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Yorodumi- EMDB-34653: SARS-CoV-2 Omicron BA.1 spike trimer (6P) in complex with YB9-258... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34653 | ||||||||||||
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Title | SARS-CoV-2 Omicron BA.1 spike trimer (6P) in complex with YB9-258 Fab, focused refinement of Fab region | ||||||||||||
Map data | |||||||||||||
Sample |
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Keywords | Spike protein / RBD / Antibody / Fab / Viral protein / VIRAL PROTEIN-IMMUNE SYSTEM complex | ||||||||||||
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 / membrane fusion / receptor-mediated endocytosis of virus by host cell / 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: 4.69 Å | ||||||||||||
Authors | Liu B / Gao X / Chen Q / Li Z / Su M / He J / Xiong X | ||||||||||||
Funding support | 3 items
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Citation | Journal: Nat Commun / Year: 2023 Title: Somatically hypermutated antibodies isolated from SARS-CoV-2 Delta infected patients cross-neutralize heterologous variants. Authors: Haisheng Yu / Banghui Liu / Yudi Zhang / Xijie Gao / Qian Wang / Haitao Xiang / Xiaofang Peng / Caixia Xie / Yaping Wang / Peiyu Hu / Jingrong Shi / Quan Shi / Pingqian Zheng / Chengqian ...Authors: Haisheng Yu / Banghui Liu / Yudi Zhang / Xijie Gao / Qian Wang / Haitao Xiang / Xiaofang Peng / Caixia Xie / Yaping Wang / Peiyu Hu / Jingrong Shi / Quan Shi / Pingqian Zheng / Chengqian Feng / Guofang Tang / Xiaopan Liu / Liliangzi Guo / Xiumei Lin / Jiaojiao Li / Chuanyu Liu / Yaling Huang / Naibo Yang / Qiuluan Chen / Zimu Li / Mengzhen Su / Qihong Yan / Rongjuan Pei / Xinwen Chen / Longqi Liu / Fengyu Hu / Dan Liang / Bixia Ke / Changwen Ke / Feng Li / Jun He / Meiniang Wang / Ling Chen / Xiaoli Xiong / Xiaoping Tang / Abstract: SARS-CoV-2 Omicron variants feature highly mutated spike proteins with extraordinary abilities in evading antibodies isolated earlier in the pandemic. Investigation of memory B cells from patients ...SARS-CoV-2 Omicron variants feature highly mutated spike proteins with extraordinary abilities in evading antibodies isolated earlier in the pandemic. Investigation of memory B cells from patients primarily with breakthrough infections with the Delta variant enables isolation of a number of neutralizing antibodies cross-reactive to heterologous variants of concern (VOCs) including Omicron variants (BA.1-BA.4). Structural studies identify altered complementarity determining region (CDR) amino acids and highly unusual heavy chain CDR2 insertions respectively in two representative cross-neutralizing antibodies-YB9-258 and YB13-292. These features are putatively introduced by somatic hypermutation and they are heavily involved in epitope recognition to broaden neutralization breadth. Previously, insertions/deletions were rarely reported for antiviral antibodies except for those induced by HIV-1 chronic infections. These data provide molecular mechanisms for cross-neutralization of heterologous SARS-CoV-2 variants by antibodies isolated from Delta variant infected patients with implications for future vaccination strategy. | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_34653.map.gz | 59.4 MB | EMDB map data format | |
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Header (meta data) | emd-34653-v30.xml emd-34653.xml | 21.7 KB 21.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_34653_fsc.xml | 11.8 KB | Display | FSC data file |
Images | emd_34653.png | 34.4 KB | ||
Filedesc metadata | emd-34653.cif.gz | 6.4 KB | ||
Others | emd_34653_half_map_1.map.gz emd_34653_half_map_2.map.gz | 59.4 MB 59.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34653 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34653 | HTTPS FTP |
-Validation report
Summary document | emd_34653_validation.pdf.gz | 822.1 KB | Display | EMDB validaton report |
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Full document | emd_34653_full_validation.pdf.gz | 821.7 KB | Display | |
Data in XML | emd_34653_validation.xml.gz | 15.5 KB | Display | |
Data in CIF | emd_34653_validation.cif.gz | 20.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34653 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34653 | HTTPS FTP |
-Related structure data
Related structure data | 8hc6MC 8hc2C 8hc3C 8hc4C 8hc5C 8hc7C 8hc8C 8hc9C 8hcaC 8hcbC 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_34653.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.65 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_34653_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_34653_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : SARS-CoV-2 Omicron BA.1 Spike (6P) in complex with YB13-292 Fab, ...
Entire | Name: SARS-CoV-2 Omicron BA.1 Spike (6P) in complex with YB13-292 Fab, focused refinement of RBD region |
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Components |
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-Supramolecule #1: SARS-CoV-2 Omicron BA.1 Spike (6P) in complex with YB13-292 Fab, ...
Supramolecule | Name: SARS-CoV-2 Omicron BA.1 Spike (6P) in complex with YB13-292 Fab, focused refinement of RBD region type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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-Supramolecule #2: SARS-CoV-2 Omicron BA.1 Spike protein
Supramolecule | Name: SARS-CoV-2 Omicron BA.1 Spike protein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1, #4 |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
-Supramolecule #3: YB13-292 Fab
Supramolecule | Name: YB13-292 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Spike protein S1
Macromolecule | Name: Spike protein S1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Molecular weight | Theoretical: 30.244215 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: PTESIVRFPN ITNLCPFDEV FNATRFASVY AWNRKRISNC VADYSVLYNL APFFTFKCYG VSPTKLNDLC FTNVYADSFV IRGDEVRQI APGQTGNIAD YNYKLPDDFT GCVIAWNSNK LDSKVSGNYN YLYRLFRKSN LKPFERDIST EIYQAGNKPC N GVAGFNCY ...String: PTESIVRFPN ITNLCPFDEV FNATRFASVY AWNRKRISNC VADYSVLYNL APFFTFKCYG VSPTKLNDLC FTNVYADSFV IRGDEVRQI APGQTGNIAD YNYKLPDDFT GCVIAWNSNK LDSKVSGNYN YLYRLFRKSN LKPFERDIST EIYQAGNKPC N GVAGFNCY FPLRSYSFRP TYGVGHQPYR VVVLSFELLH APATVCGPKK STNLVKNKCV NFNFNGLKGT GVLTESNKKF LP FQQFGRD IADTTDAVRD PQTLEILDIT UniProtKB: Spike glycoprotein |
-Macromolecule #2: Heavy chain of YB9-258 Fab
Macromolecule | Name: Heavy chain of YB9-258 Fab / 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: 23.126922 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: EVQLVESGGG LIQPGGSLRL SCAASGLTVS SNYMHWVRQA PGKGLEWVSV LYAGGSAFYA DSVKGRFTIS RNNSKNTLYL QMNSLRAED TAIYYCARGL GDYLDSWGQG TLVTVSSAST KGPSVFPLAP SSKSTSGGTA ALGCLVKDYF PEPVTVSWNS G ALTSGVHT ...String: EVQLVESGGG LIQPGGSLRL SCAASGLTVS SNYMHWVRQA PGKGLEWVSV LYAGGSAFYA DSVKGRFTIS RNNSKNTLYL QMNSLRAED TAIYYCARGL GDYLDSWGQG TLVTVSSAST KGPSVFPLAP SSKSTSGGTA ALGCLVKDYF PEPVTVSWNS G ALTSGVHT FPAVLQSSGL YSLSSVVTVP SSSLGTQTYI CNVNHKPSNT KVDKKVEPKS CD |
-Macromolecule #3: Light chain of YB9-258
Macromolecule | Name: Light chain of YB9-258 / 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: 23.177754 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: DIQMTQSPSS VSASVGDRVT ITCRASQGIG SWLAWYQQKP GKAPQLLIYA ASTLQSGVPP RFSGSGSGTD FTLTITSLQP EDFASYYCQ QANSVLALTF GGGTKVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String: DIQMTQSPSS VSASVGDRVT ITCRASQGIG SWLAWYQQKP GKAPQLLIYA ASTLQSGVPP RFSGSGSGTD FTLTITSLQP EDFASYYCQ QANSVLALTF GGGTKVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC |
-Macromolecule #4: Spike protein S1
Macromolecule | Name: Spike protein S1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Molecular weight | Theoretical: 31.1381 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QCVNLTTRTQ LPPAYTNSFT RGVYYPDKVF RSSVLHSTQD LFLPFFSNVT WFHVISGTNG TKRFDNPVLP FNDGVYFASI EKSNIIRGW IFGTTLDSKT QSLLIVNNAT NVVIKVCEFQ FCNDPFLDHK NNKSWMESEF RVYSSANNCT FEYVSQPFLM D LEGKQGNF ...String: QCVNLTTRTQ LPPAYTNSFT RGVYYPDKVF RSSVLHSTQD LFLPFFSNVT WFHVISGTNG TKRFDNPVLP FNDGVYFASI EKSNIIRGW IFGTTLDSKT QSLLIVNNAT NVVIKVCEFQ FCNDPFLDHK NNKSWMESEF RVYSSANNCT FEYVSQPFLM D LEGKQGNF KNLREFVFKN IDGYFKIYSK HTPIIVREPE DLPQGFSALE PLVDLPIGIN ITRFQTLLAL HRSYLTPGDS SS GWTAGAA AYYVGYLQPR TFLLKYNENG TITDAV UniProtKB: Spike glycoprotein |
-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: 7 / 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: 8 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |