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- EMDB-33651: SARS-CoV-2 spike glycoprotein trimer complexed with Fab fragment ... -

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Basic information

Entry
Database: EMDB / ID: EMD-33651
TitleSARS-CoV-2 spike glycoprotein trimer complexed with Fab fragment of anti-RBD antibody E7 (focused refinement on Fab-RBD interface)
Map dataFocused refinement of SARS-CoV-2 spike (S) protein receptor binding domains (RBDs) in complex with anti-RBD Fab E7
Sample
  • Complex: SARS-CoV-2 spike glycoprotein trimer complexed with Fab fragment of anti-RBD antibody E7
    • Protein or peptide: Spike glycoproteinSpike protein
    • Protein or peptide: Fab E7 light chain
    • Protein or peptide: Fab E7 heavy chain
KeywordsVIRAL 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 speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.03 Å
AuthorsChia WN / Tan CW / Tan AWK / Young B / Starr TN / Lopez E / Fibriansah G / Barr J / Cheng S / Yeoh AYY ...Chia WN / Tan CW / Tan AWK / Young B / Starr TN / Lopez E / Fibriansah G / Barr J / Cheng S / Yeoh AYY / Yap WC / Lim BL / Ng TS / Sia WR / Zhu F / Chen S / Zhang J / Greaney AJ / Chen M / Au GG / Paradkar P / Peiris M / Chung AW / Bloom JD / Lye D / Lok SM / Wang LF
Funding support Singapore, Australia, United States, 8 items
OrganizationGrant numberCountry
National Research Foundation (NRF, Singapore)NRF2016NRF-NSFC002-013 Singapore
Other governmentSTPRG-FY19-001 Singapore
Other governmentCOVID19RF-003 Singapore
Other governmentCOVID19RF-060 Singapore
Other governmentMOH-000535/MOH-OFYIRG19nov-0002 Singapore
Other governmentOFLCG19May-0034 Singapore
National Health and Medical Research Council (NHMRC, Australia)GNT 2008092 Australia
Damon Runyon Cancer Research Foundation United States
CitationJournal: Sci Adv / Year: 2023
Title: Potent pan huACE2-dependent sarbecovirus neutralizing monoclonal antibodies isolated from a BNT162b2-vaccinated SARS survivor.
Authors: Wan Ni Chia / Chee Wah Tan / Aaron Wai Kit Tan / Barnaby Young / Tyler N Starr / Ester Lopez / Guntur Fibriansah / Jennifer Barr / Samuel Cheng / Aileen Ying-Yan Yeoh / Wee Chee Yap / Beng ...Authors: Wan Ni Chia / Chee Wah Tan / Aaron Wai Kit Tan / Barnaby Young / Tyler N Starr / Ester Lopez / Guntur Fibriansah / Jennifer Barr / Samuel Cheng / Aileen Ying-Yan Yeoh / Wee Chee Yap / Beng Lee Lim / Thiam-Seng Ng / Wan Rong Sia / Feng Zhu / Shiwei Chen / Jinyan Zhang / Madeline Sheng Si Kwek / Allison J Greaney / Mark Chen / Gough G Au / Prasad N Paradkar / Malik Peiris / Amy W Chung / Jesse D Bloom / David Lye / Sheemei Lok / Lin-Fa Wang /
Abstract: The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern such as Omicron hampered efforts in controlling the ongoing coronavirus disease 2019 pandemic due to ...The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern such as Omicron hampered efforts in controlling the ongoing coronavirus disease 2019 pandemic due to their ability to escape neutralizing antibodies induced by vaccination or prior infection, highlighting the need to develop broad-spectrum vaccines and therapeutics. Most human monoclonal antibodies (mAbs) reported to date have not demonstrated true pan-sarbecovirus neutralizing breadth especially against animal sarbecoviruses. Here, we report the isolation and characterization of highly potent mAbs targeting the receptor binding domain (RBD) of huACE2-dependent sarbecovirus from a SARS-CoV survivor vaccinated with BNT162b2. Among the six mAbs identified, one (E7) showed better huACE2-dependent sarbecovirus neutralizing potency and breadth than any other mAbs reported to date. Mutagenesis and cryo-electron microscopy studies indicate that these mAbs have a unique RBD contact footprint and that E7 binds to a quaternary structure-dependent epitope.
History
DepositionJun 21, 2022-
Header (metadata) releaseAug 2, 2023-
Map releaseAug 2, 2023-
UpdateAug 9, 2023-
Current statusAug 9, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33651.png

Downloads & links

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Map

FileDownload / File: emd_33651.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFocused refinement of SARS-CoV-2 spike (S) protein receptor binding domains (RBDs) in complex with anti-RBD Fab E7
Voxel sizeX=Y=Z: 1.105 Å
Density
Contour LevelBy AUTHOR: 7.55
Minimum - Maximum-58.422398000000001 - 124.104680000000002
Average (Standard dev.)0.00000000041966 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 397.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_33651_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_33651_half_map_2.map
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 spike glycoprotein trimer complexed with Fab fragment ...

EntireName: SARS-CoV-2 spike glycoprotein trimer complexed with Fab fragment of anti-RBD antibody E7
Components
  • Complex: SARS-CoV-2 spike glycoprotein trimer complexed with Fab fragment of anti-RBD antibody E7
    • Protein or peptide: Spike glycoproteinSpike protein
    • Protein or peptide: Fab E7 light chain
    • Protein or peptide: Fab E7 heavy chain

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Supramolecule #1: SARS-CoV-2 spike glycoprotein trimer complexed with Fab fragment ...

SupramoleculeName: SARS-CoV-2 spike glycoprotein trimer complexed with Fab fragment of anti-RBD antibody E7
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
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: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 132.860156 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: VNLTTRTQLP PAYTNSFTRG VYYPDKVFRS SVLHSTQDLF LPFFSNVTWF HAIHVSGTNG TKRFDNPVLP FNDGVYFAST EKSNIIRGW IFGTTLDSKT QSLLIVNNAT NVVIKVCEFQ FCNDPFLGVY YHKNNKSWME SEFRVYSSAN NCTFEYVSQP F LMDLEGKQ ...String:
VNLTTRTQLP PAYTNSFTRG VYYPDKVFRS SVLHSTQDLF LPFFSNVTWF HAIHVSGTNG TKRFDNPVLP FNDGVYFAST EKSNIIRGW IFGTTLDSKT QSLLIVNNAT NVVIKVCEFQ FCNDPFLGVY YHKNNKSWME SEFRVYSSAN NCTFEYVSQP F LMDLEGKQ GNFKNLREFV FKNIDGYFKI YSKHTPINLV RDLPQGFSAL EPLVDLPIGI NITRFQTLLA LHRSYLTPGD SS SGWTAGA AAYYVGYLQP RTFLLKYNEN GTITDAVDCA LDPLSETKCT LKSFTVEKGI YQTSNFRVQP TESIVRFPNI TNL CPFGEV FNATRFASVY AWNRKRISNC VADYSVLYNS ASFSTFKCYG VSPTKLNDLC FTNVYADSFV IRGDEVRQIA PGQT GKIAD YNYKLPDDFT GCVIAWNSNN LDSKVGGNYN YLYRLFRKSN LKPFERDIST EIYQAGSTPC NGVEGFNCYF PLQSY GFQP TNGVGYQPYR VVVLSFELLH APATVCGPKK STNLVKNKCV NFNFNGLTGT GVLTESNKKF LPFQQFGRDI ADTTDA VRD PQTLEILDIT PCSFGGVSVI TPGTNTSNQV AVLYQDVNCT EVPVAIHADQ LTPTWRVYST GSNVFQTRAG CLIGAEH VN NSYECDIPIG AGICASYQTQ TNSPRAAASV ASQSIIAYTM SLGAENSVAY SNNSIAIPTN FTISVTTEIL PVSMTKTS V DCTMYICGDS TECSNLLLQY GSFCTQLNRA LTGIAVEQDK NTQEVFAQVK QIYKTPPIKD FGGFNFSQIL PDPSKPSKR SPIEDLLFNK VTLADAGFIK QYGDCLGDIA ARDLICAQKF NGLTVLPPLL TDEMIAQYTS ALLAGTITSG WTFGAGPALQ IPFPMQMAY RFNGIGVTQN VLYENQKLIA NQFNSAIGKI QDSLSSTPSA LGKLQDVVNQ NAQALNTLVK QLSSNFGAIS S VLNDILSR LDPPEAEVQI DRLITGRLQS LQTYVTQQLI RAAEIRASAN LAATKMSECV LGQSKRVDFC GKGYHLMSFP QS APHGVVF LHVTYVPAQE KNFTTAPAIC HDGKAHFPRE GVFVSNGTHW FVTQRNFYEP QIITTDNTFV SGNCDVVIGI VNN TVYDPL QPELDSFKEE LDKYFKNHTS PDVDLGDISG INASVVNIQK EIDRLNEVAK NLNESLIDLQ ELGKYEQYIK WP

UniProtKB: Spike glycoprotein

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Macromolecule #2: Fab E7 light chain

MacromoleculeName: Fab E7 light chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.920668 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIVMTQSPLS LPVTPGEPAS ISCRSSQSLL QNNGYNYLAW YLQKPGQSPQ LLIYLSSTRA SGVPDRFSGS GSGTDFTLKI SRVEAEDVG VYYCMQSLQI PGTFGQGTRL EIKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV ...String:
DIVMTQSPLS LPVTPGEPAS ISCRSSQSLL QNNGYNYLAW YLQKPGQSPQ LLIYLSSTRA SGVPDRFSGS GSGTDFTLKI SRVEAEDVG VYYCMQSLQI PGTFGQGTRL EIKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV TEQDSKDSTY SLSSTLTLSK ADYEKHKVYA CEVTHQGLSS PVTKSFNRGE C

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Macromolecule #3: Fab E7 heavy chain

MacromoleculeName: Fab E7 heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.339156 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLQESGPG LVKPSETLSL TCTVSGGFIG PHYWSWVRQP PGKGLEWIGY IYISGSTNYN PSLKSRLTIS VDMSKSQFSL TLSSATAAD TAVYYCARGG GYLETGPFEY WGQGTLVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV KDYFPEPVTV S WNSGALTS ...String:
QVQLQESGPG LVKPSETLSL TCTVSGGFIG PHYWSWVRQP PGKGLEWIGY IYISGSTNYN PSLKSRLTIS VDMSKSQFSL TLSSATAAD TAVYYCARGG GYLETGPFEY WGQGTLVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV KDYFPEPVTV S WNSGALTS GVHTFPAVLQ SSGLYSLSSV VTVPSSSLGT QTYICNVNHK PSNTKVDKRV EPK

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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: 7.4
Component:
ConcentrationFormulaName
50.0 mMNH2C(CH2OH)3Tris buffer
300.0 mMNaClSodium chlorideSodium chloride
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
DetailsSARS-CoV-2 spike glycoprotein trimer complexed with Fab fragment of anti-RBD antibody E7

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000
Specialist opticsEnergy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Average exposure time: 4.76 sec. / Average electron dose: 31.6 e/Å2
Details: Images were collected in counting mode at 25 frames per movie with an exposure time of 4.76 s per movie.
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 402809
Startup modelType of model: INSILICO MODEL / In silico model: Ab initio model / Details: cryoSPARC was used to generate an ab initio model.
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0-beta-2-commit-543db0) / Details: Heterogeneous refinement in cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1+220215)
Details: Non-uniform refinement followed by local refinement in cryoSPARC
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.03 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.1+220215) / Details: Local refinement in cryoSPARC / Number images used: 198525
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

6xkl


6n16

chain_id: A, residue_range: 114-213

6n16

chain_id: B, residue_range: 108-212
RefinementSpace: REAL
Output model

PDB-7y72:
SARS-CoV-2 spike glycoprotein trimer complexed with Fab fragment of anti-RBD antibody E7 (focused refinement on Fab-RBD interface)

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