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- EMDB-16678: BA.2-07 FAB IN COMPLEX WITH SARS-COV-2 BA.2.12.1 SPIKE GLYCOPROTEIN -

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Basic information

Entry
Database: EMDB / ID: EMD-16678
TitleBA.2-07 FAB IN COMPLEX WITH SARS-COV-2 BA.2.12.1 SPIKE GLYCOPROTEIN
Map dataCryoEM sharpened map BA.2.12.1 Spike complexed with BA.2-07 fab.
Sample
  • Complex: BA.2-07 FAB IN COMPLEX WITH SARS-COV-2 BA.2.12.1 SPIKE GLYCOPROTEIN
    • Complex: BA.2.12.1 SPIKE GLYCOPROTEIN
      • Protein or peptide: Spike glycoprotein,Fibritin
    • Complex: BA.2-07 FAB Heavy and Light chains
      • Protein or peptide: BA.2-07 FAB HEAVY CHAIN
      • Protein or peptide: BA.2-07 FAB LIGHT CHAIN
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsSARS-CoV2 / spike / glycoprotein / cornovavirus / antibody / fab / BA.4 / BA.5 / BA.2 / BA.2.12.1 / cross-protective / omicron variant / vaccine / therapeutic / complex / neutralising / convalescent sera / viral protein / immune system / BA.2-07 fab / VIRUS
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 / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / 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) / Enterobacteria phage T4 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsDuyvesteyn HME / Ren J / Stuart DI / Fry EE
Funding support United Kingdom, China, 4 items
OrganizationGrant numberCountry
Wellcome Trust203141/A/16/Z United Kingdom
Wellcome Trust101122/Z/13/Z United Kingdom
Chinese Academy of Sciences2018-I2M-2-002 China
Medical Research Council (MRC, United Kingdom)MR/N00065X/1 United Kingdom
CitationJournal: Res Sq / Year: 2023
Title: Isolation of a pair of potent broadly neutralizing mAb binding to RBD and SD1 domains of SARS-CoV-2
Authors: Duyvesteyn HME / Screaton G / Ren J / Stuart DI / Fry EE
History
DepositionFeb 10, 2023-
Header (metadata) releaseJul 5, 2023-
Map releaseJul 5, 2023-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16678.png

Downloads & links

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Map

FileDownload / File: emd_16678.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM sharpened map BA.2.12.1 Spike complexed with BA.2-07 fab.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 560 pix.
= 408.968 Å		0.73 Å/pix.
x 560 pix.
= 408.968 Å		0.73 Å/pix.
x 560 pix.
= 408.968 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: 0.108
Minimum - Maximum-0.41712555 - 0.7587431
Average (Standard dev.)0.00013653662 (±0.014498605)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions560560560
Spacing560560560
CellA=B=C: 408.96802 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: CryoEM half map BA.2.12.1 Spike complexed with BA.2-07 fab.

Fileemd_16678_half_map_1.map
AnnotationCryoEM half map BA.2.12.1 Spike complexed with BA.2-07 fab.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: CryoEM half map BA.2.12.1 Spike complexed with BA.2-07 fab.

Fileemd_16678_half_map_2.map
AnnotationCryoEM half map BA.2.12.1 Spike complexed with BA.2-07 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 : BA.2-07 FAB IN COMPLEX WITH SARS-COV-2 BA.2.12.1 SPIKE GLYCOPROTEIN

EntireName: BA.2-07 FAB IN COMPLEX WITH SARS-COV-2 BA.2.12.1 SPIKE GLYCOPROTEIN
Components
  • Complex: BA.2-07 FAB IN COMPLEX WITH SARS-COV-2 BA.2.12.1 SPIKE GLYCOPROTEIN
    • Complex: BA.2.12.1 SPIKE GLYCOPROTEIN
      • Protein or peptide: Spike glycoprotein,Fibritin
    • Complex: BA.2-07 FAB Heavy and Light chains
      • Protein or peptide: BA.2-07 FAB HEAVY CHAIN
      • Protein or peptide: BA.2-07 FAB LIGHT CHAIN
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: BA.2-07 FAB IN COMPLEX WITH SARS-COV-2 BA.2.12.1 SPIKE GLYCOPROTEIN

SupramoleculeName: BA.2-07 FAB IN COMPLEX WITH SARS-COV-2 BA.2.12.1 SPIKE GLYCOPROTEIN
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #2: BA.2.12.1 SPIKE GLYCOPROTEIN

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

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Supramolecule #3: BA.2-07 FAB Heavy and Light chains

SupramoleculeName: BA.2-07 FAB Heavy and Light chains / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3 / Details: Recombinantly expressed.
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Spike glycoprotein,Fibritin

MacromoleculeName: Spike glycoprotein,Fibritin / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Enterobacteria phage T4 (virus)
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: BA.2-07 FAB HEAVY CHAIN

MacromoleculeName: BA.2-07 FAB HEAVY CHAIN / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.33509 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLVQSGAE VKEPGSSVKV SCKASGGSFS TSGISWVRQA PGQGLEWMGV IIPIQGTGNY AQKFQGRVTI TADESTTTVY MELSSLRSD DTALYYCARD QHIYDSSGHG GLWFDPWGQG TLVTVSSAST KGPSVFPLAP SSKSTSGGTA ALGCLVKDYF P EPVTVSWN ...String:
EVQLVQSGAE VKEPGSSVKV SCKASGGSFS TSGISWVRQA PGQGLEWMGV IIPIQGTGNY AQKFQGRVTI TADESTTTVY MELSSLRSD DTALYYCARD QHIYDSSGHG GLWFDPWGQG TLVTVSSAST KGPSVFPLAP SSKSTSGGTA ALGCLVKDYF P EPVTVSWN SGALTSGVHT FPAVLQSSGL YSLSSVVTVP SSSLGTQTYI CNVNHKPSNT KVDKRVEPKS CDK

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Macromolecule #3: BA.2-07 FAB LIGHT CHAIN

MacromoleculeName: BA.2-07 FAB LIGHT CHAIN / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.256824 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AIRMTQSPSS LSASVGDRVT ITCRASQSIS SYLNWYQQKP GKAPKVLIYG ASSLHSGVPS RFSGSGSGTD FTLTISRLQP EDFATYYCQ QSHSSPRSFG GGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
AIRMTQSPSS LSASVGDRVT ITCRASQSIS SYLNWYQQKP GKAPKVLIYG ASSLHSGVPS RFSGSGSGTD FTLTISRLQP EDFATYYCQ QSHSSPRSFG GGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 24 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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
GridModel: C-flat-2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.5 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 165000
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

Startup modelType of model: INSILICO MODEL / Details: Ab initio model determined in cryoSPARC
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Details: Determined within cryoSPARC interface. / Number images used: 61491
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 72
Output model

PDB-8cim:
BA.2-07 FAB IN COMPLEX WITH SARS-COV-2 BA.2.12.1 SPIKE GLYCOPROTEIN

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