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- EMDB-19002: XBB-4 Fab in complex with SARS-CoV-2 BA.2.12.1 Spike Glycoprotein -
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Open data
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Basic information
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Title | XBB-4 Fab in complex with SARS-CoV-2 BA.2.12.1 Spike Glycoprotein | |||||||||||||||
![]() | Sharpened locally refined cryoEM map of XBB4 fab in complex with BA.2.12.1 Spike glycoprotein focussing on RBD and fab. | |||||||||||||||
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![]() | SARS-CoV-2 / Spike / Glycoprotein / Coronavirus / antibody / Fab / XBB.1.5 / therapeutic / complex / neutralising / RBD / receptor binding domain / convalescent sera / viral protein / immune system / XBB-4 / BA.2.12.1 / omicron variant / virus / BA.2.86 | |||||||||||||||
Function / homology | ![]() endocytosis involved in viral entry into host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / membrane Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() ![]() | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.41 Å | |||||||||||||||
![]() | Duyvesteyn HME / Ren J / Stuart DI | |||||||||||||||
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. | |||||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 322.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 23.4 KB 23.4 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 18.6 KB | Display | ![]() |
Images | ![]() | 85.5 KB | ||
Filedesc metadata | ![]() | 7.6 KB | ||
Others | ![]() ![]() | 289.8 MB 286.2 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 25.1 KB | Display | |
Data in CIF | ![]() | 33.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8r8kMC ![]() 8qrfC ![]() 8qrgC ![]() 8qsqC ![]() 8qtdC ![]() 8r80C 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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Map
File | ![]() | ||||||||||||||||||||
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Annotation | Sharpened locally refined cryoEM map of XBB4 fab in complex with BA.2.12.1 Spike glycoprotein focussing on RBD and fab. | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.7303 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Locally refined cryoEM half map of XBB4 fab...
File | emd_19002_half_map_1.map | ||||||||||||
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Annotation | Locally refined cryoEM half map of XBB4 fab in complex with BA.2.12.1 Spike glycoprotein focussing on RBD and fab. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Locally refined cryoEM half map of XBB4 fab...
File | emd_19002_half_map_2.map | ||||||||||||
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Annotation | Locally refined cryoEM half map of XBB4 fab in complex with BA.2.12.1 Spike glycoprotein focussing on RBD and fab. | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : XBB-4 Fab in complex with SARS-COV-2 BA.2.12.1 Spike Glycoprotein
Entire | Name: XBB-4 Fab in complex with SARS-COV-2 BA.2.12.1 Spike Glycoprotein |
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Components |
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-Supramolecule #1: XBB-4 Fab in complex with SARS-COV-2 BA.2.12.1 Spike Glycoprotein
Supramolecule | Name: XBB-4 Fab in complex with SARS-COV-2 BA.2.12.1 Spike Glycoprotein type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
-Supramolecule #2: XBB-4 Fab
Supramolecule | Name: XBB-4 Fab / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2 Details: Sequence from antibody isolated from convalescent sera. |
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Source (natural) | Organism: ![]() |
-Supramolecule #3: BA.2.12.1 Spike Glycoprotein Ectodomain
Supramolecule | Name: BA.2.12.1 Spike Glycoprotein Ectodomain / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3 |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Spike glycoprotein
Macromolecule | Name: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 142.72925 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MFVFLVLLPL VSSQCVNLIT RTQSYTNSFT RGVYYPDKVF RSSVLHSTQD LFLPFFSNVT WFHAIHVSGT NGTKRFDNPV LPFNDGVYF ASTEKSNIIR GWIFGTTLDS KTQSLLIVNN ATNVVIKVCE FQFCNDPFLD VYYHKNNKSW MESEFRVYSS A NNCTFEYV ...String: MFVFLVLLPL VSSQCVNLIT RTQSYTNSFT RGVYYPDKVF RSSVLHSTQD LFLPFFSNVT WFHAIHVSGT NGTKRFDNPV LPFNDGVYF ASTEKSNIIR GWIFGTTLDS KTQSLLIVNN ATNVVIKVCE FQFCNDPFLD VYYHKNNKSW MESEFRVYSS A NNCTFEYV SQPFLMDLEG KQGNFKNLRE FVFKNIDGYF KIYSKHTPIN LGRDLPQGFS ALEPLVDLPI GINITRFQTL LA LHRSYLT PGDSSSGWTA GAAAYYVGYL QPRTFLLKYN ENGTITDAVD CALDPLSETK CTLKSFTVEK GIYQTSNFRV QPT ESIVRF PNITNLCPFD EVFNATRFAS VYAWNRKRIS NCVADYSVLY NFAPFFAFKC YGVSPTKLND LCFTNVYADS FVIR GNEVS QIAPGQTGNI ADYNYKLPDD FTGCVIAWNS NKLDSKVGGN YNYQYRLFRK SNLKPFERDI STEIYQAGNK PCNGV AGFN CYFPLRSYGF RPTYGVGHQP YRVVVLSFEL LHAPATVCGP KKSTNLVKNK CVNFNFNGLT GTGVLTESNK KFLPFQ QFG RDIADTTDAV RDPQTLEILD ITPCSFGGVS VITPGTNTSN QVAVLYQGVN CTEVPVAIHA DQLTPTWRVY STGSNVF QT RAGCLIGAEY VNNSYECDIP IGAGICASYQ TQTKSHRRAR SVASQSIIAY TMSLGAENLV AYSNNSIAIP TNFTISVT T EILPVSMTKT SVDCTMYICG DSTECSNLLL QYGSFCTQLK RALTGIAVEQ DKNTQEVFAQ VKQIYKTPPI KYFGGFNFS QILPDPSKPS KRSFIEDLLF NKVTLADAGF IKQYGDCLGD IAARDLICAQ KFNGLTVLPP LLTDEMIAQY TSALLAGTIT SGWTFGAGA ALQIPFAMQM AYRFNGIGVT QNVLYENQKL IANQFNSAIG KIQDSLSSTA SALGKLQDVV NHNAQALNTL V KQLSSKFG AISSVLNDIL SRLDKVEAEV QIDRLITGRL QSLQTYVTQQ LIRAAEIRAS ANLAATKMSE CVLGQSKRVD FC GKGYHLM SFPQSAPHGV VFLHVTYVPA QEKNFTTAPA ICHDGKAHFP REGVFVSNGT HWFVTQRNFY EPQIITTDNT FVS GNCDVV IGIVNNTVYD PLQPELDSFK EELDKYFKNH TSPDVDLGDI SGINASVVNI QKEIDRLNEV AKNLNESLID LQEL GKYEQ GSGYIPEAPR DGQAYVRKDG EWVLLSTFLG RSLEVLFQGP GHHHHHHHHG SAWSHPQFEK GGGSGGGSGG SAWSH PQFE K UniProtKB: Spike glycoprotein |
-Macromolecule #2: XBB-4 Fab Heavy chain
Macromolecule | Name: XBB-4 Fab Heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 24.75566 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: EVQLVQSGGG LVKPGGSLRL SCAASGFSFT NAWMNWVRQA PGKGLEWVGR IKSKADGGTT DYAAPVKGKF TISRDDSKNT LYLQMNSLK TEDTAIYYCT SDVYDFSTGF GQRDDFDYWG QGTLVTVSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD Y FPEPVTVS ...String: EVQLVQSGGG LVKPGGSLRL SCAASGFSFT NAWMNWVRQA PGKGLEWVGR IKSKADGGTT DYAAPVKGKF TISRDDSKNT LYLQMNSLK TEDTAIYYCT SDVYDFSTGF GQRDDFDYWG QGTLVTVSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD Y FPEPVTVS WNSGALTSGV HTFPAVLQSS GLYSLSSVVT VPSSSLGTQT YICNVNHKPS NTKVDKKVEP KSCDK |
-Macromolecule #3: XBB-4 Fab Light chain
Macromolecule | Name: XBB-4 Fab Light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 23.18575 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: DIVMTQSPSS LSASVGDRVT ITCRASQSIS YFLNWYQQKP GKAPKLLISA ASSLQSGVPS RFSGSGSGTD FTLTISSLQP EDFATYYCQ QSYSSLITFG GGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String: DIVMTQSPSS LSASVGDRVT ITCRASQSIS YFLNWYQQKP GKAPKLLISA ASSLQSGVPS RFSGSGSGTD FTLTISSLQP EDFATYYCQ QSYSSLITFG GGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.7 mg/mL |
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Buffer | pH: 7.4 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.5 K / Instrument: FEI VITROBOT MARK IV |
Details | Spike ectodomain incubated with XBB-4 Fab in 2-fold molecular excess of sites (assuming three per trimeric spike unit). |
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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: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated magnification: 165000 / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 0.8 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |