[English] 日本語
Yorodumi
- EMDB-61601: Cryo-EM structure of EU-HedgehogCoV (Erinaceus/VMC/DEU/2012) S-tr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-61601
TitleCryo-EM structure of EU-HedgehogCoV (Erinaceus/VMC/DEU/2012) S-trimer in a locked-2 conformation
Map data
Sample
  • Organelle or cellular component: EU-HedgehogCoV (Erinaceus/VMC/DEU/2012/) Spike protein
    • Protein or peptide: Spike glycoprotein,Fibritin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: FOLIC ACID
  • Ligand: LINOLEIC ACID
Keywordsspike protein / VIRAL PROTEIN
Function / homology
Function and homology information


virion component / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / endocytosis involved in viral entry into 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, MERS-CoV-like / Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like / Fibritin C-terminal / Fibritin C-terminal region / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily ...Spike (S) protein S1 subunit, receptor-binding domain, MERS-CoV-like / Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like / Fibritin C-terminal / Fibritin C-terminal region / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / 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 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Fibritin / Spike glycoprotein
Similarity search - Component
Biological speciesBetacoronavirus Erinaceus/VMC/DEU/2012 / Enterobacteria phage T4 (Bacteriophage T4) (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsYuan H / Xiong X
Funding support3 items
OrganizationGrant numberCountry
Other governmentSRPG22-002
Other government2021YFA1300903
Other government2022A1515110495
CitationJournal: To Be Published
Title: A locked-1 conformation of spike protein trimer of Merbecovirus
Authors: Yuan H / Xiong X
History
DepositionSep 20, 2024-
Header (metadata) releaseJun 18, 2025-
Map releaseJun 18, 2025-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_61601.png

Downloads & links

-
Map

FileDownload / File: emd_61601.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 240 pix.
= 316.8 Å		1.32 Å/pix.
x 240 pix.
= 316.8 Å		1.32 Å/pix.
x 240 pix.
= 316.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0253
Minimum - Maximum-0.120338775 - 0.2137265
Average (Standard dev.)0.00004981695 (±0.008031746)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 316.80002 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_61601_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_61601_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : EU-HedgehogCoV (Erinaceus/VMC/DEU/2012/) Spike protein

EntireName: EU-HedgehogCoV (Erinaceus/VMC/DEU/2012/) Spike protein
Components
  • Organelle or cellular component: EU-HedgehogCoV (Erinaceus/VMC/DEU/2012/) Spike protein
    • Protein or peptide: Spike glycoprotein,Fibritin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: FOLIC ACID
  • Ligand: LINOLEIC ACID

-
Supramolecule #1: EU-HedgehogCoV (Erinaceus/VMC/DEU/2012/) Spike protein

SupramoleculeName: EU-HedgehogCoV (Erinaceus/VMC/DEU/2012/) Spike protein
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Betacoronavirus Erinaceus/VMC/DEU/2012

-
Macromolecule #1: Spike glycoprotein,Fibritin

MacromoleculeName: Spike glycoprotein,Fibritin / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Enterobacteria phage T4 (Bacteriophage T4) (virus)
Molecular weightTheoretical: 149.867672 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MIRSACLLMC LLMFIKATPS EGTCISVDMQ PSYFIKNWSM PINMSKADGV LYPVGRTYSN ITITLEGLFP HQADRGDMYV YSQSHKGRP FISNYSLVTN DFGNGIVIRI GSAANKTGSP IISNIASNFQ IMKKLYPALL FGSAVGKFPA NNKTGAYFNH S LVILPEKC ...String:
MIRSACLLMC LLMFIKATPS EGTCISVDMQ PSYFIKNWSM PINMSKADGV LYPVGRTYSN ITITLEGLFP HQADRGDMYV YSQSHKGRP FISNYSLVTN DFGNGIVIRI GSAANKTGSP IISNIASNFQ IMKKLYPALL FGSAVGKFPA NNKTGAYFNH S LVILPEKC GTVITALYCV LEPKNDTNCT GSSGYVSYVL FENFSCDATT DGNLKNSLQQ WFNIKDCLFE KNYNVTDDER EE WFGIIQD QQGVHLYTSR KNGYSNNMFL FATLPIYDQI LYYTVMPRSI NASNYASYHA FSAFYIYKLH KINYMVDFDV NGY ITRAVD CGYNDYTQLQ CSYGQFDMDS GVYSASYFNA RSRGYYYEAA ELTECDLDVL FKNDAPIIAN YSRRVFTNCN YNLT KLLSL VQVDEFVCHK TTPEALATGC YSSLTVDWFA LPFSMKSTLA IGSAEAISMF NYNQDYSNPT CRIHAAVTAN VSTAL NFTA NANYAYISRC QGVDGKPILL QPGQMTNIAC RSGVLARPSD ADYFGYSFQG RNYYLGRKSY KPKTDEGDVQ MVYVIT PKY DKGPDTVCPL KDMGAASSSL DGLLGQCIDY DIHGVVGRGV FQVCNTTGIA SQIFVYDGFG NIIGFHSKNG TYYCMAP CV SVPVSVIYDK SSDVHATLYS SVECNHIKSV ATVFSRQTES KLRSSDNGLL QTAVGCVIGF RNTSDTVEDC TLPLGQSL C AKPPSFSSRS TNVNNTFALV HMLFQNPLKV SVLNSTEFQV SIPQNFSFGI TEEFIETSIQ KVTVDCKQYV CNGFERCEQ LLVQYGQFCS KINQALHGVN LRQDDATKSL FEDIKVPQSV PLMTSLTGDY NLSLFEAPNI GSGNNNYRSA LEDLLFDKVT LSDPGYMKG YDECMKKGPP SARDLICAQY VSGYKVLPPL YDANMEAMYT ASLTGSIAGS FWTGGLSSAA ALPFAQSMFY R MNGIGITQ NVLMKNQREI ANKFNQALGA MQTGFTATNQ AFQKVQDVVN ANAQALSKLA SELANTFGAI SASIGDILKR LD VLEQEVQ IDRLINGRLT SLNAFVSQQL VRSEAAARSS QLAKEKINEC VKAQSTRSGF CGQGTHIVSF VINAPNGFYF IHV GYHPQD YVNQTAAYGL CDSSSKKCIA AKNGYFVKND SDSGSWSYTG SSFYQPEPIT TFNSRFVEPE VTFQNLSNNL PPPL LSNNT DITFEDELEE FYKNITSEIP NFGSLSQINT TMLNLSQEMS TLQQVVKDLN NSYIELKELG NHTYYQKWPG SGYIP EAPR DGQAYVRKDG EWVLLSTFLL EVLFQGPGHH HHHHHHSAWS HPQFEKGGGS GGGGSGGSAW SHPQFEKSA

UniProtKB: Spike glycoprotein, Fibritin

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

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 37 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

-
Macromolecule #5: FOLIC ACID

MacromoleculeName: FOLIC ACID / type: ligand / ID: 5 / Number of copies: 3 / Formula: FOL
Molecular weightTheoretical: 441.397 Da
Chemical component information

ChemComp-FA:
FOLIC ACID

-
Macromolecule #6: LINOLEIC ACID

MacromoleculeName: LINOLEIC ACID / type: ligand / ID: 6 / Number of copies: 3 / Formula: EIC
Molecular weightTheoretical: 280.445 Da
Chemical component information

ChemComp-EIC:
LINOLEIC ACID

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 6
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6q04

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 82386
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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