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- EMDB-50862: Structure of the Sabia Virus spike complex in a closed conformation -

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Basic information

Entry
Database: EMDB / ID: EMD-50862
TitleStructure of the Sabia Virus spike complex in a closed conformation
Map dataUnfiltered map
Sample
  • Organelle or cellular component: Spike complex of Sabia virus
    • Protein or peptide: Glycoprotein G2
    • Protein or peptide: Glycoprotein G1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: ZINC ION
  • Ligand: water
KeywordsClass-I spike complex / VIRAL PROTEIN
Function / homology
Function and homology information


host cell Golgi membrane / receptor-mediated endocytosis of virus by host cell / host cell endoplasmic reticulum membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / metal ion binding / membrane
Similarity search - Function
Arenavirus glycoprotein, zinc binding domain / Arenavirus glycoprotein / Arenavirus glycoprotein
Similarity search - Domain/homology
Pre-glycoprotein polyprotein GP complex
Similarity search - Component
Biological speciesSabia virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.64 Å
AuthorsDiskin R / Cohen-Dvashi H
Funding support Israel, 1 items
OrganizationGrant numberCountry
Israel Science Foundation209/20 Israel
CitationJournal: Nat Microbiol / Year: 2025
Title: Metal-induced conformational changes in the Sabiá virus spike complex.
Authors: Hadas Cohen-Dvashi / Michael Katz / Ron Diskin /
Abstract: Haemorrhagic fever viruses from the Arenaviridae are a source of concern owing to their potential to cause lethal outbreaks and the lack of effective therapeutics. While structures of spike proteins ...Haemorrhagic fever viruses from the Arenaviridae are a source of concern owing to their potential to cause lethal outbreaks and the lack of effective therapeutics. While structures of spike proteins from 'Old World' arenaviruses are available, the differences and similarities to 'New World' arenaviruses, such as the Sabiá virus, remain unclear owing to the lack of New World spike structures. Here we present the structure of the isolated spike complex from the Sabiá virus, which mediates viral attachment and entry to the host cells, using single-particle cryo-electron microscopy. We find two distinct conformational states of the spike, representing its native closed state at 2.6 Å resolution and an open state at 2.9 Å resolution that it assumes during cell entry. In addition, we show that the opening of the spike and subsequent cell entry are dependent on acidic pH and an unidentified metal ion. Our study suggests potential differences in the cell entry mechanisms of clade B arenaviruses compared with others in the Arenaviridae family.
History
DepositionJul 3, 2024-
Header (metadata) releaseJun 11, 2025-
Map releaseJun 11, 2025-
UpdateSep 17, 2025-
Current statusSep 17, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50862.png

Downloads & links

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Map

FileDownload / File: emd_50862.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnfiltered map
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 256 pix.
= 210.944 Å		0.82 Å/pix.
x 256 pix.
= 210.944 Å		0.82 Å/pix.
x 256 pix.
= 210.944 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.824 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.21166925 - 0.47369394
Average (Standard dev.)0.00091653696 (±0.01712462)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 210.944 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Local resolution filtered map

Fileemd_50862_additional_1.map
AnnotationLocal resolution filtered map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

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Half map: Half map A

Fileemd_50862_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_50862_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Spike complex of Sabia virus

EntireName: Spike complex of Sabia virus
Components
  • Organelle or cellular component: Spike complex of Sabia virus
    • Protein or peptide: Glycoprotein G2
    • Protein or peptide: Glycoprotein G1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: ZINC ION
  • Ligand: water

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Supramolecule #1: Spike complex of Sabia virus

SupramoleculeName: Spike complex of Sabia virus / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Sabia virus

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Macromolecule #1: Glycoprotein G2

MacromoleculeName: Glycoprotein G2 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Sabia virus
Molecular weightTheoretical: 28.552533 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GIFSWTITDA VGNDMPGGYC LERWMLVTSD LKCFGNTALA KCNLDHDSEF CDMLKLFEFN KKAIETLNDN TKNKVNLLTH SINALISDN LLMKNRLKEL LNTPYCNYTK FWYVNHTASG EHSLPRCWLV RNNSYLNESE FRNDWIIESD HLLSEMLNKE Y IDRQGKTP ...String:
GIFSWTITDA VGNDMPGGYC LERWMLVTSD LKCFGNTALA KCNLDHDSEF CDMLKLFEFN KKAIETLNDN TKNKVNLLTH SINALISDN LLMKNRLKEL LNTPYCNYTK FWYVNHTASG EHSLPRCWLV RNNSYLNESE FRNDWIIESD HLLSEMLNKE Y IDRQGKTP LTLVDICFWS TLFFTTTLFL HLVGFPTHRH IRGEPCPLPH RLNSRGGCRC GKYPELKKPI TWHKNHGGGS DY KDDDDK

UniProtKB: Pre-glycoprotein polyprotein GP complex

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Macromolecule #2: Glycoprotein G1

MacromoleculeName: Glycoprotein G1 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Sabia virus
Molecular weightTheoretical: 22.594738 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: FRIGRSTELQ NITFDMLKVF EDHPTSCMVN HSTYYVHENK NATWCLEVSV TDVTLLMAEH DRQVLNNLSN CVHPAVEHRS RMVGLLEWI FRALKYDFNH DPTPLCQKQT STVNETRVQI NITEGFGSHG FEDTILQRLG VLFGSRIAFS NIQDLGKKRF L LIRNSTWK ...String:
FRIGRSTELQ NITFDMLKVF EDHPTSCMVN HSTYYVHENK NATWCLEVSV TDVTLLMAEH DRQVLNNLSN CVHPAVEHRS RMVGLLEWI FRALKYDFNH DPTPLCQKQT STVNETRVQI NITEGFGSHG FEDTILQRLG VLFGSRIAFS NIQDLGKKRF L LIRNSTWK NQCEMNHVNS MHLMLANAGR SSGSRRPL

UniProtKB: Pre-glycoprotein polyprotein GP complex

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 12 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #7: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #8: water

MacromoleculeName: water / type: ligand / ID: 8 / Number of copies: 3 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 39.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.64 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Number images used: 116654
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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