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- EMDB-16453: SARS-CoV-2 Omicron Variant Spike Trimer in complex with three 17T... -

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Basic information

Entry
Database: EMDB / ID: EMD-16453
TitleSARS-CoV-2 Omicron Variant Spike Trimer in complex with three 17T2 Fabs
Map dataStructure map obtained after DeepEMhancer post-processing in cryosparc.
Sample
  • Complex: SARS-CoV-2 Omicron Variant Spike Trimer in complex with three 17T2 Fabs
    • Complex: Spike glycoproteinSpike protein
      • Protein or peptide: Spike glycoproteinSpike protein
    • Complex: 17T2 Fab
      • Protein or peptide: 17T2 Fab heavy chain
      • Protein or peptide: 17T2 Fab light chain
KeywordsComplex SARS-CoV-2 Spike S 17T2 / VIRAL PROTEIN
Biological speciesSevere acute respiratory syndrome coronavirus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.46 Å
AuthorsModrego A / Carlero D / Bueno-Carrasco MT / Santiago C / Carolis C / Arranz R / Blanco J / Magri G
Funding support Spain, 2 items
OrganizationGrant numberCountry
Other private
Generalitat de Catalunya Spain
CitationJournal: Nat Commun / Year: 2024
Title: A monoclonal antibody targeting a large surface of the receptor binding motif shows pan-neutralizing SARS-CoV-2 activity.
Authors: Leire de Campos-Mata / Benjamin Trinité / Andrea Modrego / Sonia Tejedor Vaquero / Edwards Pradenas / Anna Pons-Grífols / Natalia Rodrigo Melero / Diego Carlero / Silvia Marfil / César ...Authors: Leire de Campos-Mata / Benjamin Trinité / Andrea Modrego / Sonia Tejedor Vaquero / Edwards Pradenas / Anna Pons-Grífols / Natalia Rodrigo Melero / Diego Carlero / Silvia Marfil / César Santiago / Dàlia Raïch-Regué / María Teresa Bueno-Carrasco / Ferran Tarrés-Freixas / Ferran Abancó / Victor Urrea / Nuria Izquierdo-Useros / Eva Riveira-Muñoz / Ester Ballana / Mónica Pérez / Júlia Vergara-Alert / Joaquim Segalés / Carlo Carolis / Rocío Arranz / Julià Blanco / Giuliana Magri /
Abstract: Here we report the characterization of 17T2, a SARS-CoV-2 pan-neutralizing human monoclonal antibody isolated from a COVID-19 convalescent individual infected during the first pandemic wave. 17T2 is ...Here we report the characterization of 17T2, a SARS-CoV-2 pan-neutralizing human monoclonal antibody isolated from a COVID-19 convalescent individual infected during the first pandemic wave. 17T2 is a class 1 VH1-58/κ3-20 antibody, derived from a receptor binding domain (RBD)-specific IgA memory B cell, with a broad neutralizing activity against former and new SARS-CoV-2 variants, including XBB.1.16 and BA.2.86 Omicron subvariants. Consistently, 17T2 demonstrates in vivo prophylactic and therapeutic activity against Omicron BA.1.1 infection in K18-hACE2 mice. Cryo-electron microscopy reconstruction shows that 17T2 binds the BA.1 spike with the RBD in "up" position and blocks the receptor binding motif, as other structurally similar antibodies do, including S2E12. Yet, unlike S2E12, 17T2 retains its neutralizing activity against all variants tested, probably due to a larger RBD contact area. These results highlight the impact of small structural antibody changes on neutralizing performance and identify 17T2 as a potential candidate for future clinical interventions.
History
DepositionJan 12, 2023-
Header (metadata) releaseJan 10, 2024-
Map releaseJan 10, 2024-
UpdateFeb 21, 2024-
Current statusFeb 21, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16453.png

Downloads & links

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Map

FileDownload / File: emd_16453.map.gz / Format: CCP4 / Size: 454.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure map obtained after DeepEMhancer post-processing in cryosparc.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 492 pix.
= 420.66 Å		0.86 Å/pix.
x 492 pix.
= 420.66 Å		0.86 Å/pix.
x 492 pix.
= 420.66 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.855 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.034
Minimum - Maximum-0.001696685 - 1.9730217
Average (Standard dev.)0.0012242051 (±0.023971394)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions492492492
Spacing492492492
CellA=B=C: 420.66 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A obtained in the non-uniform refinement in cryosparc.

Fileemd_16453_half_map_1.map
AnnotationHalf map A obtained in the non-uniform refinement in cryosparc.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B obtained in the non-uniform refinement in cryosparc.

Fileemd_16453_half_map_2.map
AnnotationHalf map B obtained in the non-uniform refinement in cryosparc.
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 Omicron Variant Spike Trimer in complex with three 17T...

EntireName: SARS-CoV-2 Omicron Variant Spike Trimer in complex with three 17T2 Fabs
Components
  • Complex: SARS-CoV-2 Omicron Variant Spike Trimer in complex with three 17T2 Fabs
    • Complex: Spike glycoproteinSpike protein
      • Protein or peptide: Spike glycoproteinSpike protein
    • Complex: 17T2 Fab
      • Protein or peptide: 17T2 Fab heavy chain
      • Protein or peptide: 17T2 Fab light chain

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Supramolecule #1: SARS-CoV-2 Omicron Variant Spike Trimer in complex with three 17T...

SupramoleculeName: SARS-CoV-2 Omicron Variant Spike Trimer in complex with three 17T2 Fabs
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: Spike glycoprotein

SupramoleculeName: Spike glycoprotein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus

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Supramolecule #3: 17T2 Fab

SupramoleculeName: 17T2 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus
SequenceString: MPRGPVAALL LLILHGAWSC VNLTTRTQLP PAYTNSFTRG VYYPDKVFRS SVLHSTQDLF LPFFSNVTWF HVISGTNGTK RFDNPVLPFN DGVYFASIEK SNIIRGWIFG TTLDSKTQSL LIVNNATNVV IKVCEFQFCN DPFLDHKNNK SWMESEFRVY SSANNCTFEY ...String:
MPRGPVAALL LLILHGAWSC VNLTTRTQLP PAYTNSFTRG VYYPDKVFRS SVLHSTQDLF LPFFSNVTWF HVISGTNGTK RFDNPVLPFN DGVYFASIEK SNIIRGWIFG TTLDSKTQSL LIVNNATNVV IKVCEFQFCN DPFLDHKNNK SWMESEFRVY SSANNCTFEY VSQPFLMDLE GKQGNFKNLR EFVFKNIDGY FKIYSKHTPI IVREPEDLPQ GFSALEPLVD LPIGINITRF QTLLALHRSY LTPGDSSSGW TAGAAAYYVG YLQPRTFLLK YNENGTITDA VDCALDPLSE TKCTLKSFTV EKGIYQTSNF RVQPTESIVR FPNITNLCPF DEVFNATRFA SVYAWNRKRI SNCVADYSVL YNLAPFFTFK CYGVSPTKLN DLCFTNVYAD SFVIRGDEVR QIAPGQTGNI ADYNYKLPDD FTGCVIAWNS NKLDSKVSGN YNYLYRLFRK SNLKPFERDI STEIYQAGNK PCNGVAGFNC YFPLRSYSFR PTYGVGHQPY RVVVLSFELL HAPATVCGPK KSTNLVKNKC VNFNFNGLKG TGVLTESNKK FLPFQQFGRD IADTTDAVRD PQTLEILDIT PCSFGGVSVI TPGTNTSNQV AVLYQGVNCT EVPVAIHADQ LTPTWRVYST GSNVFQTRAG CLIGAEYVNN SYECDIPIGA GICASYQTQT KSHGSASSVA SQSIIAYTMS LGAENSVAYS NNSIAIPTNF TISVTTEILP VSMTKTSVDC TMYICGDSTE CSNLLLQYGS FCTQLKRALT GIAVEQDKNT QEVFAQVKQI YKTPPIKYFG GFNFSQILPD PSKPSKRSFI EDLLFNKVTL ADAGFIKQYG DCLGDIAARD LICAQKFKGL TVLPPLLTDE MIAQYTSALL AGTITSGWTF GAGAALQIPF AMQMAYRFNG IGVTQNVLYE NQKLIANQFN SAIGKIQDSL SSTASALGKL QDVVNHNAQA LNTLVKQLSS KFGAISSVLN DIFSRLDPPE AEVQIDRLIT GRLQSLQTYV TQQLIRAAEI RASANLAATK MSECVLGQSK RVDFCGKGYH LMSFPQSAPH GVVFLHVTYV PAQEKNFTTA PAICHDGKAH FPREGVFVSN GTHWFVTQRN FYEPQIITTD NTFVSGNCDV VIGIVNNTVY DPLQPELDSF KEELDKYFKN HTSPDVDLGD ISGINASVVN IQKEIDRLNE VAKNLNESLI DLQELGKYEQ LVPRGSGYIP EAPRDGQAYV RKDGEWVLLS TFLHHHHHH

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Macromolecule #2: 17T2 Fab heavy chain

MacromoleculeName: 17T2 Fab heavy chain / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: QVQLVQSGPE VKKPGTSVKV SCKAPVFTFS ISAVQWVRQA RGQRLEWIGW IVVGSGNTNY AQNFQERVTI TTDMSTGTVY MELSGLRSED TAMYYCAAPY CNRTTCYDGF DLWGQGTMVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC LVKDYFPEPV TVSWNSGALT ...String:
QVQLVQSGPE VKKPGTSVKV SCKAPVFTFS ISAVQWVRQA RGQRLEWIGW IVVGSGNTNY AQNFQERVTI TTDMSTGTVY MELSGLRSED TAMYYCAAPY CNRTTCYDGF DLWGQGTMVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC LVKDYFPEPV TVSWNSGALT SGVHTFPAVL QSSGLYSLSS VVTVPSSSLG TQTYICNVNH KPSNTKVDKR VEPKSCDKTH TCPPCPAPEL LGGPSVFLFP PKPKDTLMIS RTPEVTCVVV DVSHEDPEVK FNWYVDGVEV HNAKTKPREE QYNSTYRVVS VLTVLHQDWL NGKEYKCKVS NKALPAPIEK TISKAKGQPR EPQVYTLPPS REEMTKNQVS LTCLVKGFYP SDIAVEWESN GQPENNYKTT PPVLDSDGSF FLYSKLTVDK SRWQQGNVFS CSVMHEALHN HYTQKSLSLS PGK

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Macromolecule #3: 17T2 Fab light chain

MacromoleculeName: 17T2 Fab light chain / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: EIVLTQSPGT LSLSPGERAT LSCRASQSIS SNYLAWYQQK PGQAPRLLIY GASSRATGIP DRFSGSGSGT DFTLSINRLE PEDFAMYYCQ HYGGLSRWTF GQGTKVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN SQESVTEQDS ...String:
EIVLTQSPGT LSLSPGERAT LSCRASQSIS SNYLAWYQQK PGQAPRLLIY GASSRATGIP DRFSGSGSGT DFTLSINRLE PEDFAMYYCQ HYGGLSRWTF GQGTKVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN SQESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

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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: 7.6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS TALOS F200C
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 32.0 e/Å2
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE / Details: Ab initio generation using cryosparc
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 124570

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