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Yorodumi- EMDB-32868: Local refinement of the SARS-CoV-2 BA.1 Spike trimer in complex w... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32868 | |||||||||
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Title | Local refinement of the SARS-CoV-2 BA.1 Spike trimer in complex with 55A8 Fab | |||||||||
Map data | ||||||||||
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 | Severe acute respiratory syndrome coronavirus 2 / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Guo H / Gao Y / Lu Y / Yang H / Ji X | |||||||||
Funding support | China, 1 items
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Citation | Journal: To Be Published Title: Local refinement of the SARS-CoV-2 BA.1 Spike trimer in complex with 55A8 Fab Authors: Guo H / Gao Y / Lu Y / Yang H / Ji X | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_32868.map.gz | 483.5 MB | EMDB map data format | |
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Header (meta data) | emd-32868-v30.xml emd-32868.xml | 12 KB 12 KB | Display Display | EMDB header |
Images | emd_32868.png | 43.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32868 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32868 | HTTPS FTP |
-Validation report
Summary document | emd_32868_validation.pdf.gz | 496.3 KB | Display | EMDB validaton report |
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Full document | emd_32868_full_validation.pdf.gz | 495.9 KB | Display | |
Data in XML | emd_32868_validation.xml.gz | 8 KB | Display | |
Data in CIF | emd_32868_validation.cif.gz | 9.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32868 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32868 | HTTPS FTP |
-Related structure data
Related structure data | 7wwkMC 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_32868.map.gz / Format: CCP4 / Size: 512 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: 0.82 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : SARS-CoV-2 Omicron spike RBD complex with 55A8 Fab
Entire | Name: SARS-CoV-2 Omicron spike RBD complex with 55A8 Fab |
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Components |
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-Supramolecule #1: SARS-CoV-2 Omicron spike RBD complex with 55A8 Fab
Supramolecule | Name: SARS-CoV-2 Omicron spike RBD complex with 55A8 Fab / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all / Details: RBD-Fab local refinement |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
-Supramolecule #2: Omicron spike RBD
Supramolecule | Name: Omicron spike RBD / type: complex / ID: 2 / Chimera: Yes / Parent: 1 / Macromolecule list: #1 Details: SARS-CoV-2 Omicron variant spike protein receptor-binding domain |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #3: 55A8 Fab
Supramolecule | Name: 55A8 Fab / type: complex / ID: 3 / Chimera: Yes / Parent: 1 / Macromolecule list: #2-#3 Details: Fab fragment generated by proteolytic cleavage of IgG antibody |
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-Macromolecule #1: Spike glycoprotein
Macromolecule | Name: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Molecular weight | Theoretical: 22.065934 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: NLCPFDEVFN ATRFASVYAW NRKRISNCVA DYSVLYNLAP FFTFKCYGVS PTKLNDLCFT NVYADSFVIR GDEVRQIAPG QTGNIADYN YKLPDDFTGC VIAWNSNKLD SKVSGNYNYL YRLFRKSNLK PFERDISTEI YQAGNKPCNG VAGFNCYFPL R SYSFRPTY ...String: NLCPFDEVFN ATRFASVYAW NRKRISNCVA DYSVLYNLAP FFTFKCYGVS PTKLNDLCFT NVYADSFVIR GDEVRQIAPG QTGNIADYN YKLPDDFTGC VIAWNSNKLD SKVSGNYNYL YRLFRKSNLK PFERDISTEI YQAGNKPCNG VAGFNCYFPL R SYSFRPTY GVGHQPYRVV VLSFELLHAP ATVCGP |
-Macromolecule #2: 55A8 light chain
Macromolecule | Name: 55A8 light chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 11.868181 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: DIQMTQSPST LSASVGDRVT ITCRASQSIS SWLAWYQQKP GKAPKLLIYK ASSLESGVPS RFSGSGSGTE FTLTISSLQP DDFATYYCQ QYNSYSHTFG QGTKLEIKR |
-Macromolecule #3: 55A8 light chain
Macromolecule | Name: 55A8 light chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 13.12665 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QVQLVQSGAE VKKPGSSVKV SCKASGGTFS SYSFIWVRQA PGQGLEWMGR IIPILGIANY AQKFQGRVTI TADKSTTTAY MELSSLRSE DTAVYYCARG TEYGDYDVSH DWGQGTLVTV SS |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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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 (6k x 4k) / Average electron dose: 60.0 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: 2.8000000000000003 µm / Nominal defocus min: 1.2 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 181072 |
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Initial angle assignment | Type: COMMON LINE |
Final angle assignment | Type: COMMON LINE |