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- PDB-7phu: PfRH5 bound to monoclonal antibody R5.015 and R5.016 Fab fragments -
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Open data
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Basic information
Entry | Database: PDB / ID: 7phu | ||||||
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Title | PfRH5 bound to monoclonal antibody R5.015 and R5.016 Fab fragments | ||||||
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![]() | IMMUNE SYSTEM / malaria / Plasmodium falciparum / monoclonal antibody / vaccine | ||||||
Function / homology | ![]() rhoptry lumen / rhoptry / symbiont entry into host / host cell membrane / bicellular tight junction / apical part of cell / heparin binding / cytoplasmic vesicle / host extracellular space / host cell surface receptor binding ...rhoptry lumen / rhoptry / symbiont entry into host / host cell membrane / bicellular tight junction / apical part of cell / heparin binding / cytoplasmic vesicle / host extracellular space / host cell surface receptor binding / host cell plasma membrane / protein-containing complex / extracellular region / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ragotte, R.J. / Higgins, M.K. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 477.4 KB | Display | ![]() |
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PDB format | ![]() | 386.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 461.4 KB | Display | ![]() |
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Full document | ![]() | 472.7 KB | Display | |
Data in XML | ![]() | 40.8 KB | Display | |
Data in CIF | ![]() | 57.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7phvC ![]() 7phwC ![]() 7pi2C ![]() 7pi3C ![]() 7pi7C ![]() 4u0rS S: Starting model for refinement C: citing same article ( |
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Similar 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
-Antibody , 4 types, 4 molecules BCDE
#2: Antibody | Mass: 25478.518 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#3: Antibody | Mass: 23184.594 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#4: Antibody | Mass: 50902.977 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#5: Antibody | Mass: 23953.613 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Protein / Non-polymers , 2 types, 128 molecules A![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#1: Protein | Mass: 60053.875 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: isolate 3D7 / Gene: RH5, PFD1145c, PF3D7_0424100 / Production host: ![]() ![]() |
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#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.2 M sodium formate, 0.1 M bis-tris propane pH 6.5, 20 % PEG 3350 with an additive containing 0.08 % w/v Ellipticine, 0.20 % w/v Protamine sulfate salt, 0.20 % w/v D-(+)-Trehalose ...Details: 0.2 M sodium formate, 0.1 M bis-tris propane pH 6.5, 20 % PEG 3350 with an additive containing 0.08 % w/v Ellipticine, 0.20 % w/v Protamine sulfate salt, 0.20 % w/v D-(+)-Trehalose dihydrate, 0.20 % w/v 6-Phosphogluconic acid trisodium salt, 0.20 % w/v D-(+)-Glucose, 0.02 M HEPES sodium pH 6.8 |
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-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: Jul 31, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.53→48.22 Å / Num. obs: 316074 / % possible obs: 99.6 % / Redundancy: 6.7 % / CC1/2: 0.999 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 2.53→2.57 Å / Num. unique obs: 16521 / CC1/2: 0.575 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4U0R Resolution: 2.53→47.79 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.885 / SU R Cruickshank DPI: 0.571 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.547 / SU Rfree Blow DPI: 0.302 / SU Rfree Cruickshank DPI: 0.309
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Displacement parameters | Biso max: 119.53 Å2 / Biso mean: 63.66 Å2 / Biso min: 30 Å2
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Refine analyze | Luzzati coordinate error obs: 0.42 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.53→47.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.53→2.55 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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