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- EMDB-25105: Structure of SARS-CoV S protein in complex with Receptor Binding ... -

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Basic information

Entry
Database: EMDB / ID: EMD-25105
TitleStructure of SARS-CoV S protein in complex with Receptor Binding Domain antibody DH1047
Map datacryosparc generated map
Sample
  • Complex: SARS-CoV S protein in complex with Receptor Binding Domain antibody DH1047
    • Protein or peptide: Spike glycoproteinSpike protein
    • Protein or peptide: DH1047 Heavy chain
    • Protein or peptide: DH1047 light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Function / homology
Function and homology information


Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / Attachment and Entry / endocytosis involved in viral entry into host cell / SARS-CoV-1 activates/modulates innate immune responses / suppression by virus of host tetherin activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion / positive regulation of viral entry into host cell ...Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / Attachment and Entry / endocytosis involved in viral entry into host cell / SARS-CoV-1 activates/modulates innate immune responses / suppression by virus of host tetherin activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / 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 / host cell plasma membrane / virion membrane / membrane / identical protein binding
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV / 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 / 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-related coronavirus / Severe acute respiratory syndrome coronavirus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.43 Å
AuthorsGobeil S / Acharya P
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI145687 United States
CitationJournal: Sci Transl Med / Year: 2022
Title: A broadly cross-reactive antibody neutralizes and protects against sarbecovirus challenge in mice.
Authors: David R Martinez / Alexandra Schäfer / Sophie Gobeil / Dapeng Li / Gabriela De la Cruz / Robert Parks / Xiaozhi Lu / Maggie Barr / Victoria Stalls / Katarzyna Janowska / Esther Beaudoin / ...Authors: David R Martinez / Alexandra Schäfer / Sophie Gobeil / Dapeng Li / Gabriela De la Cruz / Robert Parks / Xiaozhi Lu / Maggie Barr / Victoria Stalls / Katarzyna Janowska / Esther Beaudoin / Kartik Manne / Katayoun Mansouri / Robert J Edwards / Kenneth Cronin / Boyd Yount / Kara Anasti / Stephanie A Montgomery / Juanjie Tang / Hana Golding / Shaunna Shen / Tongqing Zhou / Peter D Kwong / Barney S Graham / John R Mascola / David C Montefiori / S Munir Alam / Gregory Sempowski / Gregory D Sempowski / Surender Khurana / Kevin Wiehe / Kevin O Saunders / Priyamvada Acharya / Barton F Haynes / Ralph S Baric /
Abstract: Severe acute respiratory syndrome coronaviruses 1 (SARS-CoV) and 2 (SARS-CoV-2), including SARS-CoV-2 variants of concern, can cause deadly infections. The mortality associated with sarbecovirus ...Severe acute respiratory syndrome coronaviruses 1 (SARS-CoV) and 2 (SARS-CoV-2), including SARS-CoV-2 variants of concern, can cause deadly infections. The mortality associated with sarbecovirus infection underscores the importance of developing broadly effective countermeasures against them, which could be key in the prevention and mitigation of current and future zoonotic events. Here, we demonstrate the neutralization of SARS-CoV; bat coronaviruses WIV-1 and RsSHC014; and SARS-CoV-2 variants D614G, B.1.1.7, B.1.351, P.1, B.1.429, B.1.526, B.1.617.1, and B.1.617.2 by a receptor binding domain (RBD)–specific human antibody, DH1047. Prophylactic and therapeutic treatment with DH1047 was protective against SARS-CoV, WIV-1, RsSHC014, and SARS-CoV-2 B.1.351 infection in mice. Binding and structural analysis showed high affinity binding of DH1047 to an epitope that is highly conserved among sarbecoviruses. Thus, DH1047 is a broadly protective antibody that can prevent infection and mitigate outbreaks caused by SARS-related strains and SARS-CoV-2 variants. Our results also suggest that the conserved RBD epitope bound by DH1047 is a rational target for a universal sarbecovirus vaccine.
History
DepositionOct 4, 2021-
Header (metadata) releaseNov 10, 2021-
Map releaseNov 10, 2021-
UpdateFeb 9, 2022-
Current statusFeb 9, 2022Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.7
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.7
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7sg4
  • Surface level: 0.7
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_25105.png

Downloads & links

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Map

FileDownload / File: emd_25105.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcryosparc generated map
Voxel sizeX=Y=Z: 1.08 Å
Density
Contour LevelBy AUTHOR: 0.7 / Movie #1: 0.7
Minimum - Maximum-0.89491105 - 3.576813
Average (Standard dev.)0.00054165063 (±0.14894558)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 324.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z324.000324.000324.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-300-300-300
NX/NY/NZ600600600
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.8953.5770.001

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Supplemental data

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Sample components

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Entire : SARS-CoV S protein in complex with Receptor Binding Domain antibo...

EntireName: SARS-CoV S protein in complex with Receptor Binding Domain antibody DH1047
Components
  • Complex: SARS-CoV S protein in complex with Receptor Binding Domain antibody DH1047
    • Protein or peptide: Spike glycoproteinSpike protein
    • Protein or peptide: DH1047 Heavy chain
    • Protein or peptide: DH1047 light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: SARS-CoV S protein in complex with Receptor Binding Domain antibo...

SupramoleculeName: SARS-CoV S protein in complex with Receptor Binding Domain antibody DH1047
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Severe acute respiratory syndrome-related coronavirus

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Macromolecule #1: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 1
Details: C-term Expression tags: GYIPEAPRDGQAYVRKDGEWVLLSTFL = T4 fibritin trimerization motif LEVLFQ = HRV3C protease site HHHHHHHH = His Tag WSHPQFEKGGGSGGGGSGGSAWSHPQFEK = Strep tag
Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus
Molecular weightTheoretical: 140.644547 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MFIFLLFLTL TSGSDLDRCT TFDDVQAPNY TQHTSSMRGV YYPDEIFRSD TLYLTQDLFL PFYSNVTGFH TINHTFGNPV IPFKDGIYF AATEKSNVVR GWVFGSTMNN KSQSVIIINN STNVVIRACN FELCDNPFFA VSKPMGTQTH TMIFDNAFNC T FEYISDAF ...String:
MFIFLLFLTL TSGSDLDRCT TFDDVQAPNY TQHTSSMRGV YYPDEIFRSD TLYLTQDLFL PFYSNVTGFH TINHTFGNPV IPFKDGIYF AATEKSNVVR GWVFGSTMNN KSQSVIIINN STNVVIRACN FELCDNPFFA VSKPMGTQTH TMIFDNAFNC T FEYISDAF SLDVSEKSGN FKHLREFVFK NKDGFLYVYK GYQPIDVVRD LPSGFNTLKP IFKLPLGINI TNFRAILTAF SP AQDIWGT SAAAYFVGYL KPTTFMLKYD ENGTITDAVD CSQNPLAELK CSVKSFEIDK GIYQTSNFRV VPSGDVVRFP NIT NLCPFG EVFNATKFPS VYAWERKKIS NCVADYSVLY NSTFFSTFKC YGVSATKLND LCFSNVYADS FVVKGDDVRQ IAPG QTGVI ADYNYKLPDD FMGCVLAWNT RNIDATSTGN YNYKYRYLRH GKLRPFERDI SNVPFSPDGK PCTPPALNCY WPLND YGFY TTTGIGYQPY RVVVLSFELL NAPATVCGPK LSTDLIKNQC VNFNFNGLTG TGVLTPSSKR FQPFQQFGRD VSDFTD SVR DPKTSEILDI SPCSFGGVSV ITPGTNASSE VAVLYQDVNC TDVSTAIHAD QLTPAWRIYS TGNNVFQTQA GCLIGAE HV DTSYECDIPI GAGICASYHT VSLLRSTSQK SIVAYTMSLG ADSSIAYSNN TIAIPTNFSI SITTEVMPVS MAKTSVDC N MYICGDSTEC ANLLLQYGSF CTQLNRALSG IAAEQDRNTR EVFAQVKQMY KTPTLKYFGG FNFSQILPDP LKPTKRSFI EDLLFNKVTL ADAGFMKQYG ECLGDINARD LICAQKFNGL TVLPPLLTDD MIAAYTAALV SGTATAGWTF GAGAALQIPF AMQMAYRFN GIGVTQNVLY ENQKQIANQF NKAISQIQES LTTTSTALGK LQDVVNQNAQ ALNTLVKQLS SNFGAISSVL N DILSRLDP PEAEVQIDRL ITGRLQSLQT YVTQQLIRAA EIRASANLAA TKMSECVLGQ SKRVDFCGKG YHLMSFPQAA PH GVVFLHV TYVPSQERNF TTAPAICHEG KAYFPREGVF VFNGTSWFIT QRNFFSPQII TTDNTFVSGN CDVVIGIINN TVY DPLQPE LDSFKEELDK YFKNHTSPDV DLGDISGINA SVVNIQKEID RLNEVAKNLN ESLIDLQELG KYEQGSGYIP EAPR DGQAY VRKDGEWVLL STFLGRSLEV LFQGPGHHHH HHHHSAWSHP QFEKGGGSGG GGSGGSAWSH PQFEK

