[English] 日本語
Yorodumi- EMDB-34654: SARS-CoV-2 Omicron BA.1 spike trimer (6P) complex with YB9-258 Fa... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34654 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | SARS-CoV-2 Omicron BA.1 spike trimer (6P) complex with YB9-258 Fab, focused refinement of RBD-dimer region | ||||||||||||
Map data | |||||||||||||
Sample |
| ||||||||||||
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: 4.54 Å | ||||||||||||
Authors | Liu B / Gao X / Chen Q / Li Z / Su M / He J / Xiong X | ||||||||||||
Funding support | 3 items
| ||||||||||||
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 |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_34654.map.gz | 59.5 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-34654-v30.xml emd-34654.xml | 21.7 KB 21.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_34654_fsc.xml | 11.7 KB | Display | FSC data file |
Images | emd_34654.png | 37.4 KB | ||
Others | emd_34654_half_map_1.map.gz emd_34654_half_map_2.map.gz | 59.4 MB 59.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34654 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34654 | HTTPS FTP |
-Validation report
Summary document | emd_34654_validation.pdf.gz | 765.3 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_34654_full_validation.pdf.gz | 764.9 KB | Display | |
Data in XML | emd_34654_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | emd_34654_validation.cif.gz | 21 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34654 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34654 | HTTPS FTP |
-Related structure data
Related structure data | 8hc7MC 8hc2C 8hc3C 8hc4C 8hc5C 8hc6C 8hc8C 8hc9C 8hcaC 8hcbC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_34654.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.65 Å | ||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Half map: #2
File | emd_34654_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_34654_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : SARS-CoV-2 Omicron BA.1 spike trimer with in complex with YB9-258...
Entire | Name: SARS-CoV-2 Omicron BA.1 spike trimer with in complex with YB9-258 Fab, focused refinement of 2 RBD region |
---|---|
Components |
|
-Supramolecule #1: SARS-CoV-2 Omicron BA.1 spike trimer with in complex with YB9-258...
Supramolecule | Name: SARS-CoV-2 Omicron BA.1 spike trimer with in complex with YB9-258 Fab, focused refinement of 2 RBD region type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#4 |
---|
-Supramolecule #2: SARS-CoV_2 Omicron BA.1 spike protein
Supramolecule | Name: SARS-CoV_2 Omicron BA.1 spike protein / type: complex / ID: 2 / Chimera: Yes / Parent: 1 / Macromolecule list: #1-#2 |
---|---|
Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
-Supramolecule #3: YB9-258 Fab
Supramolecule | Name: YB9-258 Fab / type: complex / ID: 3 / Chimera: Yes / Parent: 1 / Macromolecule list: #3-#4 |
---|---|
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 |
---|---|
Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Molecular weight | Theoretical: 58.054379 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 TITDAVDCAL DPLSETKCTL KSFTVEKGIY QTSNFRVQPT ESIVRFPNIT NLC PFDEVF NATRFASVYA WNRKRISNCV ADYSVLYNLA PFFTFKCYGV SPTKLNDLCF TNVYADSFVI RGDEVRQIAP GQTG NIADY NYKLPDDFTG CVIAWNSNKL DSKVSGNYNY LYRLFRKSNL KPFERDISTE IYQAGNKPCN GVAGFNCYFP LRSYS FRPT YGVGHQPYRV VVLSFELLHA PATVCG |
-Macromolecule #2: Spike protein S1
Macromolecule | Name: Spike protein S1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
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 |
-Macromolecule #3: Heavy chain variable region of YB9-258
Macromolecule | Name: Heavy chain variable region of YB9-258 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 12.356818 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: EVQLVESGGG LIQPGGSLRL SCAASGLTVS SNYMHWVRQA PGKGLEWVSV LYAGGSAFYA DSVKGRFTIS RNNSKNTLYL QMNSLRAED TAIYYCARGL GDYLDSWGQG TLVTVS |
-Macromolecule #4: Light chain variable region of YB9-258
Macromolecule | Name: Light chain variable region of YB9-258 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 11.288553 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: DIQMTQSPSS VSASVGDRVT ITCRASQGIG SWLAWYQQKP GKAPQLLIYA ASTLQSGVPP RFSGSGSGTD FTLTITSLQP EDFASYYCQ QANSVLALTF GGGTKVEI |
-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 |
---|---|
Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
---|---|
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
---|---|
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 |