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- EMDB-24989: Structure of OC43 spike in complex with polyclonal Fab4 (Donor 269) -
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Open data
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Basic information
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Title | Structure of OC43 spike in complex with polyclonal Fab4 (Donor 269) | |||||||||
![]() | Sharpened map | |||||||||
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Function / homology | ![]() 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 | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
![]() | Bangaru S / Antanasijevic A / Ward A | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 137.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 21.6 KB 21.6 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 12.1 KB | Display | ![]() |
Images | ![]() | 105.9 KB | ||
Masks | ![]() | 149.9 MB | ![]() | |
Others | ![]() ![]() | 118.4 MB 118 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7sbvMC ![]() 7sb3C ![]() 7sb4C ![]() 7sb5C ![]() 7sbwC ![]() 7sbxC ![]() 7sbyC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | Sharpened map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.03 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Half map: Half map 1
File | emd_24989_half_map_1.map | ||||||||||||
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Annotation | Half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 2
File | emd_24989_half_map_2.map | ||||||||||||
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Annotation | Half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Structure of OC43 spike in complex with polyclonal Fab4 (Donor 269)
Entire | Name: Structure of OC43 spike in complex with polyclonal Fab4 (Donor 269) |
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Components |
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-Supramolecule #1: Structure of OC43 spike in complex with polyclonal Fab4 (Donor 269)
Supramolecule | Name: Structure of OC43 spike in complex with polyclonal Fab4 (Donor 269) type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() |
-Macromolecule #1: Spike protein
Macromolecule | Name: Spike protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 151.119891 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: 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 |
-Macromolecule #2: Human polyclonal Fab model with polyalanine backbone - Heavy chain
Macromolecule | Name: Human polyclonal Fab model with polyalanine backbone - Heavy chain type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 9.890183 KDa |
Sequence | 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) ...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)(UNK) |
-Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 23 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ![]() ChemComp-NAG: |
-Macromolecule #6: Sapienic acid
Macromolecule | Name: Sapienic acid / type: ligand / ID: 6 / Number of copies: 3 / Formula: 8Z9 |
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Molecular weight | Theoretical: 254.408 Da |
Chemical component information | ![]() ChemComp-8Z9: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.5 mg/mL | ||||||
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Buffer | pH: 7.4 / Component:
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Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING | ||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 4370 / Average exposure time: 9.5 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 29000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |