[English] 日本語
Yorodumi
- EMDB-70900: Cryo-EM structure of HCoV-OC43-Lab Spike glycoprotein in complex ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-70900
TitleCryo-EM structure of HCoV-OC43-Lab Spike glycoprotein in complex with 9O-acetyl GD3 sialoglycan (D1 domain local refine)
Map data
Sample
  • Complex: Human coronavirus OC43 spike glycoprotein
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: 5-acetamido-8-O-(5-acetamido-9-O-acetyl-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranonosyl)-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid
  • Ligand: water
Keywordsspike glycoprotein ectodomain / proline stablized / VIRAL PROTEIN
Function / homology
Function and homology information


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, HCoV-OC43-like / Spike (S) protein S1 subunit, N-terminal domain, murine hepatitis virus-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal ...Spike (S) protein S1 subunit, receptor-binding domain, HCoV-OC43-like / Spike (S) protein S1 subunit, N-terminal domain, murine hepatitis virus-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S2 superfamily, coronavirus / 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, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Biological speciesHuman coronavirus OC43
Methodsingle particle reconstruction / cryo EM / Resolution: 1.7 Å
AuthorsJin M / Rini JM
Funding support Canada, 1 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Nat Commun / Year: 2026
Title: OC43 clinical isolate spike proteins have distinct carbohydrate-binding properties.
Authors: Zaky Hassan / Min Jin / Ying Liu / Zhijie Li / Alan H M Wong / Marc Desforges / Adam Forman / Mark Nitz / Tarini Gunawardena / Theo J Moraes / Masahiro Narimatsu / Jeffrey L Wrana / Hai Yu / ...Authors: Zaky Hassan / Min Jin / Ying Liu / Zhijie Li / Alan H M Wong / Marc Desforges / Adam Forman / Mark Nitz / Tarini Gunawardena / Theo J Moraes / Masahiro Narimatsu / Jeffrey L Wrana / Hai Yu / Xi Chen / James M Rini /
Abstract: The human coronavirus HCoV-OC43 (OC43) is the most widespread of the four common cold-causing seasonal coronaviruses, and tissue culture-adapted strains of it have been used for ~50 years. ...The human coronavirus HCoV-OC43 (OC43) is the most widespread of the four common cold-causing seasonal coronaviruses, and tissue culture-adapted strains of it have been used for ~50 years. Nevertheless, clinical isolates of OC43 differ from tissue culture-adapted OC43 in ways that call into question the value of the latter as a model. Among these are differences in their entry mechanisms and the activities of their hemagglutinin-esterases (HE). We now show that the spike proteins of OC43 clinical isolates differ from that of the tissue culture-adapted reference strain (OC43-Lab) in their carbohydrate-binding properties and ability to bind mucins, decoy receptors cleaved by the HE. We also show that, unlike HCoV-HKU1 (HKU1), they do not bind with high affinity and specificity the 9-O-acetylated α2-8-linked disialic acid moiety implicated in viral entry for OC43-Lab and HKU1. The spike proteins of the OC43 clinical isolates possess two inserts, not found in OC43-Lab, that flank the carbohydrate-binding site. Our structural analysis of a representative clinical isolate shows that insert-2 is a determinant of these specificity differences and that the carbohydrate-binding site undergoes conformational changes on carbohydrate binding. These structural features are shared by HKU1 and suggest common mechanisms for adaptation to the human sialoglycome.
History
DepositionMay 30, 2025-
Header (metadata) releaseMay 27, 2026-
Map releaseMay 27, 2026-
UpdateMay 27, 2026-
Current statusMay 27, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_70900.png

Downloads & links

-
Map

FileDownload / File: emd_70900.map.gz / Format: CCP4 / Size: 600.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.64 Å/pix.
x 540 pix.
= 345.6 Å		0.64 Å/pix.
x 540 pix.
= 345.6 Å		0.64 Å/pix.
x 540 pix.
= 345.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.64 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 25.0
Minimum - Maximum-59.663902 - 176.771420000000006
Average (Standard dev.)-0.051464524 (±2.3625581)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions540540540
Spacing540540540
CellA=B=C: 345.6 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_70900_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_70900_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_70900_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Human coronavirus OC43 spike glycoprotein

EntireName: Human coronavirus OC43 spike glycoprotein
Components
  • Complex: Human coronavirus OC43 spike glycoprotein
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: 5-acetamido-8-O-(5-acetamido-9-O-acetyl-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranonosyl)-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid
  • Ligand: water

-
Supramolecule #1: Human coronavirus OC43 spike glycoprotein

SupramoleculeName: Human coronavirus OC43 spike glycoprotein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: Ectodomain generated by recombinant expression in HEK293 Freestyle cells
Source (natural)Organism: Human coronavirus OC43

-
Macromolecule #1: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human coronavirus OC43
Molecular weightTheoretical: 149.1025 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: VIGDLKCTSD NINDKDTGPP PISTDTVDVT NGLGTYYVLD RVYLNTTLFL NGYYPTSGST YRNMALKGSV LLSRLWFKPP FLSDFINGI FAKVKNTKVI KDRVMYSEFP AITIGSTFVN TSYSVVVQPR TINSTQDGDN KLQGLLEVSV CQYNMCEYPQ T ICHPNLGN ...String:
VIGDLKCTSD NINDKDTGPP PISTDTVDVT NGLGTYYVLD RVYLNTTLFL NGYYPTSGST YRNMALKGSV LLSRLWFKPP FLSDFINGI FAKVKNTKVI KDRVMYSEFP AITIGSTFVN TSYSVVVQPR TINSTQDGDN KLQGLLEVSV CQYNMCEYPQ T ICHPNLGN HRKELWHLDT GVVSCLYKRN FTYDVNADYL YFHFYQEGGT FYAYFTDTGV VTKFLFNVYL GMALSHYYVM PL TCNSKLT LEYWVTPLTS RQYLLAFNQD GIIFNAVDCM SDFMSEIKCK TQSIAPPTGV YELNGYTVQP IADVYRRKPN LPN CNIEAW LNDKSVPSPL NWERKTFSNC NFNMSSLMSF IQADSFTCNN IDAAKIYGMC FSSITIDKFA IPNGRKVDLQ LGNL GYLQS FNYRIDTTAT SCQLYYNLPA ANVSVSRFNP STWNKRFGFI EDSVFKPRPA GVLTNHDVVY AQHCFKAPKN FCPCK LNGS CVGSGPGKNN GIGTCPAGTN YLTCDNLCTP DPITFTGTYK CPQTKSLVGI GEHCSGLAVK SDYCGGNSCT CRPQAF LGW SADSCLQGDK CNIFANFILH DVNSGLTCST DLQKANTDII LGVCVNYDLY GILGQGIFVE VNATYYNSWQ NLLYDSN GN LYGFRDYITN RTFMIRSCYS GRVSAAFHAN SSEPALLFRN IKCNYVFNNS LTRQLQPINY FDSYLGCVVN AYNSTAIS V QTCDLTVGSG YCVDYSKNRR SRGAITTGYR FTNFEPFTVN SVNDSLEPVG GLYEIQIPSE FTIGNMVEFI QTSSPKVTI DCAAFVCGDY AACKSQLVEY GSFCDNINAI LTEVNELLDT TQLQVANSLM NGVTLSTKLK DGVNFNVDDI NFSPVLGCLG SECSKASSR SAIEDLLFDK VKLSDVGFVE AYNNCTGGAE IRDLICVQSY KGIKVLPPLL SENQISGYTL AATSASLFPP W TAAAGVPF YLNVQYRING LGVTMDVLSQ NQKLIANAFN NALYAIQEGF DAPNSALVKI QAVVNANAEA LNNLLQQLSN RF GAISASL QEILSRLDPP EAEAQIDRLI NGRLTALNAY VSQQLSDSTL VKFSAAQAME KVNECVKSQS SRINFCGNGN HII SLVQNA PYGLYFIHFS YVPTKYVTAR VSPGLCIAGD RGIAPKSGYF VNVNNTWMYT GSGYYYPEPI TENNVVVMST CAVN YTKAP YVMLNTSIPN LPDFKEELDQ WFKNQTSVAP DLSLDYINVT FLDLQVEMNR LQEAIKVLNQ SYINLKDIGT YEYYV KSGG YIPEAPRDGQ AYVRKDGEWV LLSTFLNSGR AHHHHHHGAG GLNDIFEAQK IEWHEDTAAA

UniProtKB: Spike glycoprotein

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

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

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

-
Macromolecule #4: 5-acetamido-8-O-(5-acetamido-9-O-acetyl-3,5-dideoxy-D-glycero-alp...

MacromoleculeName: 5-acetamido-8-O-(5-acetamido-9-O-acetyl-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranonosyl)-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid
type: ligand / ID: 4 / Number of copies: 1 / Formula: A1AR1
Molecular weightTheoretical: 642.561 Da

-
Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 332 / 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
Component:
ConcentrationFormulaName
10.0 mMC4H11NO3Tris
50.0 mMNaClNaCl
GridModel: C-flat-2/2 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 20
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 36.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 120000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Details: A initial 3D map was generated by ab-initio reconstruction in cryoSPARC v4
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 1.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 4195440
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
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