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- EMDB-50864: Structure of the Sabia Virus spike complex in a closed conformation -

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Basic information

Entry
Database: EMDB / ID: EMD-50864
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 G1
    • Protein or peptide: Glycoprotein G2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: POTASSIUM 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: 2.92 Å
AuthorsDiskin R / Cohen-Dvashi H
Funding support Israel, 1 items
OrganizationGrant numberCountry
Israel Science Foundation209/20 Israel
CitationJournal: To Be Published
Title: Structure of the Sabia Virus spike complex in an open conformation
Authors: Diskin R / Cohen-Dvashi H
History
DepositionJul 3, 2024-
Header (metadata) releaseJun 11, 2025-
Map releaseJun 11, 2025-
UpdateJun 11, 2025-
Current statusJun 11, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50864.png

Downloads & links

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Map

FileDownload / File: emd_50864.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnfiltered map
Projections & slices

Image control

Size
Brightness
Contrast
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: 0.035
Minimum - Maximum-0.1972377 - 0.4749515
Average (Standard dev.)0.0009098635 (±0.01588337)
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_50864_additional_1.map
AnnotationLocal resolution-filtered map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_50864_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_50864_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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 G1
    • Protein or peptide: Glycoprotein G2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: POTASSIUM 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 G1

MacromoleculeName: Glycoprotein G1 / type: protein_or_peptide / ID: 1 / 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 #2: Glycoprotein G2

MacromoleculeName: Glycoprotein G2 / type: protein_or_peptide / ID: 2 / 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 #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / 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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Macromolecule #7: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: K
Molecular weightTheoretical: 39.098 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: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Number images used: 114761
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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