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Yorodumi- EMDB-23166: Cryo-EM structure of the SARS-CoV-2 spike glycoprotein bound to F... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23166 | |||||||||
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Title | Cryo-EM structure of the SARS-CoV-2 spike glycoprotein bound to Fab 2-15 | |||||||||
Map data | Sharpened concensus map | |||||||||
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 / Attachment and Entry / membrane fusion / 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 | Homo sapiens (human) / Severe acute respiratory syndrome coronavirus 2 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.87 Å | |||||||||
Authors | Rapp M / Shapiro L | |||||||||
Citation | Journal: Cell Rep / Year: 2021 Title: Modular basis for potent SARS-CoV-2 neutralization by a prevalent VH1-2-derived antibody class. Authors: Micah Rapp / Yicheng Guo / Eswar R Reddem / Jian Yu / Lihong Liu / Pengfei Wang / Gabriele Cerutti / Phinikoula Katsamba / Jude S Bimela / Fabiana A Bahna / Seetha M Mannepalli / Baoshan ...Authors: Micah Rapp / Yicheng Guo / Eswar R Reddem / Jian Yu / Lihong Liu / Pengfei Wang / Gabriele Cerutti / Phinikoula Katsamba / Jude S Bimela / Fabiana A Bahna / Seetha M Mannepalli / Baoshan Zhang / Peter D Kwong / Yaoxing Huang / David D Ho / Lawrence Shapiro / Zizhang Sheng / Abstract: Antibodies with heavy chains that derive from the VH1-2 gene constitute some of the most potent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-neutralizing antibodies yet identified. To ...Antibodies with heavy chains that derive from the VH1-2 gene constitute some of the most potent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-neutralizing antibodies yet identified. To provide insight into whether these genetic similarities inform common modes of recognition, we determine the structures of the SARS-CoV-2 spike in complex with three VH1-2-derived antibodies: 2-15, 2-43, and H4. All three use VH1-2-encoded motifs to recognize the receptor-binding domain (RBD), with heavy-chain N53I-enhancing binding and light-chain tyrosines recognizing F486. Despite these similarities, class members bind both RBD-up and -down conformations of the spike, with a subset of antibodies using elongated CDRH3s to recognize glycan N343 on a neighboring RBD-a quaternary interaction accommodated by an increase in RBD separation of up to 12 Å. The VH1-2 antibody class, thus, uses modular recognition encoded by modular genetic elements to effect potent neutralization, with the VH-gene component specifying recognition of RBD and the CDRH3 component specifying quaternary interactions. | |||||||||
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_23166.map.gz | 204.4 MB | EMDB map data format | |
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Header (meta data) | emd-23166-v30.xml emd-23166.xml | 21.3 KB 21.3 KB | Display Display | EMDB header |
Images | emd_23166.png | 45.9 KB | ||
Others | emd_23166_additional_1.map.gz emd_23166_additional_2.map.gz emd_23166_half_map_1.map.gz emd_23166_half_map_2.map.gz | 104.2 MB 106.8 MB 202 MB 202 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23166 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23166 | HTTPS FTP |
-Validation report
Summary document | emd_23166_validation.pdf.gz | 446.5 KB | Display | EMDB validaton report |
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Full document | emd_23166_full_validation.pdf.gz | 446 KB | Display | |
Data in XML | emd_23166_validation.xml.gz | 15.4 KB | Display | |
Data in CIF | emd_23166_validation.cif.gz | 18.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23166 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23166 | HTTPS FTP |
-Related structure data
Related structure data | 7l57MC 7l56C 7l58C 7l5bC 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_23166.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Sharpened concensus map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Unsharpened local refinement of Fab & RBD
File | emd_23166_additional_1.map | ||||||||||||
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Annotation | Unsharpened local refinement of Fab & RBD | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Global refinement
File | emd_23166_additional_2.map | ||||||||||||
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Annotation | Global refinement | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Concensus half map A for FSC calculation
File | emd_23166_half_map_1.map | ||||||||||||
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Annotation | Concensus half map A for FSC calculation | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Concensus half map B for FSC calculation
File | emd_23166_half_map_2.map | ||||||||||||
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Annotation | Concensus half map B for FSC calculation | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Cryo-EM structure of the SARS-CoV-2 spike glycoprotein bound to F...
Entire | Name: Cryo-EM structure of the SARS-CoV-2 spike glycoprotein bound to Fab 2-15 |
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Components |
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-Supramolecule #1: Cryo-EM structure of the SARS-CoV-2 spike glycoprotein bound to F...
Supramolecule | Name: Cryo-EM structure of the SARS-CoV-2 spike glycoprotein bound to Fab 2-15 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
-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: 142.399375 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MFVFLVLLPL VSSQCVNLTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHAIHV SGTNGTKRFD NPVLPFNDG VYFASTEKSN IIRGWIFGTT LDSKTQSLLI VNNATNVVIK VCEFQFCNDP FLGVYYHKNN KSWMESEFRV Y SSANNCTF ...String: MFVFLVLLPL VSSQCVNLTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHAIHV SGTNGTKRFD NPVLPFNDG VYFASTEKSN IIRGWIFGTT LDSKTQSLLI VNNATNVVIK VCEFQFCNDP FLGVYYHKNN KSWMESEFRV Y SSANNCTF EYVSQPFLMD LEGKQGNFKN LREFVFKNID GYFKIYSKHT PINLVRDLPQ GFSALEPLVD LPIGINITRF QT LLALHRS YLTPGDSSSG WTAGAAAYYV GYLQPRTFLL KYNENGTITD AVDCALDPLS ETKCTLKSFT VEKGIYQTSN FRV QPTESI VRFPNITNLC PFGEVFNATR FASVYAWNRK RISNCVADYS VLYNSASFST FKCYGVSPTK LNDLCFTNVY ADSF VIRGD EVRQIAPGQT GKIADYNYKL PDDFTGCVIA WNSNNLDSKV GGNYNYLYRL FRKSNLKPFE RDISTEIYQA GSTPC NGVE GFNCYFPLQS YGFQPTNGVG YQPYRVVVLS FELLHAPATV CGPKKSTNLV KNKCVNFNFN GLTGTGVLTE SNKKFL PFQ QFGRDIADTT DAVRDPQTLE ILDITPCSFG GVSVITPGTN TSNQVAVLYQ DVNCTEVPVA IHADQLTPTW RVYSTGS NV FQTRAGCLIG AEHVNNSYEC DIPIGAGICA SYQTQTNSPG SASSVASQSI IAYTMSLGAE NSVAYSNNSI AIPTNFTI S VTTEILPVSM TKTSVDCTMY ICGDSTECSN LLLQYGSFCT QLNRALTGIA VEQDKNTQEV FAQVKQIYKT PPIKDFGGF NFSQILPDPS KPSKRSFIED LLFNKVTLAD AGFIKQYGDC LGDIAARDLI CAQKFNGLTV LPPLLTDEMI AQYTSALLAG TITSGWTFG AGAALQIPFA MQMAYRFNGI GVTQNVLYEN QKLIANQFNS AIGKIQDSLS STASALGKLQ DVVNQNAQAL N TLVKQLSS NFGAISSVLN DILSRLDPPE AEVQIDRLIT GRLQSLQTYV TQQLIRAAEI RASANLAATK MSECVLGQSK RV DFCGKGY HLMSFPQSAP HGVVFLHVTY VPAQEKNFTT APAICHDGKA HFPREGVFVS NGTHWFVTQR NFYEPQIITT DNT FVSGNC DVVIGIVNNT VYDPLQPELD SFKEELDKYF KNHTSPDVDL GDISGINASV VNIQKEIDRL NEVAKNLNES LIDL QELGK YEQGSGYIPE APRDGQAYVR KDGEWVLLST FLGRSLEVLF QGPGHHHHHH HHSAWSHPQF EKGGGSGGGG SGGSA WSHP QFEK |
-Macromolecule #2: Fab 2-15 variable domain heavy chain
Macromolecule | Name: Fab 2-15 variable domain 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: 14.008706 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: VQLVQSGAEV KKPGASVRVS CKASGYTFTG YYMHWVRQAP GQGLEWMGWI NPISDGTNYA QKFQGWVTMT RDTSISTVYM ELSRLRSDD TAVYYCARGG SRCSGGNCYG WAYDAFDIWG QGTMITV |
-Macromolecule #3: Fab 2-15 variable domain light chain
Macromolecule | Name: Fab 2-15 variable domain 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: 11.342411 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: SALTQPASVS GSPGQSITIS CTGTSSDVGG YNFVSWYQQH PGKAPKLMIY DVSKRPSGVS NRFSGSKSGN TASLTISGLQ AEDEADCYC SSYTSSSTFV FGTGTKVTVL G |
-Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 31 / 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
Buffer | pH: 5.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 52.4 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 5.87 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 16590 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |