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- EMDB-38460: Cryo-EM structure of SARS-CoV-2 Omicron BA.2.86 spike protein(6P)... -
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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | Cryo-EM structure of SARS-CoV-2 Omicron BA.2.86 spike protein(6P), 1-RBD-up state | |||||||||
![]() | Cryo-EM map(sharp) of SARS-CoV-2 Omicron BA.2.86 spike protein | |||||||||
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![]() | SARS-CoV-2 / Omicron / BA.2.86 / spike protein / VIRAL PROTEIN | |||||||||
Function / homology | ![]() 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 | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.07 Å | |||||||||
![]() | Li LJ / Gu YH / Shi KY / Qi JX / Gao GF | |||||||||
Funding support | ![]()
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![]() | ![]() 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 | ![]() | 421.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 14.3 KB 14.3 KB | Display Display | ![]() |
Images | ![]() | 100.3 KB | ||
Masks | ![]() | 476.8 MB | ![]() | |
Filedesc metadata | ![]() | 6.2 KB | ||
Others | ![]() ![]() | 442.8 MB 442.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 826.3 KB | Display | ![]() |
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Full document | ![]() | 825.9 KB | Display | |
Data in XML | ![]() | 18 KB | Display | |
Data in CIF | ![]() | 21.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8xlvMC ![]() 8xm5C ![]() 8xmgC ![]() 8xmtC ![]() 8xn2C ![]() 8xn3C ![]() 8xn5C ![]() 8xnkC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Cryo-EM map(sharp) of SARS-CoV-2 Omicron BA.2.86 spike protein | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.669 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Half map: Half-B map of SARS-CoV-2 Omicron BA.2.86 spike protein
File | emd_38460_half_map_1.map | ||||||||||||
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Annotation | Half-B map of SARS-CoV-2 Omicron BA.2.86 spike protein | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half-A map of SARS-CoV-2 Omicron BA.2.86 spike protein
File | emd_38460_half_map_2.map | ||||||||||||
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Annotation | Half-A map of SARS-CoV-2 Omicron BA.2.86 spike protein | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : SARS-CoV-2 Omicron BA.2.86 spike protein
Entire | Name: SARS-CoV-2 Omicron BA.2.86 spike protein |
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Components |
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-Supramolecule #1: SARS-CoV-2 Omicron BA.2.86 spike protein
Supramolecule | Name: SARS-CoV-2 Omicron BA.2.86 spike protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Spike glycoprotein
Macromolecule | Name: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Details: Omicron BA.2.86 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 131.772406 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MFVFLVLLPL VSSQCVMPLF NLITTTQSYT NSFTRGVYYP DKVFRSSVLH LTQDLFLPFF SNVTWFHAIS GTNGTKRFDN PVLPFNDGV YFASTEKSNI IRGWIFGTTL DSKTQSLLIV NNATNVFIKV CEFQFCNDPF LDVYHKNNKS WMESESGVYS S ANNCTFEY ...String: MFVFLVLLPL VSSQCVMPLF NLITTTQSYT NSFTRGVYYP DKVFRSSVLH LTQDLFLPFF SNVTWFHAIS GTNGTKRFDN PVLPFNDGV YFASTEKSNI IRGWIFGTTL DSKTQSLLIV NNATNVFIKV CEFQFCNDPF LDVYHKNNKS WMESESGVYS S ANNCTFEY VSQPFLMDLE GKQGNFKNLR EFVFKNIDGY FKIYSKHTPI IGRDFPQGFS ALEPLVDLPI GINITRFQTL LA LNRSYLT PGDSSSGWTA GAADYYVGYL QPRTFLLKYN ENGTITDAVD CALDPLSETK CTLKSFTVEK GIYQTSNFRV QPT ESIVRF PNVTNLCPFH EVFNATRFAS VYAWNRTRIS NCVADYSVLY NFAPFFAFKC YGVSPTKLND LCFTNVYADS FVIK GNEVS QIAPGQTGNI ADYNYKLPDD FTGCVIAWNS NKLDSKHSGN YDYWYRLFRK SKLKPFERDI STEIYQAGNK PCKGK GPNC YFPLQSYGFR PTYGVGHQPY RVVVLSFELL HAPATVCGPK KSTNLVKNKC VNFNFNGLTG TGVLTKSNKK FLPFQQ FGR DIVDTTDAVR DPQTLEILDI TPCSFGGVSV ITPGTNTSNQ VAVLYQGVNC TEVSVAIHAD QLTPTWRVYS TGSNVFQ TR AGCLIGAEYV NNSYECDIPI GAGVCASYQT QTKSRGSASS VASQSIIAYT MSLGAENSVA YSNNSIAIPT NFTISVTT E ILPVSMTKTS VDCTMYICGD STECSNLLLQ YGSFCTQLKR ALTGIAVEQD KNTQEVFAQV KQIYKTPPIK YFGGFNFSQ ILPDPSKPSK RSPIEDLLFN KVTLADAGFI KQYGDCLGDI AARDLICAQK FNGLTVLPPL LTDEMIAQYT SALLAGTITS GWTFGAGPA LQIPFPMQMA YRFNGIGVTQ NVLYENQKLI ANQFNSAIGK IQDSLFSTPS ALGKLQDVVN HNAQALNTLV K QLSSKFGA ISSVLNDILS RLDPPEAEVQ IDRLITGRLQ SLQTYVTQQL IRAAEIRASA NLAATKMSEC VLGQSKRVDF CG KGYHLMS FPQSAPHGVV FLHVTYVPAQ EKNFTTAPAI CHDGKAHFPR EGVFVSNGTH WFVTQRNFYE PQIITTDNTF VSG NCDVVI GIVNNTVYDP LQLELDSGGG SGGGSGYIPE APRDGQAYVR KDGEWVLLST FLGGGSAWSH PQFEK UniProtKB: Spike glycoprotein |
-Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 24 / 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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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
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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: ![]() |
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 |
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Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 242344 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |