+Open data
-Basic information
Entry | Database: PDB / ID: 7pi7 | ||||||
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Title | PfCyRPA bound to monoclonal antibody Cy.002 Fab fragment | ||||||
Components |
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Keywords | IMMUNE SYSTEM / malaria / Plasmodium falciparum / monoclonal antibody / vaccine | ||||||
Function / homology | Function and homology information microneme lumen / microneme / symbiont entry into host / apical part of cell / cytoplasmic vesicle / host extracellular space / host cell plasma membrane / protein-containing complex / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.72 Å | ||||||
Authors | Ragotte, R.J. / Higgins, M.K. | ||||||
Funding support | 1items
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Citation | Journal: Nat Commun / Year: 2022 Title: Heterotypic interactions drive antibody synergy against a malaria vaccine candidate. Authors: Ragotte, R.J. / Pulido, D. / Lias, A.M. / Quinkert, D. / Alanine, D.G.W. / Jamwal, A. / Davies, H. / Nacer, A. / Lowe, E.D. / Grime, G.W. / Illingworth, J.J. / Donat, R.F. / Garman, E.F. / ...Authors: Ragotte, R.J. / Pulido, D. / Lias, A.M. / Quinkert, D. / Alanine, D.G.W. / Jamwal, A. / Davies, H. / Nacer, A. / Lowe, E.D. / Grime, G.W. / Illingworth, J.J. / Donat, R.F. / Garman, E.F. / Bowyer, P.W. / Higgins, M.K. / Draper, S.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7pi7.cif.gz | 608.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7pi7.ent.gz | 504.5 KB | Display | PDB format |
PDBx/mmJSON format | 7pi7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7pi7_validation.pdf.gz | 476.2 KB | Display | wwPDB validaton report |
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Full document | 7pi7_full_validation.pdf.gz | 510.3 KB | Display | |
Data in XML | 7pi7_validation.xml.gz | 51.3 KB | Display | |
Data in CIF | 7pi7_validation.cif.gz | 71.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pi/7pi7 ftp://data.pdbj.org/pub/pdb/validation_reports/pi/7pi7 | HTTPS FTP |
-Related structure data
Related structure data | 7phuC 7phvC 7phwC 7pi2C 7pi3C 5tihS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 40184.039 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote) Strain: isolate 3D7 / Gene: CyRPA, pfd1130w, PF3D7_0423800 / Production host: Homo sapiens (human) / References: UniProt: Q8IFM8 #2: Antibody | Mass: 23525.227 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Production host: Homo sapiens (human) #3: Antibody | Mass: 23690.127 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Production host: Homo sapiens (human) #4: Water | ChemComp-HOH / | Has protein modification | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.23 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.1 M lithium sulfate, 30 % polyvinylpyrrolidone K15, 0.1 M HEPES pH7 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 4, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.72→48.55 Å / Num. obs: 169805 / % possible obs: 99.6 % / Redundancy: 3.5 % / CC1/2: 0.999 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 2.72→2.81 Å / Num. unique obs: 15709 / CC1/2: 0.864 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5TIH Resolution: 2.72→37.92 Å / Cor.coef. Fo:Fc: 0.869 / Cor.coef. Fo:Fc free: 0.841 / SU R Cruickshank DPI: 2.35 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.453 / SU Rfree Blow DPI: 0.389 / SU Rfree Cruickshank DPI: 0.403
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Displacement parameters | Biso max: 229.92 Å2 / Biso mean: 100.55 Å2 / Biso min: 30 Å2
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Refine analyze | Luzzati coordinate error obs: 0.51 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.72→37.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.72→2.74 Å / Total num. of bins used: 51
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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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