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- PDB-6x8u: Crystal structure of 3D11 Fab in complex with Plasmodium berghei ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6x8u | |||||||||||||||||||||
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Title | Crystal structure of 3D11 Fab in complex with Plasmodium berghei circumsporozoite protein Mixed peptide | |||||||||||||||||||||
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![]() | IMMUNE SYSTEM / Malaria / Antibody | |||||||||||||||||||||
Function / homology | ![]() positive regulation by symbiont of entry into host / positive regulation of development of symbiont in host / positive regulation of developmental process / adhesion of symbiont to host cell / entry into host cell by a symbiont-containing vacuole / external side of plasma membrane / cytoplasm Similarity search - Function | |||||||||||||||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||||||||
![]() | Thai, E. / Julien, J.P. | |||||||||||||||||||||
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
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 232.5 KB | Display | ![]() |
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PDB format | ![]() | 154.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Antibody | Mass: 22629.295 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Antibody | Mass: 23989.838 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
#3: Protein/peptide | Mass: 1623.676 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() | ||||
#4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.61 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 25.5% (w/v) PEG 4000, 15% (v/v) glycerol, 0.17 M ammonium acetate, 0.085 M sodium citrate pH 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 14, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033167 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→40 Å / Num. obs: 72981 / % possible obs: 100 % / Redundancy: 19.5 % / Biso Wilson estimate: 26.28 Å2 / CC1/2: 0.999 / Net I/σ(I): 19.6 |
Reflection shell | Resolution: 1.55→1.65 Å / Num. unique obs: 12222 / CC1/2: 0.843 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: internal Resolution: 1.55→29.19 Å / SU ML: 0.2288 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.0277 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.35 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→29.19 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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