[English] 日本語
Yorodumi
- EMDB-41149: Cryo-EM Structure of Spike Glycoprotein from Bat Coronavirus WIV1... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-41149
TitleCryo-EM Structure of Spike Glycoprotein from Bat Coronavirus WIV1 in Closed Conformation
Map data
Sample
  • Virus: Bat SARS-like coronavirus WIV1
    • Protein or peptide: Spike glycoproteinSpike protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: LINOLEIC ACID
  • Ligand: water
KeywordsSpike / Glycoprotein / Coronavirus / VIRAL PROTEIN
Function / homology
Function and homology information


endocytosis involved in viral entry into host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
Similarity search - Domain/homology
Biological speciesRhinolophus sinicus (Chinese rufous horseshoe bat) / Bat SARS-like coronavirus WIV1
Methodsingle particle reconstruction / cryo EM / Resolution: 1.88 Å
AuthorsBostina M / Hills FR / Eruera A
Funding support1 items
OrganizationGrant numberCountry
Other private
CitationJournal: To Be Published
Title: Cryo-EM reveals variation in structural motifs within animal SARS-related coronavirus spike proteins
Authors: Bostina M / Hills FR / Eruera A
History
DepositionJun 29, 2023-
Header (metadata) releaseMay 1, 2024-
Map releaseMay 1, 2024-
UpdateMay 1, 2024-
Current statusMay 1, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_41149.png

Downloads & links

-
Map

FileDownload / File: emd_41149.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.832 Å
Density
Contour LevelBy AUTHOR: 0.0677
Minimum - Maximum-0.39450464 - 0.8541495
Average (Standard dev.)-0.000052073836 (±0.01452661)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 374.4 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_41149_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_41149_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Bat SARS-like coronavirus WIV1

EntireName: Bat SARS-like coronavirus WIV1
Components
  • Virus: Bat SARS-like coronavirus WIV1
    • Protein or peptide: Spike glycoproteinSpike protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: LINOLEIC ACID
  • Ligand: water

-
Supramolecule #1: Bat SARS-like coronavirus WIV1

SupramoleculeName: Bat SARS-like coronavirus WIV1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 1415852 / Sci species name: Bat SARS-like coronavirus WIV1 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No

-
Macromolecule #1: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Rhinolophus sinicus (Chinese rufous horseshoe bat)
Molecular weightTheoretical: 122.841266 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: KCLDFDDRTP PANTQFLSSH RGVYYPDDIF RSNVLHLVQD HFLPFDSNVT RFITFGLNFD NPIIPFKDGI YFAATEKSNV IRGWVFGST MNNKSQSVII MNNSTNLVIR ACNFELCDNP FFVVLKSNNT QIPSYIFNNA FNCTFEYVSK DFNLDLGEKP G NFKDLREF ...String:
KCLDFDDRTP PANTQFLSSH RGVYYPDDIF RSNVLHLVQD HFLPFDSNVT RFITFGLNFD NPIIPFKDGI YFAATEKSNV IRGWVFGST MNNKSQSVII MNNSTNLVIR ACNFELCDNP FFVVLKSNNT QIPSYIFNNA FNCTFEYVSK DFNLDLGEKP G NFKDLREF VFRNKDGFLH VYSGYQPISA ASGLPTGFNA LKPIFKLPLG INITNFRTLL TAFPPRPDYW GTSAAAYFVG YL KPTTFML KYDENGTITD AVDCSQNPLA ELKCSVKSFE IDKGIYQTSN FRVAPSKEVV RFPNITNLCP FGEVFNATTF PSV YAWERK RISNCVADYS VLYNSTSFST FKCYGVSATK LNDLCFSNVY ADSFVVKGDD VRQIAPGQTG VIADYNYKLP DDFT GCVLA WNTRNIDATQ TGNYNYKYRS LRHGKLRPFE RDISNVPFSP DGKPCTPPAF NCYWPLNDYG FYITNGIGYQ PYRVV VLSF ELLNAPATVC GPKLSTDLIK NQCVNFNFNG LTGTGVLTPS SKRFQPFQQF GRDVSDFTDS VRDPKTSEIL DISPCS FGG VSVITPGTNT SSEVAVLYQD VNCTDVPVAI HADQLTPSWR VHSTGNNVFQ TQAGCLIGAE HVDTSYECDI PIGAGIC AS YHTVSSLRST SQKSIVAYTM SLGADSSIAY SNNTIAIPTN FSISITTEVM PVSMAKTSVD CNMYICGDST ECANLLLQ Y GSFCTQLNRA LSGIAVEQDR NTREVFAQVK QMYKTPTLKD FGGFNFSQIL PDPLKPTKRS FIEDLLFNKV TLADAGFMK QYGECLGDIN ARDLICAQKF NGLTVLPPLL TDDMIAAYTA ALVSGTATAG WTFGAGAALQ IPFAMQMAYR FNGIGVTQNV LYENQKQIA NQFNKAISQI QESLTTTSTA LGKLQDVVNQ NAQALNTLVK QLSSNFGAIS SVLNDILSRL DKVEAEVQID R LITGRLQS LQTYVTQQLI RAAEIRASAN LAATKMSECV LGQSKRVDFC GKGYHLMSFP QAAPHGVVFL HVTYVPSQER NF TTAPAIC HEGKAYFPRE GVFVFNGTSW FITQRNFFSP QIITTDNTFV SGSCDVVIGI INNTVYDPLQ PE

UniProtKB: Spike glycoprotein

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

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 15 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

-
Macromolecule #7: LINOLEIC ACID

MacromoleculeName: LINOLEIC ACID / type: ligand / ID: 7 / Number of copies: 3 / Formula: EIC
Molecular weightTheoretical: 280.445 Da
Chemical component information

ChemComp-EIC:
LINOLEIC ACID / Linoleic acid

-
Macromolecule #8: water

MacromoleculeName: water / type: ligand / ID: 8 / Number of copies: 207 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: OTHER / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 67.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7e7b

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 1.88 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 800000

+
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