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- EMDB-11236: Reconstruction of Tula virus surface glycoprotein lattice -

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Basic information

Entry
Database: EMDB / ID: EMD-11236
TitleReconstruction of Tula virus surface glycoprotein lattice
Map dataReconstruction of Tula virus glycoprotein spike lattice.
Sample
  • Virus: Tula orthohantavirus
    • Protein or peptide: Envelope polyprotein,Envelope polyprotein,Envelope polyprotein,Envelope polyprotein,Envelope polyprotein,Envelope polyprotein,Envelope polyprotein,Envelope polyprotein,Envelope polyprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHantavirus / Tula / Andes / TULV / ANDV / glycoprotein / lattice / spike / fusion protein / VIRAL PROTEIN
Function / homology
Function and homology information


symbiont-mediated suppression of host TRAF-mediated signal transduction / host cell Golgi membrane / host cell mitochondrion / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / host cell surface / host cell endoplasmic reticulum membrane / endocytosis involved in viral entry into host cell / symbiont-mediated activation of host autophagy / fusion of virus membrane with host endosome membrane / viral envelope ...symbiont-mediated suppression of host TRAF-mediated signal transduction / host cell Golgi membrane / host cell mitochondrion / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / host cell surface / host cell endoplasmic reticulum membrane / endocytosis involved in viral entry into host cell / symbiont-mediated activation of host autophagy / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / virion membrane / signal transduction / zinc ion binding / membrane
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 speciesTula orthohantavirus
Methodsubtomogram averaging / cryo EM / Resolution: 11.4 Å
AuthorsStass R / Li S / Huiskonen JT
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)649053 United Kingdom
CitationJournal: Cell / Year: 2020
Title: The Hantavirus Surface Glycoprotein Lattice and Its Fusion Control Mechanism.
Authors: Alexandra Serris / Robert Stass / Eduardo A Bignon / Nicolás A Muena / Jean-Claude Manuguerra / Rohit K Jangra / Sai Li / Kartik Chandran / Nicole D Tischler / Juha T Huiskonen / Felix A ...Authors: Alexandra Serris / Robert Stass / Eduardo A Bignon / Nicolás A Muena / Jean-Claude Manuguerra / Rohit K Jangra / Sai Li / Kartik Chandran / Nicole D Tischler / Juha T Huiskonen / Felix A Rey / Pablo Guardado-Calvo /
Abstract: Hantaviruses are rodent-borne viruses causing serious zoonotic outbreaks worldwide for which no treatment is available. Hantavirus particles are pleomorphic and display a characteristic square ...Hantaviruses are rodent-borne viruses causing serious zoonotic outbreaks worldwide for which no treatment is available. Hantavirus particles are pleomorphic and display a characteristic square surface lattice. The envelope glycoproteins Gn and Gc form heterodimers that further assemble into tetrameric spikes, the lattice building blocks. The glycoproteins, which are the sole targets of neutralizing antibodies, drive virus entry via receptor-mediated endocytosis and endosomal membrane fusion. Here we describe the high-resolution X-ray structures of the heterodimer of Gc and the Gn head and of the homotetrameric Gn base. Docking them into an 11.4-Å-resolution cryoelectron tomography map of the hantavirus surface accounted for the complete extramembrane portion of the viral glycoprotein shell and allowed a detailed description of the surface organization of these pleomorphic virions. Our results, which further revealed a built-in mechanism controlling Gc membrane insertion for fusion, pave the way for immunogen design to protect against pathogenic hantaviruses.
History
DepositionJun 29, 2020-
Header (metadata) releaseOct 14, 2020-
Map releaseOct 14, 2020-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 1.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6zjm
  • Surface level: 2.5
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6zjm
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11236.png

Downloads & links

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Map

FileDownload / File: emd_11236.map.gz / Format: CCP4 / Size: 4.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of Tula virus glycoprotein spike lattice.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4 Å/pix.
x 108 pix.
= 432. Å		4 Å/pix.
x 108 pix.
= 432. Å		4 Å/pix.
x 108 pix.
= 432. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.5 / Movie #1: 1.5
Minimum - Maximum-6.260702 - 8.191625
Average (Standard dev.)-0.081563696 (±0.93652344)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions108108108
Spacing108108108
CellA=B=C: 432.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z444
M x/y/z108108108
origin x/y/z0.0000.0000.000
length x/y/z432.000432.000432.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS108108108
D min/max/mean-6.2618.192-0.082

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Supplemental data

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Mask #1

Fileemd_11236_msk_1.map
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_11236_half_map_1.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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Half map: Half map (even) used to estimate resolution by FSC.

