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Open data
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Basic information
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Title | SARS Cov2 Spike RBD in complex with Fab47 | |||||||||
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Function / homology | ![]() 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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane ...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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Hallberg BM / Das H | |||||||||
Funding support | 1 items
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![]() | ![]() Title: Immunoglobulin germline gene polymorphisms influence the function of SARS-CoV-2 neutralizing antibodies. Authors: Pradeepa Pushparaj / Andrea Nicoletto / Daniel J Sheward / Hrishikesh Das / Xaquin Castro Dopico / Laura Perez Vidakovics / Leo Hanke / Mark Chernyshev / Sanjana Narang / Sungyong Kim / ...Authors: Pradeepa Pushparaj / Andrea Nicoletto / Daniel J Sheward / Hrishikesh Das / Xaquin Castro Dopico / Laura Perez Vidakovics / Leo Hanke / Mark Chernyshev / Sanjana Narang / Sungyong Kim / Julian Fischbach / Simon Ekström / Gerald McInerney / B Martin Hällberg / Ben Murrell / Martin Corcoran / Gunilla B Karlsson Hedestam / ![]() Abstract: The human immunoglobulin heavy-chain (IGH) locus is exceptionally polymorphic, with high levels of allelic and structural variation. Thus, germline IGH genotypes are personal, which may influence ...The human immunoglobulin heavy-chain (IGH) locus is exceptionally polymorphic, with high levels of allelic and structural variation. Thus, germline IGH genotypes are personal, which may influence responses to infection and vaccination. For an improved understanding of inter-individual differences in antibody responses, we isolated SARS-CoV-2 spike-specific monoclonal antibodies from convalescent health care workers, focusing on the IGHV1-69 gene, which has the highest level of allelic variation of all IGHV genes. The IGHV1-6920-using CAB-I47 antibody and two similar antibodies isolated from an independent donor were critically dependent on allele usage. Neutralization was retained when reverting the V region to the germline IGHV1-6920 allele but lost when reverting to other IGHV1-69 alleles. Structural data confirmed that two germline-encoded polymorphisms, R50 and F55, in the IGHV1-69 gene were required for high-affinity receptor-binding domain interaction. These results demonstrate that polymorphisms in IGH genes can influence the function of SARS-CoV-2 neutralizing antibodies. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 275.2 KB | ![]() | |
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Header (meta data) | ![]() ![]() | 18.7 KB 18.7 KB | Display Display | ![]() |
Images | ![]() | 80.4 KB | ||
Others | ![]() ![]() | 475.1 MB 475.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8a96MC ![]() 8a94C ![]() 8a95C ![]() 8a99C 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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Related items in Molecule of the Month |
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Map
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Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.01 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_15271_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_15271_half_map_2.map | ||||||||||||
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Density Histograms |
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Sample components
-Entire : SARS-CoV-2 Spike in Complex with Fab47
Entire | Name: SARS-CoV-2 Spike in Complex with Fab47 |
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Components |
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-Supramolecule #1: SARS-CoV-2 Spike in Complex with Fab47
Supramolecule | Name: SARS-CoV-2 Spike in Complex with Fab47 / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all / Details: Localized reconstruction |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 629 kDa/nm |
-Macromolecule #1: Spike protein S1
Macromolecule | Name: Spike protein S1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 23.017887 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: VRFPNIANLC PFGEVFNATR FASVYAWNRK RISNCVADYS VLYNSASFST FKCYGVSPTK LNDLCFTNVY ADSFVIRGDE VRQIAPGQT GKIADYNYKL PDDFTGCVIA WNSNNLDSKV GGNYNYLYRL FRKSNLKPFE RDISTEIYQA GSTPCNGVEG F NCYFPLQS ...String: VRFPNIANLC PFGEVFNATR FASVYAWNRK RISNCVADYS VLYNSASFST FKCYGVSPTK LNDLCFTNVY ADSFVIRGDE VRQIAPGQT GKIADYNYKL PDDFTGCVIA WNSNNLDSKV GGNYNYLYRL FRKSNLKPFE RDISTEIYQA GSTPCNGVEG F NCYFPLQS YGFQPTNGVG YQPYRVVVLS FELLHAPATV CGPKKST |
-Macromolecule #2: Fab47 Heavy chain (variable domain)
Macromolecule | Name: Fab47 Heavy chain (variable domain) / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 13.391934 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: VQLVQSGAEV KKPGSSVKVS CKASGGTFNT YAINWVRQAP GQGLEWMGRI IPMFGIANYA QKFQGTVTFT ADKSTSTAYM ELSSLRYED TAVYYCARSA YYSESSGYYL DYWGQGTLVT VSS |
-Macromolecule #3: Fab47 Light chain (variable domain)
Macromolecule | Name: Fab47 Light chain (variable domain) / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 11.398565 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: EIVLTQSPGT LSLSPGERAT LSCRASQSVS GSYLAWYQQK PGQAPSLLIY GASSRATGIP DRFSGSGSGT DFTLTISRLE PEDFAVYYC QQYVNSPRTF GQGTKLE |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Concentration | 0.9 mg/mL |
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Buffer | pH: 7.5 |
Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 20.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Average exposure time: 1.2 sec. / Average electron dose: 56.0 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: Details: 7A29 |
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Initial angle assignment | Type: PROJECTION MATCHING / Software - Name: cryoSPARC |
Final 3D classification | Number classes: 2 / Software - Name: cryoSPARC |
Final angle assignment | Type: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 3.2) |
Final reconstruction | Number classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 139021 |