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Yorodumi- EMDB-38463: Cryo-EM structure of SARS-CoV-2 Omicron EG.5 spike protein(6P), R... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-38463 | |||||||||
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Title | Cryo-EM structure of SARS-CoV-2 Omicron EG.5 spike protein(6P), RBD-closed state | |||||||||
Map data | ||||||||||
Sample |
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Keywords | SARS-CoV-2 / Omicron / EG.5 / spike protein / VIRAL PROTEIN | |||||||||
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 / 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 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.61 Å | |||||||||
Authors | Li LJ / Gu YH / Shi KY / Qi JX / Gao GF | |||||||||
Funding support | China, 1 items
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Citation | Journal: To Be Published Title: Structural basis of receptor binding and immune escape for SARS-CoV-2 Omicron BA.2.86, EG.5, EG.5.1 and HV.1 sub-variants Authors: Li LJ / Xu ZP / Liu KF / Gao GF | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_38463.map.gz | 449.5 MB | EMDB map data format | |
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Header (meta data) | emd-38463-v30.xml emd-38463.xml | 14.1 KB 14.1 KB | Display Display | EMDB header |
Images | emd_38463.png | 96.1 KB | ||
Masks | emd_38463_msk_1.map | 512 MB | Mask map | |
Filedesc metadata | emd-38463.cif.gz | 6.2 KB | ||
Others | emd_38463_half_map_1.map.gz emd_38463_half_map_2.map.gz | 475.6 MB 475.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-38463 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-38463 | HTTPS FTP |
-Validation report
Summary document | emd_38463_validation.pdf.gz | 722.5 KB | Display | EMDB validaton report |
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Full document | emd_38463_full_validation.pdf.gz | 722.1 KB | Display | |
Data in XML | emd_38463_validation.xml.gz | 18.8 KB | Display | |
Data in CIF | emd_38463_validation.cif.gz | 22.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38463 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38463 | HTTPS FTP |
-Related structure data
Related structure data | 8xm5MC 8xlvC 8xmgC 8xmtC 8xn2C 8xn3C 8xn5C 8xnkC 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_38463.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.808 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_38463_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_38463_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_38463_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : SARS-CoV-2 Omicron EG.5 spike protein(6P), RBD-closed state
Entire | Name: SARS-CoV-2 Omicron EG.5 spike protein(6P), RBD-closed state |
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Components |
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-Supramolecule #1: SARS-CoV-2 Omicron EG.5 spike protein(6P), RBD-closed state
Supramolecule | Name: SARS-CoV-2 Omicron EG.5 spike protein(6P), RBD-closed state type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
-Macromolecule #1: Spike glycoprotein
Macromolecule | Name: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Details: Omicron EG.5 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Molecular weight | Theoretical: 141.06675 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MGILPSPGMP ALLSLVSLLS VLLMGCVAET GTQCVNLITR TQSYTNSFTR GVYYPDKVFR SSVLHSTQDL FLPFFSNVTW FHAIHVSGT NGTKRFDNPA LPFNDGVYFA STEKSNIIRG WIFGTTLDSK TQSLLIVNNA TNVVIKVCEF QFCNDPFLDV Y QKNNKSWM ...String: MGILPSPGMP ALLSLVSLLS VLLMGCVAET GTQCVNLITR TQSYTNSFTR GVYYPDKVFR SSVLHSTQDL FLPFFSNVTW FHAIHVSGT NGTKRFDNPA LPFNDGVYFA STEKSNIIRG WIFGTTLDSK TQSLLIVNNA TNVVIKVCEF QFCNDPFLDV Y QKNNKSWM ESEFRVYSSA NNCTFEYVSQ PFLMDLEGKE GNFKNLREFV FKNIDGYFKI YSKHTPINLE RDLPQGFSAL EP LVDLPIG INITRFQTLL ALHRSYLTPV DSSSGWTAGA AAYYVGYLQP RTFLLKYNEN GTITDAVDCA LDPLSETKCT LKS FTVEKG IYQTSNFRVQ PTESIVRFPN ITNLCPFHEV FNATTFASVY AWNRKRISNC VADYSVIYNF APFFAFKCYG VSPT KLNDL CFTNVYADSF VIRGNEVSQI APGQTGNIAD YNYKLPDDFT GCVIAWNSNK LDSKPSGNYN YLYRLLRKSK LKPFE RDIS TEIYQAGNKP CNGVAGPNCY SPLQSYGFRP TYGVGHQPYR VVVLSFELLH APATVCGPKK STNLVKNKCV NFNFNG LTG TGVLTESNKK FLPFQQFGRD IADTTDAVRD PQTLEILDIT PCSFGGVSVI TPGTNTSNQV AVLYQGVNCT EVPVAIH AD QLTPTWRVYS TGSNVFQTRA GCLIGAEYVN NSYECDIPIG AGICASYQTQ TKSHRRARSV ASQSIIAYTM SLGAENSV A YSNNSIAIPT NFTISVTTEI LPVSMTKTSV DCTMYICGDS TECSNLLLQY GSFCTQLKRA LTGIAVEQDK NTQEVFAQV KQIYKTPPIK YFGGFNFSQI LPDPSKPSKR SPIEDLLFNK VTLADAGFIK QYGDCLGDIA ARDLICAQKF NGLTVLPPLL TDEMIAQYT SALLAGTITS GWTFGAGPAL QIPFPMQMAY RFNGIGVTQN VLYENQKLIA NQFNSAIGKI QDSLSSTPSA L GKLQDVVN HNAQALNTLV KQLSSKFGAI SSVLNDILSR LDPPEAEVQI DRLITGRLQS LQTYVTQQLI RAAEIRASAN LA ATKMSEC VLGQSKRVDF CGKGYHLMSF PQSAPHGVVF LHVTYVPAQE KNFTTAPAIC HDGKAHFPRE GVFVSNGTHW FVT QRNFYE PQIITTDNTF VSGNCDVVIG IVNNTVYDPL QPELDSFKEE LDKYFKNHTS PDVDLGDISG INASVVNIQK EIDR LNEVA KNLNESLIDL QELGKYEQGS GYIPEAPRDG QAYVRKDGEW VLLSTFLGSA WSHPQFEKHH HHHHHH UniProtKB: Spike glycoprotein |
-Macromolecule #2: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 27 / 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: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 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: 2.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.61 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 473611 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |