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- EMDB-19017: S1B domain of the PDCoV spike glycoprotein in complex with the 67... -

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Basic information

Entry
Database: EMDB / ID: EMD-19017
TitleS1B domain of the PDCoV spike glycoprotein in complex with the 67B12 and 46E6 antibody Fab fragments
Map data
Sample
  • Complex: PDCoV spike S1B domain in complex with the 67B12 and 46E6 antibody Fab fragments
    • Protein or peptide: Spike protein
    • Protein or peptide: 67B12 antibody heavy chain
    • Protein or peptide: 67B12 antibody light chain
    • Protein or peptide: 46E6 antibody heavy chain
    • Protein or peptide: 46E6 antibody heavy chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsSpike / coronavirus / antibody / complex / RBD / S1B / VIRAL PROTEIN
Function / homology
Function and homology information


endocytosis involved in viral entry into host cell / 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 / virion membrane / membrane
Similarity search - Function
Spike glycoprotein S1, coronavirus / Coronavirus spike glycoprotein S1 / 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 speciesHomo sapiens (human) / Porcine deltacoronavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsDebski-Antoniak O / Drulyte I / Hurdiss DL
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Innovative Medicines InitiativeLSHM19136 Switzerland
CitationJournal: To Be Published
Title: Neutralizing Antibodies Reveal Cryptic Vulnerabilities and Interdomain Crosstalk in the Porcine Deltacoronavirus Spike
Authors: Debski-Antoniak O / Drabek D / van Haperen R / van Dortmondt M / van der Lee J / Drulyte I / van Kuppeveld FJM / Grosveld F / Hurdiss DL / Bosch BJ
History
DepositionNov 30, 2023-
Header (metadata) releaseJun 5, 2024-
Map releaseJun 5, 2024-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19017.png

Downloads & links

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Map

FileDownload / File: emd_19017.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.97 Å/pix.
x 300 pix.
= 291.999 Å		0.97 Å/pix.
x 300 pix.
= 291.999 Å		0.97 Å/pix.
x 300 pix.
= 291.999 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.97333 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.168
Minimum - Maximum-0.30820972 - 0.634116
Average (Standard dev.)0.00039208593 (±0.012411781)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 291.999 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_19017_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_19017_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_19017_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 : PDCoV spike S1B domain in complex with the 67B12 and 46E6 antibod...

EntireName: PDCoV spike S1B domain in complex with the 67B12 and 46E6 antibody Fab fragments
Components
  • Complex: PDCoV spike S1B domain in complex with the 67B12 and 46E6 antibody Fab fragments
    • Protein or peptide: Spike protein
    • Protein or peptide: 67B12 antibody heavy chain
    • Protein or peptide: 67B12 antibody light chain
    • Protein or peptide: 46E6 antibody heavy chain
    • Protein or peptide: 46E6 antibody heavy chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: PDCoV spike S1B domain in complex with the 67B12 and 46E6 antibod...

SupramoleculeName: PDCoV spike S1B domain in complex with the 67B12 and 46E6 antibody Fab fragments
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 105.24 KDa

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Macromolecule #1: Spike protein

MacromoleculeName: Spike protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Porcine deltacoronavirus
Molecular weightTheoretical: 12.787479 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
LEVVQLNISA HMDFGEARLD SVTINGNTSY CVTKPYFRLE TNFMCTGCTM NLRTDTCSFD LSAVNNGMSF SQFCLSTESG ACEMKIIVT YVWNYLLRQR LYVTAVEGQT HTGTT

UniProtKB: Spike protein

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Macromolecule #2: 67B12 antibody heavy chain

MacromoleculeName: 67B12 antibody heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.964826 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: VQLVQSGAEV KKPGSSVKVS CKASGGTFSS LAISWVRQAP GQGLEWMGGI IPTFGTTNYA QNFRGRVTIT ADKSTSTAYM ELSTLISED TAVYFCARER STDTWPGDAF DIWGQGTMVT VSSASTKGPS VFPLAPSSGT AALGCLVKDY FPEPVTVSWN S GALTSGVH ...String:
VQLVQSGAEV KKPGSSVKVS CKASGGTFSS LAISWVRQAP GQGLEWMGGI IPTFGTTNYA QNFRGRVTIT ADKSTSTAYM ELSTLISED TAVYFCARER STDTWPGDAF DIWGQGTMVT VSSASTKGPS VFPLAPSSGT AALGCLVKDY FPEPVTVSWN S GALTSGVH TFPAVLQSSG LYSLSSVVTV PSSSLLGQTY ICNVNHKPSN TKVDKKVEPK

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Macromolecule #3: 67B12 antibody light chain

MacromoleculeName: 67B12 antibody light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.037592 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EILMTQSPAT LSVSPGERAT LSCWASQSVN SKLAWYQQKP GQAPRLLIYD TSTRATGIPA RFSGSGSGAE FTLTISSLQS EDFAVYYCQ QYNYWPYTFG QGTKLEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
EILMTQSPAT LSVSPGERAT LSCWASQSVN SKLAWYQQKP GQAPRLLIYD TSTRATGIPA RFSGSGSGAE FTLTISSLQS EDFAVYYCQ QYNYWPYTFG QGTKLEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS F

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Macromolecule #4: 46E6 antibody heavy chain

MacromoleculeName: 46E6 antibody heavy chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.508619 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLVESGGG VVQPGRSLRL SCAASGFTFS SYAMHWVRQA PGKGLEWVAV IWRDGSNEFY ADSVKGRFTI SRDNSKDTLY LQMNSLRAE DTAVYYCARR GIIMVRGLLG YWGQGTLVTV SSASTKGPSV FPLAPSSKSG TAALGCLVKD YFPEPVTVSW N SGALTSGV ...String:
QVQLVESGGG VVQPGRSLRL SCAASGFTFS SYAMHWVRQA PGKGLEWVAV IWRDGSNEFY ADSVKGRFTI SRDNSKDTLY LQMNSLRAE DTAVYYCARR GIIMVRGLLG YWGQGTLVTV SSASTKGPSV FPLAPSSKSG TAALGCLVKD YFPEPVTVSW N SGALTSGV HTFPAVLQSS GLYSLSSVVT VPSSSLGTQT YICNVNHKPS NTKVDKKVEP K

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Macromolecule #5: 46E6 antibody heavy chain

MacromoleculeName: 46E6 antibody heavy chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.017627 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQMTQSPPS LSASVGDRVT ITCRASQGIS NYLAWHQQKP GKVPKLLIYT ASTLQSGVPS RFSGSGSGTD FTLTISSLQP EDVATYYCQ KYNSAPFTFG PGTKVDIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
DIQMTQSPPS LSASVGDRVT ITCRASQGIS NYLAWHQQKP GKVPKLLIYT ASTLQSGVPS RFSGSGSGTD FTLTISSLQP EDVATYYCQ KYNSAPFTFG PGTKVDIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRG

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Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 1 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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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: 7.8
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.75 µm
Specialist opticsEnergy filter - Name: TFS Selectris
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / 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: OTHER / Details: ab initio
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC / Details: Non-uniform refinement
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 245068
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6bfu


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsInitial fitting was done using Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross-correlation coefficient
Output model

PDB-8r9z:
S1B domain of the PDCoV spike glycoprotein in complex with the 67B12 and 46E6 antibody Fab fragments

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