[English] 日本語
Yorodumi
- EMDB-13563: Human coronavirus OC43 spike glycoprotein ectodomain in complex w... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-13563
TitleHuman coronavirus OC43 spike glycoprotein ectodomain in complex with the 47C9 antibody Fab fragment
Map dataHuman coronavirus OC43 spike glycoprotein ectodomain in complex with the 47C9 antibody Fab fragment
Sample
  • Complex: Human coronavirus OC43 spike glycoprotein ectodomain in complex with the 47C9 antibody Fab fragment
    • Protein or peptide: 47C9 antibody heavy chain
    • Protein or peptide: 47C9 antibody light chain
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
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, HCoV-OC43-like / Spike (S) protein S1 subunit, N-terminal domain, murine hepatitis virus-like / 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, HCoV-OC43-like / Spike (S) protein S1 subunit, N-terminal domain, murine hepatitis virus-like / 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 / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Betacoronavirus spike glycoprotein S1, receptor binding / 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
Biological speciesHuman coronavirus OC43 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsHesketh EL / Townend S / Ranson NA / Hurdiss DL
Funding support Netherlands, China, 2 items
OrganizationGrant numberCountry
Health-HollandLSHM19136 Netherlands
Chinese Scholarship CouncilCSC201708620178 China
CitationJournal: Nat Commun / Year: 2022
Title: Antigenic structure of the human coronavirus OC43 spike reveals exposed and occluded neutralizing epitopes.
Authors: Chunyan Wang / Emma L Hesketh / Tatiana M Shamorkina / Wentao Li / Peter J Franken / Dubravka Drabek / Rien van Haperen / Sarah Townend / Frank J M van Kuppeveld / Frank Grosveld / Neil A ...Authors: Chunyan Wang / Emma L Hesketh / Tatiana M Shamorkina / Wentao Li / Peter J Franken / Dubravka Drabek / Rien van Haperen / Sarah Townend / Frank J M van Kuppeveld / Frank Grosveld / Neil A Ranson / Joost Snijder / Raoul J de Groot / Daniel L Hurdiss / Berend-Jan Bosch /
Abstract: Human coronavirus OC43 is a globally circulating common cold virus sustained by recurrent reinfections. How it persists in the population and defies existing herd immunity is unknown. Here we focus ...Human coronavirus OC43 is a globally circulating common cold virus sustained by recurrent reinfections. How it persists in the population and defies existing herd immunity is unknown. Here we focus on viral glycoprotein S, the target for neutralizing antibodies, and provide an in-depth analysis of its antigenic structure. Neutralizing antibodies are directed to the sialoglycan-receptor binding site in S1 domain, but, remarkably, also to S1. The latter block infection yet do not prevent sialoglycan binding. While two distinct neutralizing S1 epitopes are readily accessible in the prefusion S trimer, other sites are occluded such that their accessibility must be subject to conformational changes in S during cell-entry. While non-neutralizing antibodies were broadly reactive against a collection of natural OC43 variants, neutralizing antibodies generally displayed restricted binding breadth. Our data provide a structure-based understanding of protective immunity and adaptive evolution for this endemic coronavirus which emerged in humans long before SARS-CoV-2.
History
DepositionSep 8, 2021-
Header (metadata) releaseApr 20, 2022-
Map releaseApr 20, 2022-
UpdateNov 9, 2022-
Current statusNov 9, 2022Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_13563.png

Downloads & links

-
Map

FileDownload / File: emd_13563.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman coronavirus OC43 spike glycoprotein ectodomain in complex with the 47C9 antibody Fab fragment
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 320 pix.
= 340.8 Å		1.07 Å/pix.
x 320 pix.
= 340.8 Å		1.07 Å/pix.
x 320 pix.
= 340.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.065 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.0017475663 - 2.6206846
Average (Standard dev.)0.0023451848 (±0.03583526)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 340.80002 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Unsharpened map

Fileemd_13563_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map 1

Fileemd_13563_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map 2

Fileemd_13563_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Human coronavirus OC43 spike glycoprotein ectodomain in complex w...

EntireName: Human coronavirus OC43 spike glycoprotein ectodomain in complex with the 47C9 antibody Fab fragment
Components
  • Complex: Human coronavirus OC43 spike glycoprotein ectodomain in complex with the 47C9 antibody Fab fragment
    • Protein or peptide: 47C9 antibody heavy chain
    • Protein or peptide: 47C9 antibody light chain
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: Human coronavirus OC43 spike glycoprotein ectodomain in complex w...

SupramoleculeName: Human coronavirus OC43 spike glycoprotein ectodomain in complex with the 47C9 antibody Fab fragment
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Human coronavirus OC43 / Strain: USA/1967
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293T
Molecular weightTheoretical: 583 KDa

-
Macromolecule #1: 47C9 antibody heavy chain

MacromoleculeName: 47C9 antibody heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.521896 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLQQWGAG LLKPSETLSL TCAVYGGSFS GYYWNWIRQP PGKGLEWIGE INHSGSTNYN PSLKSRVTIS VDTSKNQFSL KLSSVTAAD TAVYYCARGN YYGSGSYVDY GMDVWGQGTT VTVSS

-
Macromolecule #2: 47C9 antibody light chain

MacromoleculeName: 47C9 antibody light chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.448732 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EIVMTQSPAT LSVSPGERAT LSCRASQSIS SNLAWYQQKP GQAPRLLIYG ASTRATGIPA RFSGSGSGTE FTLTISSLQS EDFAVYYCQ QSNNWPLTFG GGTKVEIK

-
Macromolecule #3: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human coronavirus OC43
Molecular weightTheoretical: 146.738734 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPMGSLQPLA TLYLLGMLVA SVLAVIGDLK CTSDNINDKD TGPPPISTDT VDVTNGLGTY YVLDRVYLNT TLFLNGYYPT SGSTYRNMA LKGSVLLSRL WFKPPFLSDF INGIFAKVKN TKVIKDRVMY SEFPAITIGS TFVNTSYSVV VQPRTINSTQ D GDNKLQGL ...String:
MPMGSLQPLA TLYLLGMLVA SVLAVIGDLK CTSDNINDKD TGPPPISTDT VDVTNGLGTY YVLDRVYLNT TLFLNGYYPT SGSTYRNMA LKGSVLLSRL WFKPPFLSDF INGIFAKVKN TKVIKDRVMY SEFPAITIGS TFVNTSYSVV VQPRTINSTQ D GDNKLQGL LEVSVCQYNM CEYPQTICHP NLGNHRKELW HLDTGVVSCL YKRNFTYDVN ADYLYFHFYQ EGGTFYAYFT DT GVVTKFL FNVYLGMALS HYYVMPLTCN SKLTLEYWVT PLTSRQYLLA FNQDGIIFNA VDCMSDFMSE IKCKTQSIAP PTG VYELNG YTVQPIADVY RRKPNLPNCN IEAWLNDKSV PSPLNWERKT FSNCNFNMSS LMSFIQADSF TCNNIDAAKI YGMC FSSIT IDKFAIPNGR KVDLQLGNLG YLQSFNYRID TTATSCQLYY NLPAANVSVS RFNPSTWNKR FGFIEDSVFK PRPAG VLTN HDVVYAQHCF KAPKNFCPCK LNGSCVGSGP GKNNGIGTCP AGTNYLTCDN LCTPDPITFT GTYKCPQTKS LVGIGE HCS GLAVKSDYCG GNSCTCRPQA FLGWSADSCL QGDKCNIFAN FILHDVNSGL TCSTDLQKAN TDIILGVCVN YDLYGIL GQ GIFVEVNATY YNSWQNLLYD SNGNLYGFRD YITNRTFMIR SCYSGRVSAA FHANSSEPAL LFRNIKCNYV FNNSLTRQ L QPINYFDSYL GCVVNAYNST AISVQTCDLT VGSGYCVDYS KNRRSRGAIT TGYRFTNFEP FTVNSVNDSL EPVGGLYEI QIPSEFTIGN MVEFIQTSSP KVTIDCAAFV CGDYAACKSQ LVEYGSFCDN INAILTEVNE LLDTTQLQVA NSLMNGVTLS TKLKDGVNF NVDDINFSPV LGCLGSECSK ASSRSAIEDL LFDKVKLSDV GFVEAYNNCT GGAEIRDLIC VQSYKGIKVL P PLLSENQF SGYTLAATSA SLFPPWTAAA GVPFYLNVQY RINGLGVTMD VLSQNQKLIA NAFNNALYAI QEGFDATNSA LV KIQAVVN ANAEALNNLL QQLSNRFGAI SASLQEILSR LDALEAEAQI DRLINGRLTA LNAYVSQQLS DSTLVKFSAA QAM EKVNEC VKSQSSRINF CGNGNHIISL VQNAPYGLYF IHFSYVPTKY VTARVSPGLC IAGDRGIAPK SGYFVNVNNT WMYT GSGYY YPEPITENNV VVMSTCAVNY TKAPYVMLNT SIPNLPDFKE ELDQWFKNQT SVAPDLSLDY INVTFLDLLI KRMKQ IEDK IEEIESKQKK IENEIARIKK IKLVPRGSLE WSHPQFEK

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

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 15 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMC4H11NO3Tris
150.0 mMNaClSodium chloride
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV
DetailsPurified OC43 spike ectodomain and the antibody Fab fragments were incubated together for 5 minutes at a 1:1 molar ratio

-
Electron microscopy

MicroscopeTFS KRIOS
DetailsA 30 degree stage tilt was employed during data collection to increase the number of side views visualised due to preferential orientation.
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 380 / Average exposure time: 60.0 sec. / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 144035
CTF correctionSoftware - Name: CTFFIND (ver. 4.1)
Startup modelType of model: INSILICO MODEL
In silico model: The UCSF Chimera molmap command was used to generate a 50 angstrom resolution starting model from the OC43 spike model (6OHW).
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.1) / Number images used: 45798
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: RELION (ver. 3.0.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.1)
Final 3D classificationSoftware - Name: RELION (ver. 3.1.1)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

6nzk

Output model

PDB-7po5:
Human coronavirus OC43 spike glycoprotein ectodomain in complex with the 47C9 antibody Fab fragment

+
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