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Yorodumi- EMDB-33124: Cryo-EM structure of SARS-CoV-2 Omicron spike protein (S-6P-RRAR)... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33124 | |||||||||
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Title | Cryo-EM structure of SARS-CoV-2 Omicron spike protein (S-6P-RRAR) in complex with S309 fab | |||||||||
Map data | Cryo-EM structure of SARS-CoV-2 Omicron spike protein in complex with S309 fab | |||||||||
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 | Severe acute respiratory syndrome coronavirus 2 / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.5 Å | |||||||||
Authors | Gao GF / Qi JX / Zhao ZN / Liu S / Xie YF | |||||||||
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_33124.map.gz | 483 MB | EMDB map data format | |
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Header (meta data) | emd-33124-v30.xml emd-33124.xml | 19.3 KB 19.3 KB | Display Display | EMDB header |
Images | emd_33124.png | 99.7 KB | ||
Others | emd_33124_half_map_1.map.gz emd_33124_half_map_2.map.gz | 474.5 MB 474.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33124 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33124 | HTTPS FTP |
-Validation report
Summary document | emd_33124_validation.pdf.gz | 935.9 KB | Display | EMDB validaton report |
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Full document | emd_33124_full_validation.pdf.gz | 935.5 KB | Display | |
Data in XML | emd_33124_validation.xml.gz | 18.7 KB | Display | |
Data in CIF | emd_33124_validation.cif.gz | 22.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33124 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33124 | HTTPS FTP |
-Related structure data
Related structure data | 7xcoMC 7xchC 7xciC 7xckC 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_33124.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 spike protein in complex with S309 fab | ||||||||||||||||||||
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 spike protein in...
File | emd_33124_half_map_1.map | ||||||||||||
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Annotation | Cryo-EM structure of SARS-CoV-2 Omicron spike protein in complex with S309 fab | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Cryo-EM structure of SARS-CoV-2 Omicron spike protein in...
File | emd_33124_half_map_2.map | ||||||||||||
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Annotation | Cryo-EM structure of SARS-CoV-2 Omicron spike protein in complex with S309 fab | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Cryo-EM structure of SARS-CoV-2 Omicron spike protein in complex ...
Entire | Name: Cryo-EM structure of SARS-CoV-2 Omicron spike protein in complex with S309 fab |
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Components |
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-Supramolecule #1: Cryo-EM structure of SARS-CoV-2 Omicron spike protein in complex ...
Supramolecule | Name: Cryo-EM structure of SARS-CoV-2 Omicron spike protein in complex with S309 fab type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Recombinant expression | Organism: Homo sapiens (human) |
-Supramolecule #2: SARS-CoV-2 Omicron spike protein
Supramolecule | Name: SARS-CoV-2 Omicron spike protein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
-Supramolecule #3: S309 fab
Supramolecule | Name: S309 fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3 |
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-Macromolecule #1: Spike glycoprotein
Macromolecule | Name: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Molecular weight | Theoretical: 138.306484 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 PATVCGPKKS TNLVKNKCVN FNFNGLKGTG VLTESNKKFL PFQQFGRDIA DTTDAV RDP QTLEILDITP CSFGGVSVIT PGTNTSNQVA VLYQGVNCTE VPVAIHADQL TPTWRVYSTG SNVFQTRAGC LIGAEYV NN SYECDIPIGA GICASYQTQT KSHRRARSVA SQSIIAYTMS LGAENSVAYS NNSIAIPTNF TISVTTEILP VSMTKTSV D CTMYICGDST ECSNLLLQYG SFCTQLKRAL TGIAVEQDKN TQEVFAQVKQ IYKTPPIKYF GGFNFSQILP DPSKPSKRS PIEDLLFNKV TLADAGFIKQ YGDCLGDIAA RDLICAQKFK GLTVLPPLLT DEMIAQYTSA LLAGTITSGW TFGAGPALQI PFPMQMAYR FNGIGVTQNV LYENQKLIAN QFNSAIGKIQ DSLSSTPSAL GKLQDVVNHN AQALNTLVKQ LSSKFGAISS V LNDIFSRL DPPEAEVQID RLITGRLQSL QTYVTQQLIR AAEIRASANL AATKMSECVL GQSKRVDFCG KGYHLMSFPQ SA PHGVVFL HVTYVPAQEK NFTTAPAICH DGKAHFPREG VFVSNGTHWF VTQRNFYEPQ IITTDNTFVS GNCDVVIGIV NNT VYDPLQ PELDSFKEEL DKYFKNHTSP DVDLGDISGI NASVVNIQKE IDRLNEVAKN LNESLIDLQE LGKYEQGSGY IPEA PRDGQ AYVRKDGEWV LLSTFLGSAW SHPQFEKHHH HHHHH |
-Macromolecule #2: S309 Fab heavy chain
Macromolecule | Name: S309 Fab heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / 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 #3: S309 fab light chain
Macromolecule | Name: S309 fab light chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / 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 #5: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 25 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-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 |