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Yorodumi- EMDB-33123: Cryo-EM structure of SARS-CoV-2 Omicron RBD in complex with S309 ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33123 | |||||||||
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Title | Cryo-EM structure of SARS-CoV-2 Omicron RBD in complex with S309 fab (local refinement) | |||||||||
Map data | Cryo-EM structure of SARS-CoV-2 Omicron RBD in complex with S309 fab (local refinement) | |||||||||
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 / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / 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) / Severe acute respiratory syndrome coronavirus 2 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.5 Å | |||||||||
Authors | Gao GF / Qi JX / Zhao ZN / Xie YF / Liu S | |||||||||
Funding support | China, 1 items
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Citation | Journal: Nat Commun / Year: 2022 Title: Omicron SARS-CoV-2 mutations stabilize spike up-RBD conformation and lead to a non-RBM-binding monoclonal antibody escape Authors: Zhao Z / Zhou J / Tian M / Huang M / Liu S / Xie Y / Han P / Bai C / Han P / Zheng A / Fu L / Gao Y / Peng Q / Li Y / Chai Y / Zhang Z / Zhao X / Song H / Qi J / Wang Q / Wang P / Gao GF | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33123.map.gz | 482.3 MB | EMDB map data format | |
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Header (meta data) | emd-33123-v30.xml emd-33123.xml | 18.2 KB 18.2 KB | Display Display | EMDB header |
Images | emd_33123.png | 75.8 KB | ||
Others | emd_33123_half_map_1.map.gz emd_33123_half_map_2.map.gz | 474.5 MB 474.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33123 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33123 | HTTPS FTP |
-Validation report
Summary document | emd_33123_validation.pdf.gz | 776.1 KB | Display | EMDB validaton report |
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Full document | emd_33123_full_validation.pdf.gz | 775.7 KB | Display | |
Data in XML | emd_33123_validation.xml.gz | 18.6 KB | Display | |
Data in CIF | emd_33123_validation.cif.gz | 22.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33123 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33123 | HTTPS FTP |
-Related structure data
Related structure data | 7xckMC 7xchC 7xciC 7xcoC 7xcpC 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_33123.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Cryo-EM structure of SARS-CoV-2 Omicron RBD in complex with S309 fab (local refinement) | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.67 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Cryo-EM structure of SARS-CoV-2 Omicron RBD in complex...
File | emd_33123_half_map_1.map | ||||||||||||
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Annotation | Cryo-EM structure of SARS-CoV-2 Omicron RBD in complex with S309 fab (local refinement) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Cryo-EM structure of SARS-CoV-2 Omicron RBD in complex...
File | emd_33123_half_map_2.map | ||||||||||||
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Annotation | Cryo-EM structure of SARS-CoV-2 Omicron RBD in complex with S309 fab (local refinement) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Cryo-EM structure of SARS-CoV-2 Omicron RBD in complex with S309 ...
Entire | Name: Cryo-EM structure of SARS-CoV-2 Omicron RBD in complex with S309 fab (local refinement) |
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Components |
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-Supramolecule #1: Cryo-EM structure of SARS-CoV-2 Omicron RBD in complex with S309 ...
Supramolecule | Name: Cryo-EM structure of SARS-CoV-2 Omicron RBD in complex with S309 fab (local refinement) 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) / Recombinant cell: HEK293 |
-Supramolecule #2: S309 fab
Supramolecule | Name: S309 fab / type: complex / Chimera: Yes / ID: 2 / Parent: 1 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: HEK293 |
-Supramolecule #3: SARS-CoV-2 Omicron RBD
Supramolecule | Name: SARS-CoV-2 Omicron RBD / type: complex / Chimera: Yes / ID: 3 / Parent: 1 / Macromolecule list: #3 |
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-Macromolecule #1: S309 heavy chain
Macromolecule | Name: S309 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: 24.573471 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QVQLVQSGAE VKKPGASVKV SCKASGYPFT SYGISWVRQA PGQGLEWMGW ISTYNGNTNY AQKFQGRVTM TTDTSTTTGY MELRRLRSD DTAVYYCARD YTRGAWFGES LIGGFDNWGQ GTLVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY F PEPVTVSW ...String: QVQLVQSGAE VKKPGASVKV SCKASGYPFT SYGISWVRQA PGQGLEWMGW ISTYNGNTNY AQKFQGRVTM TTDTSTTTGY MELRRLRSD DTAVYYCARD YTRGAWFGES LIGGFDNWGQ GTLVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY F PEPVTVSW NSGALTSGVH TFPAVLQSSG LYSLSSVVTV PSSSLGTQTY ICNVNHKPSN TKVDKKVEPK SC |
-Macromolecule #2: S309 light chain
Macromolecule | Name: S309 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: 23.204697 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: EIVLTQSPGT LSLSPGERAT LSCRASQTVS STSLAWYQQK PGQAPRLLIY GASSRATGIP DRFSGSGSGT DFTLTISRLE PEDFAVYYC QQHDTSLTFG GGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String: EIVLTQSPGT LSLSPGERAT LSCRASQTVS STSLAWYQQK PGQAPRLLIY GASSRATGIP DRFSGSGSGT DFTLTISRLE PEDFAVYYC QQHDTSLTFG GGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC |
-Macromolecule #3: Spike protein S1
Macromolecule | Name: Spike protein S1 / 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: 30.444469 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 PC |
-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 |
-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: 1.39 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 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: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 517940 |
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Initial angle assignment | Type: OTHER |
Final angle assignment | Type: OTHER |