoprotein Gn / ITAM motif, hantavirus type / Envelope glycoprotein precursor, Hantavirus / : / Hantavirus glycoprotein Gn, head / Hantavirus ITAM motif / Hantavirus glycoprotein Gn, base / ITAM motif hantavirus type profile. / Hantavirus glycoprotein Gc / : ...Hantavirus glycoprotein Gn / ITAM motif, hantavirus type / Envelope glycoprotein precursor, Hantavirus / : / Hantavirus glycoprotein Gn, head / Hantavirus ITAM motif / Hantavirus glycoprotein Gn, base / ITAM motif hantavirus type profile. / Hantavirus glycoprotein Gc / : / Hantavirus glycoprotein Gc, N-terminal / Hantavirus glycoprotein Gc, C-terminal
Similarity search - Domain/homology
Envelopment polyprotein
Similarity search - Component
Biological speciesPuumala orthohantavirus
Methodsubtomogram averaging / cryo EM / Resolution: 13.9 Å
AuthorsRissanen I / Stass R / Huiskonen JT / Bowden TA
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)649053 United Kingdom
CitationJournal: 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
DepositionNov 19, 2020-
Header (metadata) releaseDec 16, 2020-
Map releaseDec 16, 2020-
UpdateJan 13, 2021-
Current statusJan 13, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.98
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.98
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7b0a
  • Surface level: 0.98
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7b0a
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11966.png

Downloads & links

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Map

FileDownload / File: emd_11966.map.gz / Format: CCP4 / Size: 6.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationA reconstruction of a Puumala virus-like particle glycoprotein spike.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.52 Å/pix.
x 122 pix.
= 429.44 Å		3.52 Å/pix.
x 122 pix.
= 429.44 Å		3.52 Å/pix.
x 122 pix.
= 429.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.52 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.98 / Movie #1: 0.98
Minimum - Maximum-4.5124707 - 7.0373864
Average (Standard dev.)-0.057124995 (±0.7387445)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions122122122
Spacing122122122
CellA=B=C: 429.44 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.523.523.52
M x/y/z122122122
origin x/y/z0.0000.0000.000
length x/y/z429.440429.440429.440
α/β/γ90.00090.00090.000
start NX/NY/NZ1081340
NX/NY/NZ13584349
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS122122122
D min/max/mean-4.5127.037-0.057

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Supplemental data

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Mask #1

Fileemd_11966_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map (even) used to estimate resolution by FSC.

Fileemd_11966_half_map_1.map
AnnotationHalf map (even) used to estimate resolution by FSC.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map (odd) used to estimate resolution by FSC.

Fileemd_11966_half_map_2.map
AnnotationHalf map (odd) used to estimate resolution by FSC.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Puumala virus - Sotkamo

EntireName: Puumala virus - Sotkamo
Components
  • Virus: Puumala orthohantavirus
    • Protein or peptide: Envelope polyprotein
  • Protein or peptide: Envelope polyprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Puumala orthohantavirus

SupramoleculeName: Puumala orthohantavirus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 1980486 / Sci species name: Puumala orthohantavirus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: Yes
Host systemOrganism: Homo sapiens (human)

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Macromolecule #1: Envelope polyprotein

MacromoleculeName: Envelope polyprotein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Puumala orthohantavirus
Molecular weightTheoretical: 49.827898 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

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Macromolecule #2: Envelope polyprotein

MacromoleculeName: Envelope polyprotein / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Puumala orthohantavirus
Molecular weightTheoretical: 40.061566 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 2 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5 / Details: PBS
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 4.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 13.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Dynamo / Number subtomograms used: 4323
ExtractionNumber tomograms: 33 / Number images used: 28312
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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