[English] 日本語
Yorodumi
- EMDB-50862: Structure of the Sabia Virus spike complex in a closed conformation -

+
Open data


ID or keywords:

Loading...

-
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: To Be Published
Title: Structure of the Sabia Virus spike complex in a closed 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

-
Structure visualization

Supplemental images

emd_50862.png

Downloads & links

-
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
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: 0.04
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 °

-
Supplemental data

-
Additional map: Local resolution filtered map

Fileemd_50862_additional_1.map
AnnotationLocal resolution filtered map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map A

Fileemd_50862_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map B

Fileemd_50862_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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

-
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

-
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

-
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

-
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

-
Macromolecule #7: ZINC ION

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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
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

+
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)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more