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Macromolecule #2: DH1047 Heavy chain

MacromoleculeName: DH1047 Heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.834654 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLVQSGAE VKKPGASVQV SCQASANTFT NHYIHWVRQA PGQGLEWMGI IYPTGGNTIY AQGFQGRVTM TRDTSLNTIY LELSSLRSE DTAVYYCARD VRVDDSWSGY DLLSGGTYFD YWGQGTLVTV SSASTKGPSV FPLAPSSKST SGGTAALGCL V KDYFPEPV ...String:
QVQLVQSGAE VKKPGASVQV SCQASANTFT NHYIHWVRQA PGQGLEWMGI IYPTGGNTIY AQGFQGRVTM TRDTSLNTIY LELSSLRSE DTAVYYCARD VRVDDSWSGY DLLSGGTYFD YWGQGTLVTV SSASTKGPSV FPLAPSSKST SGGTAALGCL V KDYFPEPV TVSWNSGALT SGVHTFPAVL QSSGLYSLSS VVTVPSSSLG TQTYICNVNH KPSNTKVDKK VEPK

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Macromolecule #3: DH1047 light chain

MacromoleculeName: DH1047 light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.398033 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIVMTQSPDS LAVSLGERAT INCRSSQSVL YSSNNENYLA WYQQKPGQPP KLLIYWASTR ESGIPDRFSG SGSGTDFTLT ISRLQAEDV AVYYCQQYYS LPRTFGQGTK VEIKRTVAAP SVFIFPPSDE QLKSGTASVV CLLNNFYPRE AKVQWKVDNA L QSGNSQES ...String:
DIVMTQSPDS LAVSLGERAT INCRSSQSVL YSSNNENYLA WYQQKPGQPP KLLIYWASTR ESGIPDRFSG SGSGTDFTLT ISRLQAEDV AVYYCQQYYS LPRTFGQGTK VEIKRTVAAP SVFIFPPSDE QLKSGTASVV CLLNNFYPRE AKVQWKVDNA L QSGNSQES VTEQDSKDST YSLSSTLTLS KADYEKHKVY ACEVTHQGLS SPVTKSFNRG EC

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 47 / 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

Concentration1.5 mg/mL
BufferpH: 8
GridModel: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 54.1 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7ld1


Details: Kabat numbering for the Fab used as in this model
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.43 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 284619

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