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- EMDB-22089: CryoEM structure of the Plasmodium berghei circumsporozoite prote... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-22089 | |||||||||||||||
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Title | CryoEM structure of the Plasmodium berghei circumsporozoite protein in complex with inhibitory mouse antibody 3D11. | |||||||||||||||
![]() | Circumsporozoite protein in complex with inhibitory antibody 3D11.![]() | |||||||||||||||
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Function / homology | Plasmodium circumsporozoite protein / Thrombospondin type 1 domain / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / ![]() ![]() ![]() ![]() | |||||||||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() ![]() | |||||||||||||||
Method | ![]() ![]() | |||||||||||||||
![]() | Kucharska I / Thai E / Rubinstein J / Julien JP | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural ordering of the circumsporozoite protein repeats by inhibitory antibody 3D11. Authors: Iga Kucharska / Elaine Thai / Ananya Srivastava / John L Rubinstein / Régis Pomès / Jean-Philippe Julien / ![]() Abstract: Plasmodium sporozoites express circumsporozoite protein (CSP) on their surface, an essential protein that contains central repeating motifs. Antibodies targeting this region can neutralize infection, ...Plasmodium sporozoites express circumsporozoite protein (CSP) on their surface, an essential protein that contains central repeating motifs. Antibodies targeting this region can neutralize infection, and the partial efficacy of RTS,S/AS01 - the leading malaria vaccine against (Pf) - has been associated with the humoral response against the repeats. Although structural details of antibody recognition of PfCSP have recently emerged, the molecular basis of antibody-mediated inhibition of other Plasmodium species via CSP binding remains unclear. Here, we analyze the structure and molecular interactions of potent monoclonal antibody (mAb) 3D11 binding to CSP (PbCSP) using molecular dynamics simulations, X-ray crystallography, and cryoEM. We reveal that mAb 3D11 can accommodate all subtle variances of the PbCSP repeating motifs, and, upon binding, induces structural ordering of PbCSP through homotypic interactions. Together, our findings uncover common mechanisms of antibody evolution in mammals against the CSP repeats of Plasmodium sporozoites. | |||||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 110.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 15.8 KB 15.8 KB | Display Display | ![]() |
Images | ![]() | 350.1 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6x87MC ![]() 6x8pC ![]() 6x8qC ![]() 6x8sC ![]() 6x8uC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | Circumsporozoite protein in complex with inhibitory antibody 3D11. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Complex of Plasmodium berghei CSP protein and 3D11 Fab
Entire | Name: Complex of Plasmodium berghei CSP protein and 3D11 Fab |
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Components |
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-Supramolecule #1: Complex of Plasmodium berghei CSP protein and 3D11 Fab
Supramolecule | Name: Complex of Plasmodium berghei CSP protein and 3D11 Fab type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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-Supramolecule #2: 3D11 Fab heavy chain, 3D11 Fab kappa chain
Supramolecule | Name: 3D11 Fab heavy chain, 3D11 Fab kappa chain / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: ![]() ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() |
-Supramolecule #3: Circumsporozoite protein
Supramolecule | Name: Circumsporozoite protein / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3 |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() ![]() |
-Macromolecule #1: 3D11 Fab heavy chain
Macromolecule | Name: 3D11 Fab heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 22.830475 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: NSQAYLQQSG AELVRSGASV KMSCKASGYT FTSYNMHWVK QTPGQGLEWI GYIYPGNGVT NFNQKFKGKA TLTADTSSST AYMQISSLT SEDSAVYFCA SAAYWGQGTL VTVSSASTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFPE PVTVSWNSGA L TSGVHTFP ...String: NSQAYLQQSG AELVRSGASV KMSCKASGYT FTSYNMHWVK QTPGQGLEWI GYIYPGNGVT NFNQKFKGKA TLTADTSSST AYMQISSLT SEDSAVYFCA SAAYWGQGTL VTVSSASTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFPE PVTVSWNSGA L TSGVHTFP AVLQSSGLYS LSSVVTVPSS SLGTQTYICN VNHKPSNTKV DKKVEPKSC |
-Macromolecule #2: 3D11 Fab kappa chain
Macromolecule | Name: 3D11 Fab kappa chain / type: protein_or_peptide / ID: 2 / Number of copies: 7 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 24.19102 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: NSDVVMTQTP LTLSVTIGQP ASISCKSSQS LLYSDGKTYL NWLLQRPGQS PKRLISLVSE LDSGVPDRFT GSGSGTDFTL KISRVEAED LGVYYCWQGT HFPRTFGGGT KLEIKRTVAA PSVFIFPPSD EQLKSGTASV VCLLNNFYPR EAKVQWKVDN A LQSGNSQE ...String: NSDVVMTQTP LTLSVTIGQP ASISCKSSQS LLYSDGKTYL NWLLQRPGQS PKRLISLVSE LDSGVPDRFT GSGSGTDFTL KISRVEAED LGVYYCWQGT HFPRTFGGGT KLEIKRTVAA PSVFIFPPSD EQLKSGTASV VCLLNNFYPR EAKVQWKVDN A LQSGNSQE SVTEQDSKDS TYSLSSTLTL SKADYEKHKV YACEVTHQGL SSPVTKSFNR GEC |
-Macromolecule #3: Circumsporozoite protein
Macromolecule | Name: Circumsporozoite protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 36.397008 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: EFATMGILPS PGMPALLSLV SLLSVLLMGC VAQQKSIQAQ RNLNELCYNE GNDNKLYHVL NSKNGKIYNR NTVNRLLADA PEGKKNEKK NEKIERNNKL KQPPPPPNPN DPPPPNPNDP PPPNPNDPPP PNPNDPPPPN ANDPPPPNAN DPAPPNANDP A PPNANDPA ...String: EFATMGILPS PGMPALLSLV SLLSVLLMGC VAQQKSIQAQ RNLNELCYNE GNDNKLYHVL NSKNGKIYNR NTVNRLLADA PEGKKNEKK NEKIERNNKL KQPPPPPNPN DPPPPNPNDP PPPNPNDPPP PNPNDPPPPN ANDPPPPNAN DPAPPNANDP A PPNANDPA PPNANDPAPP NANDPPPPNP NDPAPPNAND PPPPNPNDPA PPQGNNNPQP QPRPQPQPQP QPQPQPQPQP QP RPQPQPQ PGGNNNNKNN NNDDSYIPSA EKILEFVKQI RDSITEEWSQ CQVTCGSGIR VRKRKGSNKK AEDLTLEDID TEI CKMDKC SPHHHHHH |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Concentration | 3.0 mg/mL | |||||||||||||||
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Buffer | pH: 8 Component:
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Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 90 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK III |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 2080 / Average electron dose: 42.7 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Particle selection | Number selected: 669223 |
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CTF correction | Software - Name: cryoSPARC (ver. 2) |
Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: NOT APPLICABLE |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2) / Number images used: 165747 |