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Yorodumi- PDB-7f9l: Crystal structure of the variable region of Plasmodium RIFIN #6 (... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7f9l | ||||||
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Title | Crystal structure of the variable region of Plasmodium RIFIN #6 (PF3D7_1400600) in complex with LAIR1 (with T67L, N69S and A77T mutations) | ||||||
Components |
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Keywords | IMMUNE SYSTEM / malaria / Plasmodium falciparum / RIFIN | ||||||
Function / homology | Function and homology information antigenic variation / tertiary granule membrane / specific granule membrane / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / adaptive immune response / membrane => GO:0016020 / Neutrophil degranulation / host cell plasma membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Xie, Y. / Song, H. / Li, X. / Qi, J. / Gao, G.F. | ||||||
Citation | Journal: Cell Rep / Year: 2021 Title: Structural basis of malarial parasite RIFIN-mediated immune escape against LAIR1. Authors: Xie, Y. / Li, X. / Chai, Y. / Song, H. / Qi, J. / Gao, G.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7f9l.cif.gz | 367.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7f9l.ent.gz | 242.9 KB | Display | PDB format |
PDBx/mmJSON format | 7f9l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f9/7f9l ftp://data.pdbj.org/pub/pdb/validation_reports/f9/7f9l | HTTPS FTP |
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-Related structure data
Related structure data | 7f9kC 7f9mC 7f9nC 3kgrS 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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3 |
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4 |
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5 |
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6 |
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Unit cell |
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-Components
#1: Protein | Mass: 17002.520 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote) Strain: isolate 3D7 / Gene: PF3D7_1400600 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q8IM82 #2: Protein | Mass: 12436.640 Da / Num. of mol.: 6 / Mutation: T67L, N69S, A77T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LAIR1, CD305 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q6GTX8 #3: Water | ChemComp-HOH / | |
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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: 3.56 Å3/Da / Density % sol: 65.48 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.1 M sodium acetate trihydrate pH 3.6, 40% v/v polyethylene glycol 300 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97853 Å |
Detector | Type: SDMS / Detector: CCD / Date: Mar 14, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 68571 / % possible obs: 99.9 % / Redundancy: 7.7 % / Biso Wilson estimate: 45.87 Å2 / CC1/2: 0.997 / Net I/σ(I): 14.17 |
Reflection shell | Resolution: 2.7→2.8 Å / Num. unique obs: 68571 / CC1/2: 0.519 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3KGR Resolution: 2.7→41.88 Å / SU ML: 0.3755 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.646 / Stereochemistry target values: GeoStd + Monomer Library
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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: 47.12 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→41.88 Å
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Refine LS restraints |
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LS refinement shell |
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