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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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Basic information

Entry
Database: EMDB / ID: EMD-19002
TitleXBB-4 Fab in complex with SARS-CoV-2 BA.2.12.1 Spike Glycoprotein
Map dataSharpened locally refined cryoEM map of XBB4 fab in complex with BA.2.12.1 Spike glycoprotein focussing on RBD and fab.
Sample
  • Complex: XBB-4 Fab in complex with SARS-COV-2 BA.2.12.1 Spike Glycoprotein
    • Complex: XBB-4 Fab
      • Protein or peptide: Spike glycoprotein,Fibritin
      • Protein or peptide: XBB-4 Fab Heavy chain
    • Complex: BA.2.12.1 Spike Glycoprotein Ectodomain
      • Protein or peptide: XBB-4 Fab Light chain
KeywordsSARS-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
Function and homology information


virion component / 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 ...virion component / 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 / symbiont-mediated suppression of host innate immune response / 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
Fibritin C-terminal / Fibritin C-terminal region / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. ...Fibritin C-terminal / Fibritin C-terminal region / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Spike glycoprotein / Fibritin
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human) / Tequatrovirus T4
Methodsingle particle reconstruction / cryo EM / Resolution: 3.41 Å
AuthorsDuyvesteyn HME / Ren J / Stuart DI
Funding support United Kingdom, 4 items
OrganizationGrant numberCountry
Wellcome Trust203141/A/16/Z United Kingdom
Wellcome Trust101122/Z/13/Z United Kingdom
CAMS Innovation Fund for Medical Sciences (CIFMS)2018-I2M-2-002 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/N00065X/1 United Kingdom
CitationJournal: Cell Rep Med / Year: 2024
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
DepositionNov 29, 2023-
Header (metadata) releaseMay 8, 2024-
Map releaseMay 8, 2024-
UpdateAug 14, 2024-
Current statusAug 14, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19002.png

Downloads & links

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Map

FileDownload / File: emd_19002.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened locally refined cryoEM map of XBB4 fab in complex with BA.2.12.1 Spike glycoprotein focussing on RBD and fab.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 450 pix.
= 328.635 Å		0.73 Å/pix.
x 450 pix.
= 328.635 Å		0.73 Å/pix.
x 450 pix.
= 328.635 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.7303 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.139
Minimum - Maximum-0.57079434 - 0.8938954
Average (Standard dev.)0.00041230576 (±0.016529169)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 328.635 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Locally refined cryoEM half map of XBB4 fab...

Fileemd_19002_half_map_1.map
AnnotationLocally refined cryoEM half map of XBB4 fab in complex with BA.2.12.1 Spike glycoprotein focussing on RBD and fab.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Locally refined cryoEM half map of XBB4 fab...

Fileemd_19002_half_map_2.map
AnnotationLocally refined cryoEM half map of XBB4 fab in complex with BA.2.12.1 Spike glycoprotein focussing on RBD and fab.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : XBB-4 Fab in complex with SARS-COV-2 BA.2.12.1 Spike Glycoprotein

EntireName: XBB-4 Fab in complex with SARS-COV-2 BA.2.12.1 Spike Glycoprotein
Components
  • Complex: XBB-4 Fab in complex with SARS-COV-2 BA.2.12.1 Spike Glycoprotein
    • Complex: XBB-4 Fab
      • Protein or peptide: Spike glycoprotein,Fibritin
      • Protein or peptide: XBB-4 Fab Heavy chain
    • Complex: BA.2.12.1 Spike Glycoprotein Ectodomain
      • Protein or peptide: XBB-4 Fab Light chain

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Supramolecule #1: XBB-4 Fab in complex with SARS-COV-2 BA.2.12.1 Spike Glycoprotein

SupramoleculeName: XBB-4 Fab in complex with SARS-COV-2 BA.2.12.1 Spike Glycoprotein
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #2: XBB-4 Fab

SupramoleculeName: XBB-4 Fab / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Details: Sequence from antibody isolated from convalescent sera.
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: BA.2.12.1 Spike Glycoprotein Ectodomain

SupramoleculeName: BA.2.12.1 Spike Glycoprotein Ectodomain / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Macromolecule #1: Spike glycoprotein,Fibritin

MacromoleculeName: Spike glycoprotein,Fibritin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tequatrovirus T4
Molecular weightTheoretical: 142.72925 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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, Fibritin

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Macromolecule #2: XBB-4 Fab Heavy chain

MacromoleculeName: XBB-4 Fab Heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.75566 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

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Macromolecule #3: XBB-4 Fab Light chain

MacromoleculeName: XBB-4 Fab Light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.18575 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.7 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.5 K / Instrument: FEI VITROBOT MARK IV
DetailsSpike 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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 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 stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3282771 / Details: Blob picker in cryoSPARC live interface.
Startup modelType of model: INSILICO MODEL
In silico model: Ab initio model generated in cryoSPARC from 17,585 randomly selected picked particles.
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.41 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC
Details: Determined by cryoSPARC. Local refinement job centred around one fab and RBD.
Number images used: 61333
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 8 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

8cim


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8r8k:
XBB-4 Fab in complex with SARS-CoV-2 BA.2.12.1 Spike Glycoprotein

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