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Yorodumi- EMDB-25794: Cryo-EM structure of SARS-CoV-2 spike in complex with antibodies ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-25794 | |||||||||
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Title | Cryo-EM structure of SARS-CoV-2 spike in complex with antibodies B1-182.1 and A19-61.1 | |||||||||
Map data | cryo-EM map of SARS-CoV-2 spike in complex with antibody B1-182.1 and A19-61.1 | |||||||||
Sample |
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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 / entry receptor-mediated virion attachment to host cell ...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 / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / membrane fusion / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / 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 / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.83 Å | |||||||||
Authors | Zhou T / Tsybovsky T / Kwong PD | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Science / Year: 2022 Title: Structural basis for potent antibody neutralization of SARS-CoV-2 variants including B.1.1.529. Authors: Tongqing Zhou / Lingshu Wang / John Misasi / Amarendra Pegu / Yi Zhang / Darcy R Harris / Adam S Olia / Chloe Adrienna Talana / Eun Sung Yang / Man Chen / Misook Choe / Wei Shi / I-Ting Teng ...Authors: Tongqing Zhou / Lingshu Wang / John Misasi / Amarendra Pegu / Yi Zhang / Darcy R Harris / Adam S Olia / Chloe Adrienna Talana / Eun Sung Yang / Man Chen / Misook Choe / Wei Shi / I-Ting Teng / Adrian Creanga / Claudia Jenkins / Kwanyee Leung / Tracy Liu / Erik-Stephane D Stancofski / Tyler Stephens / Baoshan Zhang / Yaroslav Tsybovsky / Barney S Graham / John R Mascola / Nancy J Sullivan / Peter D Kwong / Abstract: The rapid spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) B.1.1.529 (Omicron) variant and its resistance to neutralization by vaccinee and convalescent sera are driving a ...The rapid spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) B.1.1.529 (Omicron) variant and its resistance to neutralization by vaccinee and convalescent sera are driving a search for monoclonal antibodies with potent neutralization. To provide insight into effective neutralization, we determined cryo-electron microscopy structures and evaluated receptor binding domain (RBD) antibodies for their ability to bind and neutralize B.1.1.529. Mutations altered 16% of the B.1.1.529 RBD surface, clustered on an RBD ridge overlapping the angiotensin-converting enzyme 2 (ACE2)-binding surface and reduced binding of most antibodies. Substantial inhibitory activity was retained by select monoclonal antibodies-including A23-58.1, B1-182.1, COV2-2196, S2E12, A19-46.1, S309, and LY-CoV1404-that accommodated these changes and neutralized B.1.1.529. We identified combinations of antibodies with synergistic neutralization. The analysis revealed structural mechanisms for maintenance of potent neutralization against emerging variants. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_25794.map.gz | 268.4 MB | EMDB map data format | |
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Header (meta data) | emd-25794-v30.xml emd-25794.xml | 25.9 KB 25.9 KB | Display Display | EMDB header |
Images | emd_25794.png | 113.1 KB | ||
Masks | emd_25794_msk_1.map | 536.4 MB | Mask map | |
Others | emd_25794_additional_1.map.gz emd_25794_half_map_1.map.gz emd_25794_half_map_2.map.gz | 507.1 MB 497.4 MB 497.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-25794 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25794 | HTTPS FTP |
-Validation report
Summary document | emd_25794_validation.pdf.gz | 962 KB | Display | EMDB validaton report |
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Full document | emd_25794_full_validation.pdf.gz | 961.6 KB | Display | |
Data in XML | emd_25794_validation.xml.gz | 19.2 KB | Display | |
Data in CIF | emd_25794_validation.cif.gz | 22.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25794 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25794 | HTTPS FTP |
-Related structure data
Related structure data | 7tb8MC 7tbfC 7tc9C 7tcaC 7tccC 7u0dC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_25794.map.gz / Format: CCP4 / Size: 536.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | cryo-EM map of SARS-CoV-2 spike in complex with antibody B1-182.1 and A19-61.1 | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.873 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_25794_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: sharpened cryo-EM map of SARS-CoV-2 spike in complex...
File | emd_25794_additional_1.map | ||||||||||||
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Annotation | sharpened cryo-EM map of SARS-CoV-2 spike in complex with antibody B1-182.1 and A19-61.1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: cryo-EM half map of SARS-CoV-2 spike in complex...
File | emd_25794_half_map_1.map | ||||||||||||
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Annotation | cryo-EM half map of SARS-CoV-2 spike in complex with antibody B1-182.1 and A19-61.1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: cryo-EM half map of SARS-CoV-2 spike in complex...
File | emd_25794_half_map_2.map | ||||||||||||
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Annotation | cryo-EM half map of SARS-CoV-2 spike in complex with antibody B1-182.1 and A19-61.1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : SARS-CoV-2 spike in complex with antibodies B1-182.1 and A19-61.1
Entire | Name: SARS-CoV-2 spike in complex with antibodies B1-182.1 and A19-61.1 |
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Components |
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-Supramolecule #1: SARS-CoV-2 spike in complex with antibodies B1-182.1 and A19-61.1
Supramolecule | Name: SARS-CoV-2 spike in complex with antibodies B1-182.1 and A19-61.1 type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Recombinant expression | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 570 KDa |
-Macromolecule #1: Spike glycoprotein
Macromolecule | Name: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Molecular weight | Theoretical: 132.306406 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 TQTNSPGSAS SVASQSIIAY TMSLGAENSV AYSNNSIAIP TNFTISVTTE ILPVSMTK T SVDCTMYICG DSTECSNLLL QYGSFCTQLN RALTGIAVEQ DKNTQEVFAQ VKQIYKTPPI KDFGGFNFSQ ILPDPSKPS KRSFIEDLLF NKVTLADAGF IKQYGDCLGD IAARDLICAQ KFNGLTVLPP LLTDEMIAQY TSALLAGTIT SGWTFGAGAA LQIPFAMQM AYRFNGIGVT QNVLYENQKL IANQFNSAIG KIQDSLSSTA 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 LQELGKYEQ |
-Macromolecule #2: The heavy chain of SARS-CoV-2 antibody A19-61.1
Macromolecule | Name: The heavy chain of SARS-CoV-2 antibody A19-61.1 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 13.934431 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QVQLVESGGG VVQPGRSLRL SCAASGFTFS SYAFHWVRQA PGKGLEWVAV ISYDGSNQYY ADSVKGRFTI SRDNSKNTLY LQMNSLRAD DTAVYYCARD LAIAVAGTWH YYNGMDVWGQ GTTVTVSS |
-Macromolecule #3: The light chain of SARS-COV-2 antibody A19-61.1
Macromolecule | Name: The light chain of SARS-COV-2 antibody A19-61.1 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 11.571899 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: DIQMTQSPSS VSASVGDRVI ITCRASQGIS SWLAWYQQKP GKAPKVLIYD ASSLQSGVPS RFSGSGYGTD FTLTISSLQP EDSATYYCQ QAKSFPITFG QGTRLEIK |
-Macromolecule #4: The heavy chain of SARS-CoV-2 antiboddy antibody B1-182.1
Macromolecule | Name: The heavy chain of SARS-CoV-2 antiboddy antibody B1-182.1 type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 13.473101 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QMQLVQSGPE VKKPGTSVKV SCKASGFTFT SSAVQWVRQA RGQRLEWIGW IVVGSGNTNY AQKFQERVTI TRDMSTSTAY MELSSLRSE DTAVYYCAAP YCSGGSCFDG FDIWGQGTMV TVSS |
-Macromolecule #5: The light chain of SARS-COV-2 antibody B1-182.1
Macromolecule | Name: The light chain of SARS-COV-2 antibody B1-182.1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 11.775985 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: EIVLTQSPGT LSLSPGERAT LSCRASQSVS SSYLAWYQQK PGQAPRLLIY GASSRATGFP DRFSGSGSGT DFTLTISRLE PEDFAVYYC QQYGNSPWTF GQGTKVEIR |
-Macromolecule #8: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 8 / Number of copies: 25 / 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 | 0.5 mg/mL |
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Buffer | pH: 7.4 / Details: 100 mM HEPES, pH 7.4, 150 mM NaCl |
Grid | Material: GOLD |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Blot for 2-3.5 seconds before plugging.. |
Details | Spike at 0.5 mg/mL concentration in the buffer, Fabs are 1.2 fold in molar ratio. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: OTHER / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |