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- EMDB-18639: Locally refined SARS-CoV-2 BA-2.86 Spike receptor binding domain ... -
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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | Locally refined SARS-CoV-2 BA-2.86 Spike receptor binding domain (RBD) complexed with angiotensin converting enzyme 2 (ACE2) | |||||||||
![]() | Sharpened refined map of BA-2.86 spike with ACE2. | |||||||||
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Function / homology | ![]() positive regulation of amino acid transport / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Ren J / Stuart DI / Duyvesteyn HME | |||||||||
Funding support | ![]()
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![]() | ![]() Title: A structure-function analysis shows SARS-CoV-2 BA.2.86 balances antibody escape and ACE2 affinity. Authors: Chang Liu / Daming Zhou / Aiste Dijokaite-Guraliuc / Piyada Supasa / Helen M E Duyvesteyn / Helen M Ginn / Muneeswaran Selvaraj / Alexander J Mentzer / Raksha Das / Thushan I de Silva / ...Authors: Chang Liu / Daming Zhou / Aiste Dijokaite-Guraliuc / Piyada Supasa / Helen M E Duyvesteyn / Helen M Ginn / Muneeswaran Selvaraj / Alexander J Mentzer / Raksha Das / Thushan I de Silva / Thomas G Ritter / Megan Plowright / Thomas A H Newman / Lizzie Stafford / Barbara Kronsteiner / Nigel Temperton / Yuan Lui / Martin Fellermeyer / Philip Goulder / Paul Klenerman / Susanna J Dunachie / Michael I Barton / Mikhail A Kutuzov / Omer Dushek / / Elizabeth E Fry / Juthathip Mongkolsapaya / Jingshan Ren / David I Stuart / Gavin R Screaton / ![]() ![]() ![]() Abstract: BA.2.86, a recently described sublineage of SARS-CoV-2 Omicron, contains many mutations in the spike gene. It appears to have originated from BA.2 and is distinct from the XBB variants responsible ...BA.2.86, a recently described sublineage of SARS-CoV-2 Omicron, contains many mutations in the spike gene. It appears to have originated from BA.2 and is distinct from the XBB variants responsible for many infections in 2023. The global spread and plethora of mutations in BA.2.86 has caused concern that it may possess greater immune-evasive potential, leading to a new wave of infection. Here, we examine the ability of BA.2.86 to evade the antibody response to infection using a panel of vaccinated or naturally infected sera and find that it shows marginally less immune evasion than XBB.1.5. We locate BA.2.86 in the antigenic landscape of recent variants and look at its ability to escape panels of potent monoclonal antibodies generated against contemporary SARS-CoV-2 infections. We demonstrate, and provide a structural explanation for, increased affinity of BA.2.86 to ACE2, which may increase transmissibility. #1: ![]() Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix Authors: Liebschner D / Afonine PV #2: ![]() Title: cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination Authors: Punjani A / Rubinstein JL | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 79.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 24 KB 24 KB | Display Display | ![]() |
Images | ![]() | 56.8 KB | ||
Filedesc metadata | ![]() | 7.4 KB | ||
Others | ![]() ![]() | 77.7 MB 77.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8qsqMC ![]() 8qrfC ![]() 8qrgC ![]() 8qtdC ![]() 8r80C ![]() 8r8kC 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
File | ![]() | ||||||||||||||||||||||||||||||||||||
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Annotation | Sharpened refined map of BA-2.86 spike with ACE2. | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.46 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half map A of BA-2.86 spike with ACE2.
File | emd_18639_half_map_1.map | ||||||||||||
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Annotation | Half map A of BA-2.86 spike with ACE2. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map B of BA-2.86 spike with ACE2.
File | emd_18639_half_map_2.map | ||||||||||||
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Annotation | Half map B of BA-2.86 spike with ACE2. | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : BA-2.86 variant SARS-CoV2 S protein complexed with angiotensin co...
Entire | Name: BA-2.86 variant SARS-CoV2 S protein complexed with angiotensin converting enzyme 2 (ACE2) |
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Components |
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-Supramolecule #1: BA-2.86 variant SARS-CoV2 S protein complexed with angiotensin co...
