[English] 日本語
Yorodumi
- PDB-9r6s: Prefusion stabilized spike glycoprotein of human coronavirus OC43. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9r6s
TitlePrefusion stabilized spike glycoprotein of human coronavirus OC43.
ComponentsSpike glycoprotein
KeywordsVIRAL PROTEIN / fusion glycoprotein / membrane 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
Sapienic acid / Spike glycoprotein
Similarity search - Component
Biological speciesHuman coronavirus OC43
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsMelchers, J.M. / Hulswit, R.J.G. / Hurdiss, D.L.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Other private Netherlands
CitationJournal: To Be Published
Title: AI-guided prefusion stabilization of the human coronavirus OC43 spike protein enables universal Embecovirus antigen design.
Authors: Melchers, J.M. / Juraszek, J. / Hulswit, R.J.G. / van Overveld, D. / Le, L. / van Kuppeveld, F. / Hurdiss, D.L. / Bosch, B.J. / Langedijk, J.P.M. / Bakkers, M.J.G.
History
DepositionMay 13, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 11, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Spike glycoprotein
B: Spike glycoprotein
C: Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)447,73057
Polymers432,0283
Non-polymers15,70254
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "C"
d_2ens_1chain "B"
d_3ens_1chain "A"

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11VALVALASNASNCC15 - 122915 - 1229
d_12NAGNAGNAGNAGCUA1302
d_13NAGNAGNAGNAGCVA1303
d_14NAGNAGNAGNAGPP1
d_15NAGNAGNAGNAGQQ1
d_16NAGNAGNAGNAGQQ2
d_17NAGNAGNAGNAGPP2
d_18NAGNAGNAGNAGCWA1304
d_19NAGNAGNAGNAGCXA1305
d_110NAGNAGNAGNAGRR1
d_111NAGNAGNAGNAGRR2
d_112NAGNAGNAGNAGCYA1306
d_113NAGNAGNAGNAGSS1
d_114NAGNAGNAGNAGSS2
d_115NAGNAGNAGNAGTT1
d_116NAGNAGNAGNAGTT2
d_117NAGNAGNAGNAGCZA1307
d_118NAGNAGNAGNAGCAB1308
d_119NAGNAGNAGNAGCBB1309
d_120NAGNAGNAGNAGCCB1310
d_121NAGNAGNAGNAGUU1
d_122NAGNAGNAGNAGUU2
d_1238Z98Z98Z98Z9BSA1312
d_124NAGNAGNAGNAGCDB1311
d_125NAGNAGNAGNAGCEB1312
d_21VALVALASNASNBB15 - 122915 - 1229
d_22NAGNAGNAGNAGBHA1301
d_23NAGNAGNAGNAGBIA1302
d_24NAGNAGNAGNAGJJ1
d_25NAGNAGNAGNAGKK1
d_26NAGNAGNAGNAGKK2
d_27NAGNAGNAGNAGJJ2
d_28NAGNAGNAGNAGBJA1303
d_29NAGNAGNAGNAGBKA1304
d_210NAGNAGNAGNAGLL1
d_211NAGNAGNAGNAGLL2
d_212NAGNAGNAGNAGBLA1305
d_213NAGNAGNAGNAGMM1
d_214NAGNAGNAGNAGMM2
d_215NAGNAGNAGNAGNN1
d_216NAGNAGNAGNAGNN2
d_217NAGNAGNAGNAGBMA1306
d_218NAGNAGNAGNAGBNA1307
d_219NAGNAGNAGNAGBOA1308
d_220NAGNAGNAGNAGBPA1309
d_221NAGNAGNAGNAGOO1
d_222NAGNAGNAGNAGOO2
d_2238Z98Z98Z98Z9AGA1312
d_224NAGNAGNAGNAGBQA1310
d_225NAGNAGNAGNAGBRA1311
d_31VALVALASNASNAA15 - 122915 - 1229
d_32NAGNAGNAGNAGAV1301
d_33NAGNAGNAGNAGAW1302
d_34NAGNAGNAGNAGDD1
d_35NAGNAGNAGNAGEE1
d_36NAGNAGNAGNAGEE2
d_37NAGNAGNAGNAGDD2
d_38NAGNAGNAGNAGAX1303
d_39NAGNAGNAGNAGAY1304
d_310NAGNAGNAGNAGFF1
d_311NAGNAGNAGNAGFF2
d_312NAGNAGNAGNAGAZ1305
d_313NAGNAGNAGNAGGG1
d_314NAGNAGNAGNAGGG2
d_315NAGNAGNAGNAGHH1
d_316NAGNAGNAGNAGHH2
d_317NAGNAGNAGNAGAAA1306
d_318NAGNAGNAGNAGABA1307
d_319NAGNAGNAGNAGACA1308
d_320NAGNAGNAGNAGADA1309
d_321NAGNAGNAGNAGII1
d_322NAGNAGNAGNAGII2
d_3238Z98Z98Z98Z9CTA1301
d_324NAGNAGNAGNAGAEA1310
d_325NAGNAGNAGNAGAFA1311

NCS oper:
IDCodeMatrixVector
1given(-0.499985563361, 0.866033737499, 4.40993794767E-5), (-0.86603373861, -0.499985562448, -3.05329156729E-5), (-4.39348202566E-6, -5.34575675224E-5, 0.999999998561)132.484094043, 494.506849995, 0.0161293412641
2given(-0.500132488484, -0.865948890145, 0.0001167021337), (0.865948884453, -0.500132499959, -0.000109536576206), (0.000153219606474, 4.62752820533E-5, 0.999999987191)494.494216428, 132.580381046, -0.0331883759127

-
Components

#1: Protein Spike glycoprotein / S glycoprotein / E2 / Peplomer protein


Mass: 144009.203 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human coronavirus OC43 / Cell line (production host): Expi293 / Production host: Homo sapiens (human) / References: UniProt: A0A3S6FHI0
#2: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 18
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Sugar...
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 33 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-8Z9 / Sapienic acid


Mass: 254.408 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H30O2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Trimeric spike glycoprotein / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.452 MDa / Experimental value: YES
Source (natural)Organism: Human coronavirus OC43 / Strain: ANZ78834.1 / Cellular location: membrane
Source (recombinant)Organism: Homo sapiens (human) / Cell: Expi293
Buffer solutionpH: 7.4 / Details: 20 mM Tris-HCL, 150 mM NaCl, pH 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTris1
2150 mMsodium chlorideNaCl1
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

-
Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2EPUimage acquisition
4cryoSPARCCTF correction
7UCSF ChimeraX1.9model fitting
8ISOLDEmodel fitting
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
13cryoSPARC3D reconstruction
14PHENIX1.20.1_4487:model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 92153 / Symmetry type: POINT
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
16NZK

6nzk

16NZK1PDBexperimental model
21AlphaFoldin silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 32.33 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.001729088
ELECTRON MICROSCOPYf_angle_d0.449139576
ELECTRON MICROSCOPYf_chiral_restr0.0414638
ELECTRON MICROSCOPYf_plane_restr0.00375022
ELECTRON MICROSCOPYf_dihedral_angle_d4.57884254
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2CCELECTRON MICROSCOPYNCS constraints1.11752181924E-10
ens_1d_3CCELECTRON MICROSCOPYNCS constraints2.23560831186E-12

+
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