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- EMDB-24994: Structure of OC43 spike in complex with polyclonal Fab9 (Donor 1412) -

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Basic information

Entry
Database: EMDB / ID: EMD-24994
TitleStructure of OC43 spike in complex with polyclonal Fab9 (Donor 1412)
Map dataSharpened map
Sample
  • Complex: Structure of OC43 spike in complex with polyclonal Fab9 (Donor 1412)
    • Protein or peptide: OC43 prefusion spike
Biological speciesHuman coronavirus OC43
Methodsingle particle reconstruction / cryo EM / Resolution: 7.1 Å
AuthorsWard AB / Bangaru S / Antanasijevic A
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 26, 2021-
Header (metadata) releaseMay 4, 2022-
Map releaseMay 4, 2022-
UpdateMay 18, 2022-
Current statusMay 18, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_24994.png

Downloads & links

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Map

FileDownload / File: emd_24994.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
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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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025
Minimum - Maximum-0.02367367 - 0.085071556
Average (Standard dev.)0.0009419944 (±0.0054536774)
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_24994_msk_1.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_24994_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_24994_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

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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 Fab9 (Donor 1412)

EntireName: Structure of OC43 spike in complex with polyclonal Fab9 (Donor 1412)
Components
  • Complex: Structure of OC43 spike in complex with polyclonal Fab9 (Donor 1412)
    • Protein or peptide: OC43 prefusion spike

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Supramolecule #1: Structure of OC43 spike in complex with polyclonal Fab9 (Donor 1412)

SupramoleculeName: Structure of OC43 spike in complex with polyclonal Fab9 (Donor 1412)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human coronavirus OC43
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: 293F cells

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Macromolecule #1: OC43 prefusion spike

MacromoleculeName: OC43 prefusion spike / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Human coronavirus OC43
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MFLILLISLP TAFAVIGDLK CPLDSRTGSL NNIDTGPPSI STATVDVTNG LGTYYVLDRV YLNTTLFLNG YYPTSGSTYR NMALKGTDKL STLWFKPPFL SDFINGIFAK VKNTKVFKDG VMYSEFPAIT IGSTFVNTSY SVVVQPRTIN STQDGVNKLQ GLLEVSVCQY ...String:
MFLILLISLP TAFAVIGDLK CPLDSRTGSL NNIDTGPPSI STATVDVTNG LGTYYVLDRV YLNTTLFLNG YYPTSGSTYR NMALKGTDKL STLWFKPPFL SDFINGIFAK VKNTKVFKDG VMYSEFPAIT IGSTFVNTSY SVVVQPRTIN STQDGVNKLQ GLLEVSVCQY NMCEYPHTIC HPKLGNHFKE LWHMDTGVVS CLYKRNFTYD VNATYLYFHF YQEGGTFYAY FTDTGVVTKF LFNVYLGMAL SHYYVMPLTC ISRRDIGFTL EYWVTPLTSR QYLLAFNQDG IIFNAVDCMS DFMSEIKCKT QSIAPPTGVY ELNGYTVQPI ADVYRRKPDL PNCNIEAWLN DKSVPSPLNW ERKTFSNCNF NMSSLMSFIQ ADSFTCNNID AAKIYGMCFS SITIDKFAIP NGRKVDLQLG NLGYLQSFNY RIDTTATSCQ LYYNLPAANV SVSRFNPSTW NKRFGFIENS VFKPQPAGVL TNHDVVYAQH CFKAPKNFCP CKLNSSLCVG SGPGKNNGIG TCPAGTNYLT CHNLCNPDPI TFTGPYKCPQ TKSLVGIGEH CSGLAVKSDY CGGNPCTCQP QAFLGWSADS CLQGDKCNIF ANLILHDVNS GLTCSTDLQK ANTDIKLGVC VNYDLYGISG QGIFVEVNAT YYNSWQNLLY DSNGNLYGFR DYITNRTFMI RSCYSGRVSA AFHANSSEPA LLFRNIKCNY VFNNSLIRQL QPINYFDSYL GCVVNAYNST AISVQTCDLT VGSGYCVDYS KNRRSRRAIT TGYRFTNFEP FTVNSVNDSL EPVGGLYEIQ IPSEFTIGNM EEFIQTSSPK VTIDCAAFVC GDYAACKSQL VEYGSFCDNI NAILTEVNEL LDTTQLQVAN SLMNGVTLST KLKDGVNFNV DDINFSSVLG CLGSECSKAS SRSAIEDLLF DKVKLSDVGF VAAYNNCTGG AEIRDLICVQ SYKGIKVLPP LLSENQISGY TLAATSASLF PPWTAAAGVP FYLNVQYRIN GLGVTMDVLS QNQKLIANAF NNALDAIQEG FDATNSALVK IQAVVNANAE ALNNLLQQLS NRFGAISSSL QEILSRLDPP EAEAQIDRLI NGRLTALNAY VSQQLSDSTL VKFSAAQAME KVNECVKSQS SRINFCGNGN HIISLVQNAP YGLYFIHFSY VPTKYVTAKV SPGLCIAGDR GIAPKSGYFV NVNNTWMYTG SGYYYPEPIT ENNVVVMSTC AVNYTKAPYV MLNTSTPNLP DFREELDQWF KNQTSVAPDL SLDYINVTFL DLQVEMNRLQ EAIKVLNGSG YIPEAPRDGQ AYVRKDGEWV LLSTFLGRSL EVLFQGPGHH HHHHHHSAWS HPQFEKGGGS GGGGSGGSAW SHPQFEK

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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
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

CTF correctionSoftware - Name: Gctf (ver. 1.06)
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: 7.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 4846
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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