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Yorodumi- EMDB-23507: Cryo-EM structure of the SARS-CoV-2 spike glycoprotein bound to F... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23507 | |||||||||
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Title | Cryo-EM structure of the SARS-CoV-2 spike glycoprotein bound to Fab 2-7 | |||||||||
Map data | Sharpened global refinement | |||||||||
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 / 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 | |||||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.72 Å | |||||||||
Authors | Rapp M / Shapiro L | |||||||||
Citation | Journal: bioRxiv / Year: 2021 Title: Structural Basis for Accommodation of Emerging B.1.351 and B.1.1.7 Variants by Two Potent SARS-CoV-2 Neutralizing Antibodies. Authors: Gabriele Cerutti / Micah Rapp / Yicheng Guo / Fabiana Bahna / Jude Bimela / Eswar R Reddem / Jian Yu / Pengfei Wang / Lihong Liu / Yaoxing Huang / David D Ho / Peter D Kwong / Zizhang Sheng / Lawrence Shapiro Abstract: Emerging SARS-CoV-2 strains, B.1.1.7 and B.1.351, from the UK and South Africa, respectively show decreased neutralization by monoclonal antibodies and convalescent or vaccinee sera raised against ...Emerging SARS-CoV-2 strains, B.1.1.7 and B.1.351, from the UK and South Africa, respectively show decreased neutralization by monoclonal antibodies and convalescent or vaccinee sera raised against the original wild-type virus, and are thus of clinical concern. However, the neutralization potency of two antibodies, 1-57 and 2-7, which target the receptor-binding domain (RBD) of spike, was unaffected by these emerging strains. Here, we report cryo-EM structures of 1-57 and 2-7 in complex with spike, revealing each of these antibodies to utilize a distinct mechanism to bypass or accommodate RBD mutations. Notably, each antibody represented a response with recognition distinct from those of frequent antibody classes. Moreover, many epitope residues recognized by 1-57 and 2-7 were outside hotspots of evolutionary pressure for both ACE2 binding and neutralizing antibody escape. We suggest the therapeutic use of antibodies like 1-57 and 2-7, which target less prevalent epitopes, could ameliorate issues of monoclonal antibody escape. | |||||||||
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_23507.map.gz | 204.2 MB | EMDB map data format | |
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Header (meta data) | emd-23507-v30.xml emd-23507.xml | 31 KB 31 KB | Display Display | EMDB header |
Images | emd_23507.png | 87.4 KB | ||
Masks | emd_23507_msk_1.map | 216 MB | Mask map | |
Others | emd_23507_additional_1.map.gz emd_23507_additional_2.map.gz emd_23507_additional_3.map.gz emd_23507_additional_4.map.gz emd_23507_additional_5.map.gz emd_23507_additional_6.map.gz emd_23507_half_map_1.map.gz emd_23507_half_map_2.map.gz | 108.3 MB 204.2 MB 107.9 MB 200.6 MB 200.6 MB 1.4 MB 200.3 MB 200.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23507 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23507 | HTTPS FTP |
-Related structure data
Related structure data | 7lssMC 7ls9C 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_23507.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Sharpened global refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.058 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_23507_msk_1.map | ||||||||||||
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Density Histograms |
-Additional map: Unsharpened global refinement
File | emd_23507_additional_1.map | ||||||||||||
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Annotation | Unsharpened global refinement | ||||||||||||
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Density Histograms |
-Additional map: Sharpened local refinement
File | emd_23507_additional_2.map | ||||||||||||
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Annotation | Sharpened local refinement | ||||||||||||
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Density Histograms |
-Additional map: Unsharpened local refinement
File | emd_23507_additional_3.map | ||||||||||||
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Annotation | Unsharpened local refinement | ||||||||||||
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Density Histograms |
-Additional map: Local refinement half map A
File | emd_23507_additional_4.map | ||||||||||||
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Annotation | Local refinement half map A | ||||||||||||
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Density Histograms |
-Additional map: Local refinement half map B
File | emd_23507_additional_5.map | ||||||||||||
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Annotation | Local refinement half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Density modified consensus map
File | emd_23507_additional_6.map | ||||||||||||
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Annotation | Density modified consensus map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Global refinement half map A
File | emd_23507_half_map_1.map | ||||||||||||
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Annotation | Global refinement half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Global refinement half map B
File | emd_23507_half_map_2.map | ||||||||||||
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Annotation | Global refinement half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : SARS-CoV-2 spike glycoprotein in complex with Fab 2-7 variable domain
Entire | Name: SARS-CoV-2 spike glycoprotein in complex with Fab 2-7 variable domain |
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Components |
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-Supramolecule #1: SARS-CoV-2 spike glycoprotein in complex with Fab 2-7 variable domain
Supramolecule | Name: SARS-CoV-2 spike glycoprotein in complex with Fab 2-7 variable domain type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
-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 2-7 variable light chain
Macromolecule | Name: Fab 2-7 variable light 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: 11.182218 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: SALAQPASVS GSPGQSITIS CTGTSSDVGA YNYVSWYQQH PGKAPKLMIY DVSKRPSGVS NRFSGSKSGN TASLTISGLQ AEDEADYYC SSYTTSSTVF GGGTKLTVL |
-Macromolecule #3: Fab 2-7 variable heavy chain
Macromolecule | Name: Fab 2-7 variable heavy 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: 13.319156 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QITLKESGPT LVKPTQTLTL TCTFSGFSLS TSGVGVGWIR QPPGKALEWL ALIYWDDDKR YSPSLKSRLT ITKDTSKNQV VLTMTNMDP VDTATYYCAH HKIERIFDYW GQGTLVTVSS |
-Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 30 / 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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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 51.69 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
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Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.72 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 165576 |