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- EMDB-14250: Structure of the SARS-CoV-2 spike glycoprotein in complex with th... -

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Entry
Database: EMDB / ID: EMD-14250
TitleStructure of the SARS-CoV-2 spike glycoprotein in complex with the 87G7 antibody Fab fragment
Map dataComposite map
Sample
  • Complex: SARS-CoV-2 spike glycoprotein in complex with the 87G7 antibody Fab fragment
    • Complex: SARS-CoV-2 spike glycoprotein
      • Protein or peptide: Spike glycoproteinSpike protein
    • Complex: 87G7 antibody Fab fragment
      • Protein or peptide: 87G7 light chain variable region
      • Protein or peptide: 87G7 heavy chain variable region
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsCoronavirus / Spike / Antibody / Complex / VIRAL PROTEIN
Function / homology
Function and homology information


Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / membrane / identical protein binding / plasma membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsHurdiss DL / Drulyte I
Funding supportEuropean Union, Germany, 3 items
OrganizationGrant numberCountry
European Commission101003651European Union
German Research Foundation (DFG)398066876/GRK 2485/1 Germany
German Federal Ministry for Education and Research01KI1723G Germany
CitationJournal: Sci Immunol / Year: 2022
Title: An ACE2-blocking antibody confers broad neutralization and protection against Omicron and other SARS-CoV-2 variants of concern.
Authors: Wenjuan Du / Daniel L Hurdiss / Dubravka Drabek / Anna Z Mykytyn / Franziska K Kaiser / Mariana González-Hernández / Diego Muñoz-Santos / Mart M Lamers / Rien van Haperen / Wentao Li / ...Authors: Wenjuan Du / Daniel L Hurdiss / Dubravka Drabek / Anna Z Mykytyn / Franziska K Kaiser / Mariana González-Hernández / Diego Muñoz-Santos / Mart M Lamers / Rien van Haperen / Wentao Li / Ieva Drulyte / Chunyan Wang / Isabel Sola / Federico Armando / Georg Beythien / Malgorzata Ciurkiewicz / Wolfgang Baumgärtner / Kate Guilfoyle / Tony Smits / Joline van der Lee / Frank J M van Kuppeveld / Geert van Amerongen / Bart L Haagmans / Luis Enjuanes / Albert D M E Osterhaus / Frank Grosveld / Berend-Jan Bosch /
Abstract: The ongoing evolution of SARS-CoV-2 has resulted in the emergence of Omicron, which displays notable immune escape potential through mutations at key antigenic sites on the spike protein. Many of ...The ongoing evolution of SARS-CoV-2 has resulted in the emergence of Omicron, which displays notable immune escape potential through mutations at key antigenic sites on the spike protein. Many of these mutations localize to the spike protein ACE2 receptor binding domain, annulling the neutralizing activity of therapeutic antibodies that were effective against other variants of concern (VOCs) earlier in the pandemic. Here, we identified a receptor-blocking human monoclonal antibody, 87G7, that retained potent in vitro neutralizing activity against SARS-CoV-2 variants including the Alpha, Beta, Gamma, Delta, and Omicron (BA.1/BA.2) VOCs. Using cryo-electron microscopy and site-directed mutagenesis experiments, we showed that 87G7 targets a patch of hydrophobic residues in the ACE2-binding site that are highly conserved in SARS-CoV-2 variants, explaining its broad neutralization capacity. 87G7 protected mice and hamsters prophylactically against challenge with all current SARS-CoV-2 VOCs and showed therapeutic activity against SARS-CoV-2 challenge in both animal models. Our findings demonstrate that 87G7 holds promise as a prophylactic or therapeutic agent for COVID-19 that is more resilient to SARS-CoV-2 antigenic diversity.
History
DepositionFeb 8, 2022-
Header (metadata) releaseApr 20, 2022-
Map releaseApr 20, 2022-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14250.png

Downloads & links

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Map

FileDownload / File: emd_14250.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.24 Å/pix.
x 300 pix.
= 372. Å		1.24 Å/pix.
x 300 pix.
= 372. Å		1.24 Å/pix.
x 300 pix.
= 372. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.24 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.004284906 - 3.62477
Average (Standard dev.)0.0013926498 (±0.027411383)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 372.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_14250_msk_1.map
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Additional map: Mask used for refinement

Fileemd_14250_additional_1.map
AnnotationMask used for refinement
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Additional map: Local resolution filtered map

Fileemd_14250_additional_2.map
AnnotationLocal resolution filtered map
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Additional map: DeepEMhancer sharpened map

Fileemd_14250_additional_3.map
AnnotationDeepEMhancer sharpened map
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Additional map: Unsharpened map

Fileemd_14250_additional_4.map
AnnotationUnsharpened map
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Additional map: Sharpened map

Fileemd_14250_additional_5.map
AnnotationSharpened map
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Half map: Half map 1

Fileemd_14250_half_map_1.map
AnnotationHalf map 1
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Half map: Half map 2

Fileemd_14250_half_map_2.map
AnnotationHalf map 2
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Sample components

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Entire : SARS-CoV-2 spike glycoprotein in complex with the 87G7 antibody F...

EntireName: SARS-CoV-2 spike glycoprotein in complex with the 87G7 antibody Fab fragment
Components
  • Complex: SARS-CoV-2 spike glycoprotein in complex with the 87G7 antibody Fab fragment
    • Complex: SARS-CoV-2 spike glycoprotein
      • Protein or peptide: Spike glycoproteinSpike protein
    • Complex: 87G7 antibody Fab fragment
      • Protein or peptide: 87G7 light chain variable region
      • Protein or peptide: 87G7 heavy chain variable region
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: SARS-CoV-2 spike glycoprotein in complex with the 87G7 antibody F...

SupramoleculeName: SARS-CoV-2 spike glycoprotein in complex with the 87G7 antibody Fab fragment
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Molecular weightTheoretical: 500 KDa

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Supramolecule #2: SARS-CoV-2 spike glycoprotein

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

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Supramolecule #3: 87G7 antibody Fab fragment

SupramoleculeName: 87G7 antibody Fab fragment / 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 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 141.048734 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QCVNLTTRTQ LPPAYTNSFT RGVYYPDKVF RSSVLHSTQD LFLPFFSNVT WFHAIHVSGT NGTKRFDNPV LPFNDGVYFA STEKSNIIR GWIFGTTLDS KTQSLLIVNN ATNVVIKVCE FQFCNDPFLG VYYHKNNKSW MESEFRVYSS ANNCTFEYVS Q PFLMDLEG ...String:
QCVNLTTRTQ LPPAYTNSFT RGVYYPDKVF RSSVLHSTQD LFLPFFSNVT WFHAIHVSGT NGTKRFDNPV LPFNDGVYFA STEKSNIIR GWIFGTTLDS KTQSLLIVNN ATNVVIKVCE FQFCNDPFLG VYYHKNNKSW MESEFRVYSS ANNCTFEYVS Q PFLMDLEG KQGNFKNLRE FVFKNIDGYF KIYSKHTPIN LVRDLPQGFS ALEPLVDLPI GINITRFQTL LALHRSYLTP GD SSSGWTA GAAAYYVGYL QPRTFLLKYN ENGTITDAVD CALDPLSETK CTLKSFTVEK GIYQTSNFRV QPTESIVRFP NIT NLCPFG EVFNATRFAS VYAWNRKRIS NCVADYSVLY NSASFSTFKC YGVSPTKLND LCFTNVYADS FVIRGDEVRQ IAPG QTGKI ADYNYKLPDD FTGCVIAWNS NNLDSKVGGN YNYLYRLFRK SNLKPFERDI STEIYQAGST PCNGVEGFNC YFPLQ SYGF QPTNGVGYQP YRVVVLSFEL LHAPATVCGP KKSTNLVKNK CVNFNFNGLT GTGVLTESNK KFLPFQQFGR DIADTT DAV RDPQTLEILD ITPCSFGGVS VITPGTNTSN QVAVLYQDVN CTEVPVAIHA DQLTPTWRVY STGSNVFQTR AGCLIGA EH VNNSYECDIP IGAGICASYQ TQTNSPAAAR SVASQSIIAY TMSLGAENSV AYSNNSIAIP TNFTISVTTE ILPVSMTK T SVDCTMYICG DSTECSNLLL QYGSFCTQLN RALTGIAVEQ DKNTQEVFAQ VKQIYKTPPI KDFGGFNFSQ ILPDPSKPS KRSPIEDLLF NKVTLADAGF IKQYGDCLGD IAARDLICAQ KFNGLTVLPP LLTDEMIAQY TSALLAGTIT SGWTFGAGPA LQIPFPMQM AYRFNGIGVT QNVLYENQKL IANQFNSAIG KIQDSLSSTP SALGKLQDVV NQNAQALNTL VKQLSSNFGA I SSVLNDIL SRLDPPEAEV QIDRLITGRL QSLQTYVTQQ LIRAAEIRAS ANLAATKMSE CVLGQSKRVD FCGKGYHLMS FP QSAPHGV VFLHVTYVPA QEKNFTTAPA ICHDGKAHFP REGVFVSNGT HWFVTQRNFY EPQIITTDNT FVSGNCDVVI GIV NNTVYD PLQPELDSFK EELDKYFKNH TSPDVDLGDI SGINASVVNI QKEIDRLNEV AKNLNESLID LQELGKYEQG SGYI PEAPR DGQAYVRKDG EWVLLSTFLG RSLEVLFQGP GHHHHHHHHS AWSHPQFEKG GGSGGGGSGG SAWSHPQFEK