Supramolecule | Name: BA-2.86 variant SARS-CoV2 S protein complexed with angiotensin converting enzyme 2 (ACE2) type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 Details: Spike protein recombinantly expressed using sequence of human-derived BA-2.86 variant of SARS-CoV2. Angiotensin converting enzyme 2 (ACE2) recombinantely expressed. |
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-Supramolecule #2: Angiotensin converting enzyme 2 (ACE2)
Supramolecule | Name: Angiotensin converting enzyme 2 (ACE2) / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2 Details: Human Angiotensin converting enzyme 2 (hACE2) recombinantely expressed |
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Source (natural) | Organism: ![]() ![]() |
-Supramolecule #3: BA-2.86 variant SARS-CoV2 S protein
Supramolecule | Name: BA-2.86 variant SARS-CoV2 S protein / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1 Details: Spike protein recombinantly expressed using sequence of human-derived BA-2.86 variant of SARS-CoV2. |
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Source (natural) | Organism: ![]() ![]() ![]() |
-Macromolecule #1: Spike protein S2'
Macromolecule | Name: Spike protein S2' / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 22.159053 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: VTNLCPFHEV FNATRFASVY AWNRTRISNC VADYSVLYNF APFFAFKCYG VSPTKLNDLC FTNVYADSFV IKGNEVSQIA PGQTGNIAD YNYKLPDDFT GCVIAWNSNK LDSKHSGNYD YWYRLFRKSK LKPFERDIST EIYQAGNKPC KGKGPNCYFP L QSYGFRPT ...String: VTNLCPFHEV FNATRFASVY AWNRTRISNC VADYSVLYNF APFFAFKCYG VSPTKLNDLC FTNVYADSFV IKGNEVSQIA PGQTGNIAD YNYKLPDDFT GCVIAWNSNK LDSKHSGNYD YWYRLFRKSK LKPFERDIST EIYQAGNKPC KGKGPNCYFP L QSYGFRPT YGVGHQPYRV VVLSFELLHA PATVCGP UniProtKB: ![]() |
-Macromolecule #2: Processed angiotensin-converting enzyme 2
Macromolecule | Name: Processed angiotensin-converting enzyme 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 69.982562 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: STIEEQAKTF LDKFNHEAED LFYQSSLASW NYNTNITEEN VQNMNNAGDK WSAFLKEQST LAQMYPLQEI QNLTVKLQLQ ALQQNGSSV LSEDKSKRLN TILNTMSTIY STGKVCNPDN PQECLLLEPG LNEIMANSLD YNERLWAWES WRSEVGKQLR P LYEEYVVL ...String: STIEEQAKTF LDKFNHEAED LFYQSSLASW NYNTNITEEN VQNMNNAGDK WSAFLKEQST LAQMYPLQEI QNLTVKLQLQ ALQQNGSSV LSEDKSKRLN TILNTMSTIY STGKVCNPDN PQECLLLEPG LNEIMANSLD YNERLWAWES WRSEVGKQLR P LYEEYVVL KNEMARANHY EDYGDYWRGD YEVNGVDGYD YSRGQLIEDV EHTFEEIKPL YEHLHAYVRA KLMNAYPSYI SP IGCLPAH LLGDMWGRFW TNLYSLTVPF GQKPNIDVTD AMVDQAWDAQ RIFKEAEKFF VSVGLPNMTQ GFWENSMLTD PGN VQKAVC HPTAWDLGKG DFRILMCTKV TMDDFLTAHH EMGHIQYDMA YAAQPFLLRN GANEGFHEAV GEIMSLSAAT PKHL KSIGL LSPDFQEDNE TEINFLLKQA LTIVGTLPFT YMLEKWRWMV FKGEIPKDQW MKKWWEMKRE IVGVVEPVPH DETYC DPAS LFHVSNDYSF IRYYTRTLYQ FQFQEALCQA AKHEGPLHKC DISNSTEAGQ KLFNMLRLGK SEPWTLALEN VVGAKN MNV RPLLNYFEPL FTWLKDQNKN SFVGWSTDWS PYADHHHHHH UniProtKB: ![]() |
-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: 6 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ![]() ChemComp-NAG: |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
Details | BA-2.86 Spike with angiotensin converting enzyme 2 (ACE2) at a 6-fold excess of S protein. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD![]() |
Specialist optics | Energy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 9818 / Average electron dose: 50.0 e/Å2 / Details: Images were collected in EER format. |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Particle selection | Number selected: 504319 |
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Startup model | Type of model: PDB ENTRY PDB model - PDB ID: Details: Initial RBD-Spike from related deposition. ACE2 model. Also compared with 8IOV. |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC |
Final 3D classification | Number classes: 5 / Software - Name: cryoSPARC (ver. v.4.3.1) Details: Following classification into 8 classes, classification without alignment, focussing on RBD/ACE2 region. |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v.4.3.1) |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v.4.3.1) / Details: CryoSPARC. / Number images used: 15883 |
-Atomic model buiding 1
Initial model |
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Details | Phenix real space refinement with manual checks using coot. | ||||||||
Refinement | Space: REAL / Protocol: OTHER | ||||||||
Output model | ![]() PDB-8qsq: |