[English] 日本語
Yorodumi
- EMDB-53687: Prefusion stabilized spike glycoprotein of equine coronavirus. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-53687
TitlePrefusion stabilized spike glycoprotein of equine coronavirus.
Map dataEM map of the equine coronavirus spike glycoprotein.
Sample
  • Complex: Trimeric spike glycoprotein
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: Sapienic acid
Keywordsfusion glycoprotein / membrane protein / viral protein
Biological speciesEquine coronavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.76 Å
AuthorsMelchers JM / Hulswit RJG / Hurdiss DL
Funding support Netherlands, 1 items
OrganizationGrant numberCountry
Other private Netherlands
CitationJournal: PLoS Pathog / Year: 2026
Title: AI-guided prefusion stabilization of the human coronavirus OC43 spike protein enables universal embecovirus antigen design.
Authors: Jelle M Melchers / Jarek Juraszek / Ruben J G Hulswit / Daan van Overveld / Lam Le / Frank J M van Kuppeveld / Daniel L Hurdiss / Berend-Jan Bosch / Johannes P M Langedijk / Mark J G Bakkers /
Abstract: The continued threat of zoonotic coronavirus spillovers underscores the need for cross-species applicable vaccine design strategies. The genus Embecovirus includes human coronaviruses OC43 and HKU1 ...The continued threat of zoonotic coronavirus spillovers underscores the need for cross-species applicable vaccine design strategies. The genus Embecovirus includes human coronaviruses OC43 and HKU1 as well as relevant veterinary pathogens. The coronavirus spike (S) fusion glycoprotein, key to viral entry and protective immunity, is inherently metastable, complicating vaccine development. Using the ReCaP AI tool, we stabilized the prefusion conformation of OC43 S through rationally combined amino acid substitutions, resulting in markedly enhanced expression and thermal stability. The substitutions were transferable to equine coronavirus (ECoV) S and HKU1. Cryo-EM structures of stabilized OC43 and ECoV S revealed that stabilization was achieved by arresting the release of the fusion peptide and keeping the S1B receptor binding domain in the 'down' state by improving the complex polar interactions of neighboring S1B domains and the bound free fatty acid at the interprotomer S1B interface. This work provides the first ECoV S structure and a broadly applicable framework for engineering stabilized Embecovirus S antigens.
History
DepositionMay 13, 2025-
Header (metadata) releaseMar 11, 2026-
Map releaseMar 11, 2026-
UpdateApr 1, 2026-
Current statusApr 1, 2026Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_53687.png

Downloads & links

-
Map

FileDownload / File: emd_53687.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM map of the equine coronavirus spike glycoprotein.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 360 pix.
= 300.96 Å		0.84 Å/pix.
x 360 pix.
= 300.96 Å		0.84 Å/pix.
x 360 pix.
= 300.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.836 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.73191214 - 0.97892576
Average (Standard dev.)0.0006376272 (±0.021337064)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 300.96002 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Half map of equine coronavirus spike glycoprotein.

Fileemd_53687_half_map_1.map
AnnotationHalf map of equine coronavirus spike glycoprotein.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map of equine coronavirus spike glycoprotein.

Fileemd_53687_half_map_2.map
AnnotationHalf map of equine coronavirus spike glycoprotein.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Trimeric spike glycoprotein

EntireName: Trimeric spike glycoprotein
Components
  • Complex: Trimeric spike glycoprotein
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: Sapienic acid

-
Supramolecule #1: Trimeric spike glycoprotein

SupramoleculeName: Trimeric spike glycoprotein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Equine coronavirus / Location in cell: membrane
Molecular weightTheoretical: 435 KDa

-
Macromolecule #1: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Equine coronavirus
Molecular weightTheoretical: 143.631375 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MVLLLLFFLP TAFAVVGDVK CTTIGVNDVN TGAPVISTET VDVTNGLGTY YVLDRVYLNT TLLLNGYYPT SGANYRNLAL KASELLSTL WYKPPFLSEF NDGVFAKVKN TKVTKNGIVY SEFPTMVIGT TFVNTSYTVV VQPRTTVVNS KLQGLLEITI C QYSMCEYP ...String:
MVLLLLFFLP TAFAVVGDVK CTTIGVNDVN TGAPVISTET VDVTNGLGTY YVLDRVYLNT TLLLNGYYPT SGANYRNLAL KASELLSTL WYKPPFLSEF NDGVFAKVKN TKVTKNGIVY SEFPTMVIGT TFVNTSYTVV VQPRTTVVNS KLQGLLEITI C QYSMCEYP NTVCNSGIGS PRKELWHYEK AVASCLYRRN FTYDVNSDWL YFHFYQQGGT FYAYYTDSGF ITTFLFNIYL GT SLSHYYV MPLSCSGKLD LQYWVTPLTN RQFLLVFNQD GIIYNAVDCA SDYMSEIKCK TQNVKPSTGV YDLTGYTVQP IAD VYRRIP NLPDCNMEDW LSAPTVASPL NWERRTFSNC NFNMSSLLSF IQADSFSCSN IDAAKLYGMC FGSVTIDKFA IPNS RKVDL QLGNRGYLQR FNYRIDTTAT SCQLYYSLGA DNVTVTRSNP SAWNRRYGFN DTMFKPQPAG FFTNHDVVYS KQCFK VPNT YCPCKNNGAT CVGNGVSAGV SGTTTGSGTC PVGTSYRTCF NPIQCACTCD PEPINAILTS GPRACPQVKS LVGLGE HCS GLGIHEDFCG GSPCSCPANA FMAWSVDSCL QDGRCNIFSN LILNGVNSGA TCSTDLQRSN TEIVVGVCVK YDLYGIT GQ GIFIEVNATY YNSWQNLLYD SNGNLYGFRD YLTNRTFMIR SCYSGRVSAA YHSDASEPAL LYRNLKCNYV FNNTIARE G NPINYFDSYL GCIVNADNST SSVVDTCVLT MGSGYCVDYS TASRAGGSPS TGYRLTNFEP FNVRLVNDSV EPVGGLYEI QIPSEFTIGN FEEFIQTNSP KVTIDCAAFV CGDYAACREQ LVGYGSFCDN IEAILTEVND LLDTTQFQVA NSLMNGVTLS SRLKTGINF NVDDINFSSV LGCVGSDCNT VSSRSAIEDL LFNKVRLSDV GFVEAYNNCT GGAEIRDLLC VQTFNGIKVL P PVLSENQI SGYTLAATSA QLFPPWTAAA GIPFYLNVQY RINGLGVTMD VLSQNQKMIA NAFNNALGAI QNGFDPTNSA LV KIQAVVN ANAEALNNLL QQLSNRFGAI SSSLQEILSR LDPPEAQAQI DKLINGRLTA LNAFVSQQLS DTTLVKFSAS QAI EKVNEC VKSQSLRVNF CGNGNHIISL VQNAPYGLYF IHFNYVPTKY VTAKVSPGLC IAGDRGIAPK SGYFVNVNNM WMFT GSGYY YPEPITENNV VVMSTCAVNY TKAPDVMLNI LIPNLSDFKE ELDQWFKNQT SVAPDLSLDY INVTFLNLQD EMNRL QESI KVLNQSYINL KDKGTYEY

-
Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 12 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

-
Macromolecule #4: Sapienic acid

MacromoleculeName: Sapienic acid / type: ligand / ID: 4 / Number of copies: 3 / Formula: 8Z9
Molecular weightTheoretical: 254.408 Da
Chemical component information

ChemComp-8Z9:
Sapienic acid

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1.1 mg/mL
BufferpH: 7.4
Component:
ConcentrationNameFormula
20.0 mMTris
150.0 mMsodium chlorideNaCl

Details: 20 mM Tris-HCL, 150 mM NaCl, pH 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
SoftwareName: EPU
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 906875
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab initio
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.76 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 397300
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: in silico model / Details: ModelAngelo
SoftwareName: UCSF ChimeraX (ver. 1.9)
RefinementProtocol: OTHER
Output model

PDB-9r6t:
Prefusion stabilized spike glycoprotein of equine coronavirus.

+
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