+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32395 | |||||||||
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Title | local structure of hu33 and spike | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Surface glycoprotein Function and homology information | |||||||||
Biological species | Homo sapiens (human) / Severe acute respiratory syndrome coronavirus 2 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
Authors | Pulan L | |||||||||
Funding support | China, 1 items
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Citation | Journal: Signal Transduct Target Ther / Year: 2022 Title: A non-ACE2-blocking neutralizing antibody against Omicron-included SARS-CoV-2 variants. Authors: Xiaomin Duan / Rui Shi / Pulan Liu / Qingrui Huang / Fengze Wang / Xinyu Chen / Hui Feng / Weijin Huang / Junyu Xiao / Jinghua Yan / | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_32395.map.gz | 230.1 MB | EMDB map data format | |
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Header (meta data) | emd-32395-v30.xml emd-32395.xml | 11.3 KB 11.3 KB | Display Display | EMDB header |
Images | emd_32395.png | 39.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32395 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32395 | HTTPS FTP |
-Validation report
Summary document | emd_32395_validation.pdf.gz | 418.7 KB | Display | EMDB validaton report |
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Full document | emd_32395_full_validation.pdf.gz | 418.3 KB | Display | |
Data in XML | emd_32395_validation.xml.gz | 7.1 KB | Display | |
Data in CIF | emd_32395_validation.cif.gz | 8.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32395 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32395 | HTTPS FTP |
-Related structure data
Related structure data | 7wb5MC 7wbhC 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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-Map
File | Download / File: emd_32395.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : local structure of R33 and RBD
Entire | Name: local structure of R33 and RBD |
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Components |
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-Supramolecule #1: local structure of R33 and RBD
Supramolecule | Name: local structure of R33 and RBD / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
-Macromolecule #1: hu33 heavy chain
Macromolecule | Name: hu33 heavy chain / 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: 13.162599 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QVQLVQSGSE LKKPGASVKV SCKASGYTFT DYGMNWVRQA PGQGLEWMGW INTYSGEPTY ADDFRGRFVF SLDTSVSTAY LQICSLKAE DTAVYYCARG GNWDWYFDVW GQGTLVTVS |
-Macromolecule #2: hu33 light chain
Macromolecule | Name: hu33 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: 11.717014 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: DIQMTQSPSS LSASVGDRVT ITCRASQSVS NFLHWYQQKP GKAPKLLIYY ASQSISGVPS RFSGSGSGTD FTLTISSLQP EDFATYYCQ QSNTWPLTFG QGTKLEIK |
-Macromolecule #3: Surface glycoprotein
Macromolecule | Name: Surface glycoprotein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Molecular weight | Theoretical: 20.745172 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: NLCPFGEVFN ATRFASVYAW NRKRISNCVA DYSVLYNSAS FSTFKCYGVS PTKLNDLCFT NVYADSFVIR GDEVRQIAPG QTGNIADYN YKLPDDFTGC VIAWNSNNLD SKVGGNYNYL YRLFRKSNLK PFERDISTEI YQAGSTPCNG VKGFNCYFPL Q SYGFQPTY GVGYQPYRVV VLSFE |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.2 |
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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: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 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: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 222776 |
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Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |