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- EMDB-24970: Structure of OC43 spike in complex with polyclonal Fab3 (Donor 1412) -

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Basic information

Entry
Database: EMDB / ID: EMD-24970
TitleStructure of OC43 spike in complex with polyclonal Fab3 (Donor 1412)
Map dataSharpened map
Sample
  • Complex: Structure of OC43 spike in complex with polyclonal Fab3 (Donor 1412)
    • Protein or peptide: Spike protein
    • Protein or peptide: Human polyclonal Fab model with polyalanine backbone - Heavy chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: PALMITIC ACID
KeywordsHCoV / spike / OC43 / polyclonal antibody / EMPEM / VIRAL PROTEIN / VIRAL PROTEIN-Immune System complex
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: 4.2 Å
AuthorsBangaru S / Antanasijevic A / Ward A / Jackson AM
Funding support United States, 2 items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1170236 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI110657 United States
CitationJournal: Sci Adv / Year: 2022
Title: Structural mapping of antibody landscapes to human betacoronavirus spike proteins.
Authors: Sandhya Bangaru / Aleksandar Antanasijevic / Nurgun Kose / Leigh M Sewall / Abigail M Jackson / Naveenchandra Suryadevara / Xiaoyan Zhan / Jonathan L Torres / Jeffrey Copps / Alba Torrents ...Authors: Sandhya Bangaru / Aleksandar Antanasijevic / Nurgun Kose / Leigh M Sewall / Abigail M Jackson / Naveenchandra Suryadevara / Xiaoyan Zhan / Jonathan L Torres / Jeffrey Copps / Alba Torrents de la Peña / James E Crowe / Andrew B Ward /
Abstract: Preexisting immunity against seasonal coronaviruses (CoVs) represents an important variable in predicting antibody responses and disease severity to severe acute respiratory syndrome CoV-2 (SARS-CoV- ...Preexisting immunity against seasonal coronaviruses (CoVs) represents an important variable in predicting antibody responses and disease severity to severe acute respiratory syndrome CoV-2 (SARS-CoV-2) infections. We used electron microscopy-based polyclonal epitope mapping (EMPEM) to characterize the antibody specificities against β-CoV spike proteins in prepandemic (PP) sera or SARS-CoV-2 convalescent (SC) sera. We observed that most PP sera had antibodies specific to seasonal human CoVs (HCoVs) OC43 and HKU1 spike proteins while the SC sera showed reactivity across all human β-CoVs. Detailed molecular mapping of spike-antibody complexes revealed epitopes that were differentially targeted by preexisting antibodies and SC serum antibodies. Our studies provide an antigenic landscape to β-HCoV spikes in the general population serving as a basis for cross-reactive epitope analyses in SARS-CoV-2-infected individuals.
History
DepositionSep 23, 2021-
Header (metadata) releaseMay 4, 2022-
Map releaseMay 4, 2022-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_24970.png

Downloads & links

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Map

FileDownload / File: emd_24970.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 340 pix.
= 350.2 Å		1.03 Å/pix.
x 340 pix.
= 350.2 Å		1.03 Å/pix.
x 340 pix.
= 350.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.0128836995 - 0.057524394
Average (Standard dev.)0.00035103556 (±0.0030614228)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 350.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_24970_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_24970_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_24970_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Structure of OC43 spike in complex with polyclonal Fab3 (Donor 1412)

EntireName: Structure of OC43 spike in complex with polyclonal Fab3 (Donor 1412)
Components
  • Complex: Structure of OC43 spike in complex with polyclonal Fab3 (Donor 1412)
    • Protein or peptide: Spike protein
    • Protein or peptide: Human polyclonal Fab model with polyalanine backbone - Heavy chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: PALMITIC ACID

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Supramolecule #1: Structure of OC43 spike in complex with polyclonal Fab3 (Donor 1412)

SupramoleculeName: Structure of OC43 spike in complex with polyclonal Fab3 (Donor 1412)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Human coronavirus OC43

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Macromolecule #1: Spike protein

MacromoleculeName: Spike protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human coronavirus OC43
Molecular weightTheoretical: 151.119891 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MFLILLISLP TAFAVIGDLK CPLDSRTGSL NNIDTGPPSI STATVDVTNG LGTYYVLDRV YLNTTLFLNG YYPTSGSTYR NMALKGTDK LSTLWFKPPF LSDFINGIFA KVKNTKVFKD GVMYSEFPAI TIGSTFVNTS YSVVVQPRTI NSTQDGVNKL Q GLLEVSVC ...String:
MFLILLISLP TAFAVIGDLK CPLDSRTGSL NNIDTGPPSI STATVDVTNG LGTYYVLDRV YLNTTLFLNG YYPTSGSTYR NMALKGTDK LSTLWFKPPF LSDFINGIFA KVKNTKVFKD GVMYSEFPAI TIGSTFVNTS YSVVVQPRTI NSTQDGVNKL Q GLLEVSVC QYNMCEYPHT ICHPKLGNHF KELWHMDTGV VSCLYKRNFT YDVNATYLYF HFYQEGGTFY AYFTDTGVVT KF LFNVYLG MALSHYYVMP LTCISRRDIG FTLEYWVTPL TSRQYLLAFN QDGIIFNAVD CMSDFMSEIK CKTQSIAPPT GVY ELNGYT VQPIADVYRR KPDLPNCNIE AWLNDKSVPS PLNWERKTFS NCNFNMSSLM SFIQADSFTC NNIDAAKIYG MCFS SITID KFAIPNGRKV DLQLGNLGYL QSFNYRIDTT ATSCQLYYNL PAANVSVSRF NPSTWNKRFG FIENSVFKPQ PAGVL TNHD VVYAQHCFKA PKNFCPCKLN SSLCVGSGPG KNNGIGTCPA GTNYLTCHNL CNPDPITFTG PYKCPQTKSL VGIGEH CSG LAVKSDYCGG NPCTCQPQAF LGWSADSCLQ GDKCNIFANL ILHDVNSGLT CSTDLQKANT DIKLGVCVNY DLYGISG QG IFVEVNATYY NSWQNLLYDS NGNLYGFRDY ITNRTFMIRS CYSGRVSAAF HANSSEPALL FRNIKCNYVF NNSLIRQL Q PINYFDSYLG CVVNAYNSTA ISVQTCDLTV GSGYCVDYSK NRRSRRAITT GYRFTNFEPF TVNSVNDSLE PVGGLYEIQ IPSEFTIGNM EEFIQTSSPK VTIDCAAFVC GDYAACKSQL VEYGSFCDNI NAILTEVNEL LDTTQLQVAN SLMNGVTLST KLKDGVNFN VDDINFSSVL GCLGSECSKA SSRSAIEDLL FDKVKLSDVG FVAAYNNCTG GAEIRDLICV QSYKGIKVLP P LLSENQIS GYTLAATSAS LFPPWTAAAG VPFYLNVQYR INGLGVTMDV LSQNQKLIAN AFNNALDAIQ EGFDATNSAL VK IQAVVNA NAEALNNLLQ QLSNRFGAIS SSLQEILSRL DPPEAEAQID RLINGRLTAL NAYVSQQLSD STLVKFSAAQ AME KVNECV KSQSSRINFC GNGNHIISLV QNAPYGLYFI HFSYVPTKYV TAKVSPGLCI AGDRGIAPKS GYFVNVNNTW MYTG SGYYY PEPITENNVV VMSTCAVNYT KAPYVMLNTS TPNLPDFREE LDQWFKNQTS VAPDLSLDYI NVTFLDLQVE MNRLQ EAIK VLNGSGYIPE APRDGQAYVR KDGEWVLLST FLGRSLEVLF QGPGHHHHHH HHSAWSHPQF EKGGGSGGGG SGGSAW SHP QFEK

UniProtKB: Spike glycoprotein

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Macromolecule #2: Human polyclonal Fab model with polyalanine backbone - Heavy chain

MacromoleculeName: Human polyclonal Fab model with polyalanine backbone - Heavy chain
type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.805078 KDa
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 31 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #6: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 6 / Number of copies: 3 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID

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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

Concentration0.5 mg/mL
BufferpH: 7.4 / Component:
ConcentrationFormula
50.0 mMTris-Cl
150.0 mMNaCl
/ Details: TBS 1X
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 7 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 2321 / Average exposure time: 10.0 sec. / Average electron dose: 50.0 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: 1.3 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 29000
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

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6ohw

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 12703
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.0)
Final 3D classificationSoftware - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

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