Fileemd_11236_half_map_2.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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Sample components

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Entire : Tula orthohantavirus

EntireName: Tula orthohantavirus
Components
  • Virus: Tula orthohantavirus
    • Protein or peptide: Envelope polyprotein,Envelope polyprotein,Envelope polyprotein,Envelope polyprotein,Envelope polyprotein,Envelope polyprotein,Envelope polyprotein,Envelope polyprotein,Envelope polyprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Tula orthohantavirus

SupramoleculeName: Tula orthohantavirus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 1980494 / Sci species name: Tula orthohantavirus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No

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Macromolecule #1: Envelope polyprotein,Envelope polyprotein,Envelope polyprotein,En...

MacromoleculeName: Envelope polyprotein,Envelope polyprotein,Envelope polyprotein,Envelope polyprotein,Envelope polyprotein,Envelope polyprotein,Envelope polyprotein,Envelope polyprotein,Envelope polyprotein
type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Tula orthohantavirus
Molecular weightTheoretical: 112.691258 KDa
Recombinant expressionOrganism: Drosophila melanogaster (fruit fly)
SequenceString: KTIYELKMEC PHTVGLGQGY IIGSTELGLI SIEAASDIKL ESSCNFDLHT TSMAQKSFTQ VEWRKKSDTT DTTNAASTTF EAQTKTVNL RGTCILAPEL YDTLKKVKKT VLCYDLTCNQ THCQPTVYLI APVLTCMSIR SCMASVFTSR IQVIYEKTHC V TGQLIEGQ ...String:
KTIYELKMEC PHTVGLGQGY IIGSTELGLI SIEAASDIKL ESSCNFDLHT TSMAQKSFTQ VEWRKKSDTT DTTNAASTTF EAQTKTVNL RGTCILAPEL YDTLKKVKKT VLCYDLTCNQ THCQPTVYLI APVLTCMSIR SCMASVFTSR IQVIYEKTHC V TGQLIEGQ CFNPAHTLTL SQPAHTYDTV TLPISCFFTP KKSEQLKVIK TFEGILTKTG CTENALQGYY VCFLGSHSEP LI VPSLEDI RSAEVVSRML VHPRGEDHDA IQNSQSHLRI VGPITAKVPS TSSTDTLKGT AFAGVPMYSS LSTLVRNADP EFV FSPGIV PESNHSTCDK KTVPITWTGY LPISGEMEGG SGLVPRGSGG GSGGGSWSHP QFEKGGGTGG GTLVPRGSGT GGET PLMES GWSDTAHGVG EIPMKTDLEL DFSLPSSSSY SYRRKLTNPA NKEESIPFHF QMEKQVIHAE IQPLGHWMDA TFNIK TAFH CYGACQKYSY PWQTSKCFFE KDYQYETGWG CNPGDCPGVG TGCTACGVYL DKLKSVGKAY KIISLKYTRK VCIQLG TEQ TCKHIDANDC LVTPSVKVCI VGTVSKLQPS DTLLFLGPLE QGGIILKQWC TTSCAFGDPG DIMSTPSGMR CPEHTGS FR KICGFATTPV CEYQGNTISG YKRMMATKDS FQSFNLTEPH ITTNKLEWID PDGNTRDFVN LVLNRDVSFQ DLSDNPCK V DLHTQAIEGA WGSGVGFTLT CTVGLTECPS FMTSIKACDL AMCYGSTVTN LARGSNTVKV VGKGGHSGSS FKCCHDTDC SSEGLLASAP HLERVTGFNQ IDSDKVYDDG APPCTFKCWF TKSGEWLLGI LNGNGPFEDD DDKAGWSHPQ FEKGGGSGGG SGGGSWSHP QFEKKVTGCT VFCTLAGPGA SCEAYSENGI FNISSPTCLV NKVQRFRGSE QKINFICQRV DQDVVVYCNG Q KKVILTKT LVIGQCIYTF TSLFSLMPDV AHSLAVELCV PGLHGGPFED DDDKAGWSHP QFEKGGGSGG GSGGGSWSHP QF EK

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 6 / 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
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI POLARA 300
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 4.71 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 11.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Dynamo / Number subtomograms used: 18064
ExtractionNumber tomograms: 49 / Number images used: 107820 / Reference model: EMD-4867 / Method: Template matching / Software - Name: Dynamo
Final 3D classificationNumber classes: 8 / Software - Name: RELION
Final angle assignmentType: OTHER / Software - Name: Dynamo / Details: template matching
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

6y5f

source_name: PDB, initial_model_type: experimental model

6yrq

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Correlation coefficient
Output model

PDB-6zjm:
Atomic model of Andes virus glycoprotein spike tetramer generated by fitting into a Tula virus reconstruction

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