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- EMDB-27511: Cryo-EM structure of SARS-CoV-2 Gamma (P.1) spike protein in comp... -

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Entry
Database: EMDB / ID: EMD-27511
TitleCryo-EM structure of SARS-CoV-2 Gamma (P.1) spike protein in complex with Fab 4-8
Map datastructure of SARS-CoV-2 Gamma (P.1) spike protein in complex with Fab 4-8
Sample
  • Complex: SARS-CoV-2 Gamma (P.1) spike protein in complex with Fab 4-8
    • Complex: SARS-CoV-2 Gamma (P.1) spike protein
      • Protein or peptide: SARS-CoV-2 Gamma (P.1) spike protein
    • Complex: Fab 4-8
      • Protein or peptide: Fab 4-8 heavy chain
      • Protein or peptide: Fab 4-8 light chain
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.59 Å
AuthorsZhu X / Mannar D / Saville JW / Srivastava SS / Berezuk AM / Zhou S / Tuttle KS / Subramaniam S
Funding support Canada, 2 items
OrganizationGrant numberCountry
Canada Excellence Research Chair AwardPrecision Cancer Drug Design Canada
Other governmentCOVID-19 research
CitationJournal: Nat Commun / Year: 2022
Title: SARS-CoV-2 variants of concern: spike protein mutational analysis and epitope for broad neutralization.
Authors: Dhiraj Mannar / James W Saville / Zehua Sun / Xing Zhu / Michelle M Marti / Shanti S Srivastava / Alison M Berezuk / Steven Zhou / Katharine S Tuttle / Michele D Sobolewski / Andrew Kim / ...Authors: Dhiraj Mannar / James W Saville / Zehua Sun / Xing Zhu / Michelle M Marti / Shanti S Srivastava / Alison M Berezuk / Steven Zhou / Katharine S Tuttle / Michele D Sobolewski / Andrew Kim / Benjamin R Treat / Priscila Mayrelle Da Silva Castanha / Jana L Jacobs / Simon M Barratt-Boyes / John W Mellors / Dimiter S Dimitrov / Wei Li / Sriram Subramaniam /
Abstract: Mutations in the spike glycoproteins of SARS-CoV-2 variants of concern have independently been shown to enhance aspects of spike protein fitness. Here, we describe an antibody fragment (V ab6) that ...Mutations in the spike glycoproteins of SARS-CoV-2 variants of concern have independently been shown to enhance aspects of spike protein fitness. Here, we describe an antibody fragment (V ab6) that neutralizes all major variants including the recently emerged BA.1 and BA.2 Omicron subvariants, with a unique mode of binding revealed by cryo-EM studies. Further, we provide a comparative analysis of the mutational effects within previously emerged variant spikes and identify the structural role of mutations within the NTD and RBD in evading antibody neutralization. Our analysis shows that the highly mutated Gamma N-terminal domain exhibits considerable structural rearrangements, partially explaining its decreased neutralization by convalescent sera. Our results provide mechanistic insights into the structural, functional, and antigenic consequences of SARS-CoV-2 spike mutations and highlight a spike protein vulnerability that may be exploited to achieve broad protection against circulating variants.
History
DepositionJul 8, 2022-
Header (metadata) releaseAug 31, 2022-
Map releaseAug 31, 2022-
UpdateAug 31, 2022-
Current statusAug 31, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27511.png

Downloads & links

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Map

FileDownload / File: emd_27511.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationstructure of SARS-CoV-2 Gamma (P.1) spike protein in complex with Fab 4-8
Voxel sizeX=Y=Z: 1 Å
Density
Contour LevelBy AUTHOR: 0.0998
Minimum - Maximum-0.28606042 - 0.88201094
Average (Standard dev.)-0.00050688605 (±0.019968148)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 400.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map 1

Fileemd_27511_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_27511_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 : SARS-CoV-2 Gamma (P.1) spike protein in complex with Fab 4-8

EntireName: SARS-CoV-2 Gamma (P.1) spike protein in complex with Fab 4-8
Components
  • Complex: SARS-CoV-2 Gamma (P.1) spike protein in complex with Fab 4-8
    • Complex: SARS-CoV-2 Gamma (P.1) spike protein
      • Protein or peptide: SARS-CoV-2 Gamma (P.1) spike protein
    • Complex: Fab 4-8
      • Protein or peptide: Fab 4-8 heavy chain
      • Protein or peptide: Fab 4-8 light chain

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Supramolecule #1: SARS-CoV-2 Gamma (P.1) spike protein in complex with Fab 4-8

SupramoleculeName: SARS-CoV-2 Gamma (P.1) spike protein in complex with Fab 4-8
type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #2: SARS-CoV-2 Gamma (P.1) spike protein

SupramoleculeName: SARS-CoV-2 Gamma (P.1) spike protein / type: complex / Chimera: Yes / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Recombinant expressionOrganism: Homo sapiens (human)

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Supramolecule #3: Fab 4-8

SupramoleculeName: Fab 4-8 / type: complex / Chimera: Yes / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Homo sapiens (human)

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Macromolecule #1: SARS-CoV-2 Gamma (P.1) spike protein

MacromoleculeName: SARS-CoV-2 Gamma (P.1) spike protein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
SequenceString: MFVFLVLLPL VSSQCVNFTN RTQLPSAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHAIHV SGTNGTKRFD NPVLPFNDGV YFASTEKSNI IRGWIFGTTL DSKTQSLLIV NNATNVVIKV CEFQFCNYPF LGVYYHKNNK SWMESEFRVY SSANNCTFEY ...String:
MFVFLVLLPL VSSQCVNFTN RTQLPSAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHAIHV SGTNGTKRFD NPVLPFNDGV YFASTEKSNI IRGWIFGTTL DSKTQSLLIV NNATNVVIKV CEFQFCNYPF LGVYYHKNNK SWMESEFRVY SSANNCTFEY VSQPFLMDLE GKQGNFKNLS EFVFKNIDGY FKIYSKHTPI NLVRDLPQGF SALEPLVDLP IGINITRFQT LLALHRSYLT PGDSSSGWTA GAAAYYVGYL QPRTFLLKYN ENGTITDAVD CALDPLSETK CTLKSFTVEK GIYQTSNFRV QPTESIVRFP NITNLCPFGE VFNATRFASV YAWNRKRISN CVADYSVLYN SASFSTFKCY GVSPTKLNDL CFTNVYADSF VIRGDEVRQI APGQTGTIAD YNYKLPDDFT GCVIAWNSNN LDSKVGGNYN YLYRLFRKSN LKPFERDIST EIYQAGSTPC NGVKGFNCYF PLQSYGFQPT YGVGYQPYRV VVLSFELLHA PATVCGPKKS TNLVKNKCVN FNFNGLTGTG VLTESNKKFL PFQQFGRDIA DTTDAVRDPQ TLEILDITPC SFGGVSVITP GTNTSNQVAV LYQGVNCTEV PVAIHADQLT PTWRVYSTGS NVFQTRAGCL IGAEYVNNSY ECDIPIGAGI CASYQTQTNS PGSASSVASQ SIIAYTMSLG AENSVAYSNN SIAIPTNFTI SVTTEILPVS MTKTSVDCTM YICGDSTECS NLLLQYGSFC TQLNRALTGI AVEQDKNTQE VFAQVKQIYK TPPIKDFGGF NFSQILPDPS KPSKRSPIED LLFNKVTLAD AGFIKQYGDC LGDIAARDLI CAQKFNGLTV LPPLLTDEMI AQYTSALLAG TITSGWTFGA GPALQIPFPM QMAYRFNGIG VTQNVLYENQ KLIANQFNSA IGKIQDSLSS TPSALGKLQD VVNQNAQALN TLVKQLSSNF GAISSVLNDI LSRLDPPEAE VQIDRLITGR LQSLQTYVTQ QLIRAAEIRA SANLAAIKMS ECVLGQSKRV DFCGKGYHLM SFPQSAPHGV VFLHVTYVPA QEKNFTTAPA ICHDGKAHFP REGVFVSNGT HWFVTQRNFY EPQIITTDNT FVSGNCDVVI GIVNNTVYDP LQPELDSFKE ELDKYFKNHT SPDVDLGDIS GINASFVNIQ KEIDRLNEVA KNLNESLIDL QELGKYEQGS GYIPEAPRDG QAYVRKDGEW VLLSTFLGRS LEVLFQGPGH HHHHHHHSAW SHPQFEKGGG SGGGGSGGSA WSHPQFEK

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Macromolecule #2: Fab 4-8 heavy chain

MacromoleculeName: Fab 4-8 heavy chain / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MDWTWRVFCL LAVAPGAHSQ VQLVQSGAEV KKAGSSVKVS CKASGGTFSS HTITWVRQAP GQGLEWMGRI IPILGIANYA QKFQGRVTIT ADKSTSTAYM ELSSLRSEDT AVYYCASLQT VDTAIEKYYG MDVWGQGTTV TVSSASTKGP SVFPLAPSSK STSGGTAALG ...String:
MDWTWRVFCL LAVAPGAHSQ VQLVQSGAEV KKAGSSVKVS CKASGGTFSS HTITWVRQAP GQGLEWMGRI IPILGIANYA QKFQGRVTIT ADKSTSTAYM ELSSLRSEDT AVYYCASLQT VDTAIEKYYG MDVWGQGTTV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP VTVSWNSGAL TSGVHTFPAV LQSSGLYSLS SVVTVPSSSL GTQTYICNVN HKPSNTKVDK KVEPKSCGSH HHHHH

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Macromolecule #3: Fab 4-8 light chain

MacromoleculeName: Fab 4-8 light chain / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MVLQTQVFIS LLLWISGAYG SYELTQPPSV SVSPGQTASI TCSGDKLGDK YACWYQQKPG QSPVLVIYQD NKRPSGIPER FSGSNSGNTA TLTISGTQAM DEADYYCQAW DSSTAVFGGG TKLTVLGQPK ANPTVTLFPP SSEELQANKA TLVCLISDFY PGAVTVAWKA ...String:
MVLQTQVFIS LLLWISGAYG SYELTQPPSV SVSPGQTASI TCSGDKLGDK YACWYQQKPG QSPVLVIYQD NKRPSGIPER FSGSNSGNTA TLTISGTQAM DEADYYCQAW DSSTAVFGGG TKLTVLGQPK ANPTVTLFPP SSEELQANKA TLVCLISDFY PGAVTVAWKA DGSPVKAGVE TTKPSKQSNN KYAASSYLSL TPEQWKSHRS YSCQVTHEGS TVEKTVAPTE CS

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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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.59 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 312649
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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