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Yorodumi- EMDB-25105: Structure of SARS-CoV S protein in complex with Receptor Binding ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-25105 | |||||||||
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Title | Structure of SARS-CoV S protein in complex with Receptor Binding Domain antibody DH1047 | |||||||||
Map data | cryosparc generated map | |||||||||
Sample |
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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 / symbiont-mediated suppression of host innate immune response / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / identical protein binding / membrane Similarity search - Function | |||||||||
Biological species | Severe acute respiratory syndrome-related coronavirus / Severe acute respiratory syndrome coronavirus / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.43 Å | |||||||||
Authors | Gobeil S / Acharya P | |||||||||
Funding support | United States, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_25105.map.gz | 96.8 MB | EMDB map data format | |
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Header (meta data) | emd-25105-v30.xml emd-25105.xml | 16.3 KB 16.3 KB | Display Display | EMDB header |
Images | emd_25105.png | 73 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-25105 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25105 | HTTPS FTP |
-Validation report
Summary document | emd_25105_validation.pdf.gz | 420.5 KB | Display | EMDB validaton report |
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Full document | emd_25105_full_validation.pdf.gz | 420.1 KB | Display | |
Data in XML | emd_25105_validation.xml.gz | 6.5 KB | Display | |
Data in CIF | emd_25105_validation.cif.gz | 7.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25105 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25105 | HTTPS FTP |
-Related structure data
Related structure data | 7sg4MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_25105.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | cryosparc generated map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : SARS-CoV S protein in complex with Receptor Binding Domain antibo...
Entire | Name: SARS-CoV S protein in complex with Receptor Binding Domain antibody DH1047 |
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Components |
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-Supramolecule #1: SARS-CoV S protein in complex with Receptor Binding Domain antibo...
Supramolecule | Name: SARS-CoV S protein in complex with Receptor Binding Domain antibody DH1047 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Severe acute respiratory syndrome-related coronavirus |
-Macromolecule #1: Spike glycoprotein
Macromolecule | Name: 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 |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus |
Molecular weight | Theoretical: 140.644547 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Macromolecule #2: DH1047 Heavy chain
Macromolecule | Name: DH1047 Heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 24.834654 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Macromolecule #3: DH1047 light chain
Macromolecule | Name: DH1047 light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 24.398033 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 47 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.5 mg/mL |
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Buffer | pH: 8 |
Grid | Model: Quantifoil R1.2/1.3 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Instrument: LEICA EM GP |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 54.1 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: Details: Kabat numbering for the Fab used as in this model |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.43 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 284619 |
Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: NOT APPLICABLE |