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Yorodumi- EMDB-33552: Local structure of BD55-5514 and BD55-5840 Fab and Omicron BA.1 R... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33552 | |||||||||
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Title | Local structure of BD55-5514 and BD55-5840 Fab and Omicron BA.1 RBD complex | |||||||||
Map data | Local map of BD5514_5840_Omicron_S6P | |||||||||
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 | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.42 Å | |||||||||
Authors | Zhang Z / Xiao J | |||||||||
Funding support | China, 1 items
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Citation | Journal: Cell Rep / Year: 2022 Title: Rational identification of potent and broad sarbecovirus-neutralizing antibody cocktails from SARS convalescents. Authors: Yunlong Cao / Fanchong Jian / Zhiying Zhang / Ayijiang Yisimayi / Xiaohua Hao / Linlin Bao / Fei Yuan / Yuanling Yu / Shuo Du / Jing Wang / Tianhe Xiao / Weiliang Song / Ying Zhang / Pulan ...Authors: Yunlong Cao / Fanchong Jian / Zhiying Zhang / Ayijiang Yisimayi / Xiaohua Hao / Linlin Bao / Fei Yuan / Yuanling Yu / Shuo Du / Jing Wang / Tianhe Xiao / Weiliang Song / Ying Zhang / Pulan Liu / Ran An / Peng Wang / Yao Wang / Sijie Yang / Xiao Niu / Yuhang Zhang / Qingqing Gu / Fei Shao / Yaling Hu / Weidong Yin / Aihua Zheng / Youchun Wang / Chuan Qin / Ronghua Jin / Junyu Xiao / Xiaoliang Sunney Xie / Abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron sublineages have escaped most receptor-binding domain (RBD)-targeting therapeutic neutralizing antibodies (NAbs), which proves ...Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron sublineages have escaped most receptor-binding domain (RBD)-targeting therapeutic neutralizing antibodies (NAbs), which proves that previous NAb drug screening strategies are deficient against the fast-evolving SARS-CoV-2. Better broad NAb drug candidate selection methods are needed. Here, we describe a rational approach for identifying RBD-targeting broad SARS-CoV-2 NAb cocktails. Based on high-throughput epitope determination, we propose that broad NAb drugs should target non-immunodominant RBD epitopes to avoid herd-immunity-directed escape mutations. Also, their interacting antigen residues should focus on sarbecovirus conserved sites and associate with critical viral functions, making the antibody-escaping mutations less likely to appear. Following these criteria, a featured non-competing antibody cocktail, SA55+SA58, is identified from a large collection of broad sarbecovirus NAbs isolated from SARS-CoV-2-vaccinated SARS convalescents. SA55+SA58 potently neutralizes ACE2-utilizing sarbecoviruses, including circulating Omicron variants, and could serve as broad SARS-CoV-2 prophylactics to offer long-term protection, especially for individuals who are immunocompromised or with high-risk comorbidities. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33552.map.gz | 168.1 MB | EMDB map data format | |
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Header (meta data) | emd-33552-v30.xml emd-33552.xml | 18.4 KB 18.4 KB | Display Display | EMDB header |
Images | emd_33552.png | 63 KB | ||
Others | emd_33552_half_map_1.map.gz emd_33552_half_map_2.map.gz | 164.9 MB 164.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33552 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33552 | HTTPS FTP |
-Validation report
Summary document | emd_33552_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_33552_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_33552_validation.xml.gz | 14.9 KB | Display | |
Data in CIF | emd_33552_validation.cif.gz | 17.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33552 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33552 | HTTPS FTP |
-Related structure data
Related structure data | 7y0wMC 7wrjC 7wryC 7y0cC 7y0vC 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_33552.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Local map of BD5514_5840_Omicron_S6P | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.04 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: half A map of BD5514 5840 Omicron S6P
File | emd_33552_half_map_1.map | ||||||||||||
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Annotation | half A map of BD5514_5840_Omicron_S6P | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half B map of BD5514 5840 Omicron S6P
File | emd_33552_half_map_2.map | ||||||||||||
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Annotation | half B map of BD5514_5840_Omicron_S6P | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Local structure of BD55-5514 and BD55-5840 Fab and Omicron BA.1 R...
Entire | Name: Local structure of BD55-5514 and BD55-5840 Fab and Omicron BA.1 RBD complex |
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Components |
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-Supramolecule #1: Local structure of BD55-5514 and BD55-5840 Fab and Omicron BA.1 R...
Supramolecule | Name: Local structure of BD55-5514 and BD55-5840 Fab and Omicron BA.1 RBD complex type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: BD55-5514H
Macromolecule | Name: BD55-5514H / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 13.237812 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QVQLVQSGAE VKKPGSSVKV SCKASGGTFR SHVISWVRQA PGQGLEWMGG FIPLFGTTIY AQAFQGRVMI SADESTSTAY MELSSLRSE DTAVYFCARL FPNGDPNSPE DGFDIWGQGT LVTV |
-Macromolecule #2: BD55-5514L
Macromolecule | Name: BD55-5514L / 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: 11.750876 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: DIQMTQSPSS LSASVGDRVT ITCQASQDIG NYLNWYQQKP GKAPKLLIYD ASHLETGVPS RFSGSGSGTD FTFTISSLQP EDIATYYCQ RYDDLPSYTF GQGTKVEI |
-Macromolecule #3: BD55-5840H
Macromolecule | Name: BD55-5840H / 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: 13.136394 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: VQLAQSGSEL RKPGASVKVS CDTSGHSFTS NAIHWVRQAP GQGLEWMGWI NTDTGTPTYA QGFTGRFVFS LDTSARTAYL QISSLKADD TAVFYCARER DYSDYFFDYW GQGTLVTVSS |
-Macromolecule #4: BD55-5840L
Macromolecule | Name: BD55-5840L / 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: 11.635954 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: EVVMTQSPAS LSVSPGERAT LSCRARASLG ISTDLAWYQQ RPGQAPRLLI YGASTRATGI PARFSGSGSG TEFTLTISSL QSEDSAVYY CQQYSNWPLT FGGGTKVEIK |
-Macromolecule #5: Spike protein S1
Macromolecule | Name: Spike protein S1 / 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: 21.983895 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: LCPFDEVFNA TRFASVYAWN RKRISNCVAD YSVLYNLAPF FTFKCYGVSP TKLNDLCFTN VYADSFVIRG DEVRQIAPGQ TGNIADYNY KLPDDFTGCV IAWNSNKLDS KVSGNYNYLY RLFRKSNLKP FERDISTEIY QAGNKPCNGV AGFNCYFPLR S YSFRPTYG ...String: LCPFDEVFNA TRFASVYAWN RKRISNCVAD YSVLYNLAPF FTFKCYGVSP TKLNDLCFTN VYADSFVIRG DEVRQIAPGQ TGNIADYNY KLPDDFTGCV IAWNSNKLDS KVSGNYNYLY RLFRKSNLKP FERDISTEIY QAGNKPCNGV AGFNCYFPLR S YSFRPTYG VGHQPYRVVV LSFELLHAPA TVCGK |
-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: OTHER |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 1.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: OTHER / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.42 Å / Resolution method: FSC 1/2 BIT CUT-OFF / Number images used: 3985 |
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Initial angle assignment | Type: OTHER |
Final angle assignment | Type: OTHER |