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- EMDB-16676: Delta-RBD complex with BA.2-07 fab, SARS1-34 fab and C1 nanobody -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-16676
TitleDelta-RBD complex with BA.2-07 fab, SARS1-34 fab and C1 nanobody
Map data
Sample
  • Complex: Delta-RBD complex with BA.2-07 fab, SARS1-34 fab and C1 nanobody
    • Complex: SARS1-34 fab
      • Protein or peptide: SARS1-34 fab Heavy Chain
      • Protein or peptide: SARS1-34 fab Light Chain
    • Complex: BA.2-07 fab
      • Protein or peptide: BA.2-07 fab Heavy Chain
      • Protein or peptide: BA.2-07 fab Light Chain
    • Complex: C1 nanobody
      • Protein or peptide: C1 nanobody
    • Complex: Delta-RBD
      • Protein or peptide: Spike protein S2'
KeywordsSARS-CoV2 / spike / glycoprotein / cornovavirus / antibody / fab / BA.4 / BA.5 / BA.2 / Delta variant / cross-protective / omicron variant / vaccine / therapeutic / complex / neutralising / convalescent sera / viral protein / immune system / C1 nanobody / SARS1-34 fab / BA.2-07 fab / VIRUS
Function / homology
Function and homology information


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 / Attachment and Entry / membrane fusion / 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 / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / membrane / identical protein binding / plasma membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / 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 ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / 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 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human) / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 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: To Be Published
Title: Potent cross-reactive mAbs from BA.4/5 breakthrough infection
Authors: Duyvesteyn HME / Screaton G / Ren J / Stuart DI / Fry EE
History
DepositionFeb 9, 2023-
Header (metadata) releaseFeb 21, 2024-
Map releaseFeb 21, 2024-
UpdateFeb 21, 2024-
Current statusFeb 21, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16676.png

Downloads & links

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Map

FileDownload / File: emd_16676.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 400 pix.
= 292.12 Å		0.73 Å/pix.
x 400 pix.
= 292.12 Å		0.73 Å/pix.
x 400 pix.
= 292.12 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: 0.0992
Minimum - Maximum-0.17540833 - 0.3850543
Average (Standard dev.)0.00003099344 (±0.0069553736)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 292.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_16676_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_16676_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Delta-RBD complex with BA.2-07 fab, SARS1-34 fab and C1 nanobody

EntireName: Delta-RBD complex with BA.2-07 fab, SARS1-34 fab and C1 nanobody
Components
  • Complex: Delta-RBD complex with BA.2-07 fab, SARS1-34 fab and C1 nanobody
    • Complex: SARS1-34 fab
      • Protein or peptide: SARS1-34 fab Heavy Chain
      • Protein or peptide: SARS1-34 fab Light Chain
    • Complex: BA.2-07 fab
      • Protein or peptide: BA.2-07 fab Heavy Chain
      • Protein or peptide: BA.2-07 fab Light Chain
    • Complex: C1 nanobody
      • Protein or peptide: C1 nanobody
    • Complex: Delta-RBD
      • Protein or peptide: Spike protein S2'

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Supramolecule #1: Delta-RBD complex with BA.2-07 fab, SARS1-34 fab and C1 nanobody

SupramoleculeName: Delta-RBD complex with BA.2-07 fab, SARS1-34 fab and C1 nanobody
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #2: SARS1-34 fab

SupramoleculeName: SARS1-34 fab / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: BA.2-07 fab

SupramoleculeName: BA.2-07 fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4-#5
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: C1 nanobody

SupramoleculeName: C1 nanobody / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #6
Source (natural)Organism: Lama glama (llama)

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Supramolecule #5: Delta-RBD

SupramoleculeName: Delta-RBD / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Macromolecule #1: Spike protein S2'

MacromoleculeName: Spike protein S2' / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.935734 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: HHHHHHTNLC PFGEVFNATR FASVYAWNRK RISNCVADYS VLYNSASFST FKCYGVSPTK LNDLCFTNVY ADSFVIRGDE VRQIAPGQT GKIADYNYKL PDDFTGCVIA WNSNNLDSKV GGNYNYRYRL FRKSNLKPFE RDISTEIYQA GSKPCNGVEG F NCYFPLQS ...String:
HHHHHHTNLC PFGEVFNATR FASVYAWNRK RISNCVADYS VLYNSASFST FKCYGVSPTK LNDLCFTNVY ADSFVIRGDE VRQIAPGQT GKIADYNYKL PDDFTGCVIA WNSNNLDSKV GGNYNYRYRL FRKSNLKPFE RDISTEIYQA GSKPCNGVEG F NCYFPLQS YGFQPTNGVG YQPYRVVVLS FELLHAPATV CGKK

UniProtKB: Spike glycoprotein

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Macromolecule #2: SARS1-34 fab Heavy Chain

MacromoleculeName: SARS1-34 fab Heavy Chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.447453 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: QVQLVESGPG LVKPSETLSL TCTVSGDSVT SYHWSWIRQP PGKGLEWIGY IYYSGFTTYN PSLKSRVTMS LDTSKNQFSL RLSSVTAAD TAVYYCVRLL SGSLYWNHWF DPWGQGTLVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC LVKDYFPEPV T VSWNSGAL ...String:
QVQLVESGPG LVKPSETLSL TCTVSGDSVT SYHWSWIRQP PGKGLEWIGY IYYSGFTTYN PSLKSRVTMS LDTSKNQFSL RLSSVTAAD TAVYYCVRLL SGSLYWNHWF DPWGQGTLVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC LVKDYFPEPV T VSWNSGAL TSGVHTFPAV LQSSGLYSLS SVVTVPSSSL GTQTYICNVN HKPSNTKVDK RVEPKSCDK

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Macromolecule #3: SARS1-34 fab Light Chain

MacromoleculeName: SARS1-34 fab Light Chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.334879 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: AIQLTQSPST LSASVGDRVT ITCRASQSID NWLAWYQQKP GKAPKLLIYD GSSLQSGVPS RFSGSGSGTE FTLTISSLQP DDFATYYCQ QYNSLFLTFG GGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
AIQLTQSPST LSASVGDRVT ITCRASQSID NWLAWYQQKP GKAPKLLIYD GSSLQSGVPS RFSGSGSGTE FTLTISSLQP DDFATYYCQ QYNSLFLTFG GGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

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Macromolecule #4: BA.2-07 fab Heavy Chain

MacromoleculeName: BA.2-07 fab Heavy Chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / 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 #5: BA.2-07 fab Light Chain

MacromoleculeName: BA.2-07 fab Light Chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / 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 #6: C1 nanobody

MacromoleculeName: C1 nanobody / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 14.659114 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
QVQLVESGGG LVQPGGSLRL SCAASGFTND FYSIAWFRQA PGKEREGVSW LSVSDNTPTY VDSVKDRFTI SRHNANNTVY LQMNMLKPE DTAIYYCAAG RFAGRDTWPS SYDYWGQGTQ VTVSSKHHHH HH

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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

BufferpH: 7.4
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300
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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / 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
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Average electron dose: 50.0 e/Å2
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
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 1207910

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Atomic model buiding 1

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

PDB-8cii:
Delta-RBD complex with BA.2-07 fab, SARS1-34 fab and C1 nanobody

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