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- EMDB-13564: Human coronavirus OC43 spike glycoprotein ectodomain in complex w... -

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Entry
Database: EMDB / ID: EMD-13564
TitleHuman coronavirus OC43 spike glycoprotein ectodomain in complex with the 37F1 antibody Fab fragment
Map dataHuman coronavirus OC43 spike glycoprotein ectodomain in complex with the 37F1 antibody Fab fragment
Sample
  • Complex: Human coronavirus OC43 spike glycoprotein ectodomain in complex with the 37F1 antibody Fab fragment
    • Complex: Human coronavirus OC43 spike glycoprotein ectodomain
      • Protein or peptide: Human coronavirus OC43 spike glycoprotein
    • Complex: 37F1 antibody Fab fragment
      • Protein or peptide: 37F1 antibody heavy chain
      • Protein or peptide: 37F1 antibody light chain
KeywordsCoronavirus / Glycoprotein / Antibody / Spike / VIRAL PROTEIN
Biological speciesHuman coronavirus OC43 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsHesketh EL / Townend S / Ranson NA / Hurdiss DL
Funding support Netherlands, China, 2 items
OrganizationGrant numberCountry
Other governmentLSHM19136 Netherlands
Other governmentCSC201708620178 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 1, 2023-
Current statusNov 1, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_13564.png

Downloads & links

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Map

FileDownload / File: emd_13564.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 37F1 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: 0.02
Minimum - Maximum-0.0015638045 - 1.2310252
Average (Standard dev.)0.001800218 (±0.021110939)
SymmetrySpace group: 1
Details

EMDB XML:

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

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Supplemental data

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Additional map: Unsharpened map

Fileemd_13564_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_13564_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_13564_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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

EntireName: Human coronavirus OC43 spike glycoprotein ectodomain in complex with the 37F1 antibody Fab fragment
Components
  • Complex: Human coronavirus OC43 spike glycoprotein ectodomain in complex with the 37F1 antibody Fab fragment
    • Complex: Human coronavirus OC43 spike glycoprotein ectodomain
      • Protein or peptide: Human coronavirus OC43 spike glycoprotein
    • Complex: 37F1 antibody Fab fragment
      • Protein or peptide: 37F1 antibody heavy chain
      • Protein or peptide: 37F1 antibody light chain

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

SupramoleculeName: Human coronavirus OC43 spike glycoprotein ectodomain in complex with the 37F1 antibody Fab fragment
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human coronavirus OC43 / Strain: USA/1967
Molecular weightTheoretical: 583 KDa

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Supramolecule #2: Human coronavirus OC43 spike glycoprotein ectodomain

SupramoleculeName: Human coronavirus OC43 spike glycoprotein ectodomain / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: 37F1 antibody Fab fragment

SupramoleculeName: 37F1 antibody Fab fragment / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3

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Macromolecule #1: Human coronavirus OC43 spike glycoprotein

MacromoleculeName: Human coronavirus OC43 spike glycoprotein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Human coronavirus OC43 / Strain: USA/1967
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPMGSLQPLA TLYLLGMLVA SVLAVIGDLK CTSDNINDKD TGPPPISTDT VDVTNGLGTY YVLDRVYLNT TLFLNGYYPT SGSTYRNMAL KGSVLLSRLW FKPPFLSDFI NGIFAKVKNT KVIKDRVMYS EFPAITIGST FVNTSYSVVV QPRTINSTQD GDNKLQGLLE ...String:
MPMGSLQPLA TLYLLGMLVA SVLAVIGDLK CTSDNINDKD TGPPPISTDT VDVTNGLGTY YVLDRVYLNT TLFLNGYYPT SGSTYRNMAL KGSVLLSRLW FKPPFLSDFI NGIFAKVKNT KVIKDRVMYS EFPAITIGST FVNTSYSVVV QPRTINSTQD GDNKLQGLLE VSVCQYNMCE YPQTICHPNL GNHRKELWHL DTGVVSCLYK RNFTYDVNAD YLYFHFYQEG GTFYAYFTDT GVVTKFLFNV YLGMALSHYY VMPLTCNSKL TLEYWVTPLT SRQYLLAFNQ DGIIFNAVDC MSDFMSEIKC KTQSIAPPTG VYELNGYTVQ PIADVYRRKP NLPNCNIEAW LNDKSVPSPL NWERKTFSNC NFNMSSLMSF IQADSFTCNN IDAAKIYGMC FSSITIDKFA IPNGRKVDLQ LGNLGYLQSF NYRIDTTATS CQLYYNLPAA NVSVSRFNPS TWNKRFGFIE DSVFKPRPAG VLTNHDVVYA QHCFKAPKNF CPCKLNGSCV GSGPGKNNGI GTCPAGTNYL TCDNLCTPDP ITFTGTYKCP QTKSLVGIGE HCSGLAVKSD YCGGNSCTCR PQAFLGWSAD SCLQGDKCNI FANFILHDVN SGLTCSTDLQ KANTDIILGV CVNYDLYGIL GQGIFVEVNA TYYNSWQNLL YDSNGNLYGF RDYITNRTFM IRSCYSGRVS AAFHANSSEP ALLFRNIKCN YVFNNSLTRQ LQPINYFDSY LGCVVNAYNS TAISVQTCDL TVGSGYCVDY SKNGGSGGAI TTGYRFTNFE PFTVNSVNDS LEPVGGLYEI QIPSEFTIGN MVEFIQTSSP KVTIDCAAFV CGDYAACKSQ LVEYGSFCDN INAILTEVNE LLDTTQLQVA NSLMNGVTLS TKLKDGVNFN VDDINFSPVL GCLGSECSKA SSRSAIEDLL FDKVKLSDVG FVEAYNNCTG GAEIRDLICV QSYKGIKVLP PLLSENQFSG YTLAATSASL FPPWTAAAGV PFYLNVQYRI NGLGVTMDVL SQNQKLIANA FNNALYAIQE GFDATNSALV KIQAVVNANA EALNNLLQQL SNRFGAISAS LQEILSRLDA LEAEAQIDRL INGRLTALNA YVSQQLSDST LVKFSAAQAM EKVNECVKSQ SSRINFCGNG NHIISLVQNA PYGLYFIHFS YVPTKYVTAR VSPGLCIAGD RGIAPKSGYF VNVNNTWMYT GSGYYYPEPI TENNVVVMST CAVNYTKAPY VMLNTSIPNL PDFKEELDQW FKNQTSVAPD LSLDYINVTF LDLLIKRMKQ IEDKIEEIES KQKKIENEIA RIKKIKLVPR GSLEWSHPQF EK

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Macromolecule #2: 37F1 antibody heavy chain

MacromoleculeName: 37F1 antibody heavy chain / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLQESGPG LVKPSGTLSL TCAVSGGSIS STYNWWSWVR QPPGKGLEWI GEIYHSGNTN YNPSLKSRVT ISVDKSKNQF SLKLSSVTAA DTAVYYCARE DFDWLRDYYY GLDVWGQGTT VTVSS

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Macromolecule #3: 37F1 antibody light chain

MacromoleculeName: 37F1 antibody light chain / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIQLTQSPSF LSASVGDRVT ITCRASQGIA SFLAWYQQKP GKAPKLLIYA ASTLQSGVPS RFSGSGSGTE FTLTISSLQP EDFATYFCQQ LNSYPYTFGQ GTKLEIK

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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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 / Pretreatment - Time: 30 sec.
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

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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: 759 / 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

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Image processing

Particle selectionNumber selected: 635273
Startup modelType of model: OTHER / Details: Ab initio model generation
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.1) / Number images used: 23452
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)

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