UniProtKB: Spike glycoprotein

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Macromolecule #2: 87G7 light chain variable region

MacromoleculeName: 87G7 light chain variable region / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.550207 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EIVLTQSPAT LSLSPGERAT LSCRASQSFH NYLAWYQQKP GRAPRLLIFD ASNRATGIPA RFSGSGSGTD FTLTISSLEP EDFAVYYCQ QRFNWPLTFG GGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
EIVLTQSPAT LSLSPGERAT LSCRASQSFH NYLAWYQQKP GRAPRLLIFD ASNRATGIPA RFSGSGSGTD FTLTISSLEP EDFAVYYCQ QRFNWPLTFG GGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

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Macromolecule #3: 87G7 heavy chain variable region

MacromoleculeName: 87G7 heavy chain variable region / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.915703 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLLESGGG LVQPGGSLRL SCVASGFTFS SYVMSWVRQA PGKGLEWVAA ISGSGGNTYY ADSVKGRFTI SRDNSKNTLY LQMNSLRAE DTAVYYCAKE GTYYYGSGSF WGQGTLVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV KDYFPEPVTV S WNSGALTS ...String:
EVQLLESGGG LVQPGGSLRL SCVASGFTFS SYVMSWVRQA PGKGLEWVAA ISGSGGNTYY ADSVKGRFTI SRDNSKNTLY LQMNSLRAE DTAVYYCAKE GTYYYGSGSF WGQGTLVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV KDYFPEPVTV S WNSGALTS GVHTFPAVLQ SSGLYSLSSV VTVPSSSLGT QTYICNVNHK PSNTKVDKKV EPKSCDKTH

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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: 27 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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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

Concentration4 mg/mL
BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 130000
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 2 / Number real images: 3831 / Average electron dose: 51.5 e/Å2
Details: 1331 images collected from grid 1 (0.02% FOM) and 2500 images collected from grid 2 (0% FOM)
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 934811
Details: 313636 particles were picked from 1331 images from 0.02% FOM dataset and 621175 particles were picked from 2500 images without FOM.
Startup modelType of model: OTHER / Details: Generated ab initio using cryoSPARC
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 133550
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

7b62

chain_id: A, residue_range: 14-308, source_name: PDB, initial_model_type: experimental model

7k4n

chain_id: A, residue_range: 309-332, source_name: PDB, initial_model_type: experimental model

7k4n

chain_id: A, residue_range: 527-1145, source_name: PDB, initial_model_type: experimental model

6m0j

chain_id: E, residue_range: 333-526, source_name: PDB, initial_model_type: experimental model
Output model

PDB-7r40:
Structure of the SARS-CoV-2 spike glycoprotein in complex with the 87G7 antibody Fab fragment

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