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Yorodumi- PDB-8a44: Plasmodium vivax Duffy binding protein region II bound the DARC e... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8a44 | ||||||
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Title | Plasmodium vivax Duffy binding protein region II bound the DARC ectodomain and monoclonal antibody DB1 | ||||||
Components |
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Keywords | CELL ADHESION / Plasmodium vivax / malaria / reticulocyte invasion / Duffy binding protein / DARC / sulphotyrosine. | ||||||
Function / homology | Function and homology information chemokine binding / chemokine-mediated signaling pathway / G protein-coupled receptor activity / recycling endosome / early endosome / host cell surface receptor binding / inflammatory response / membrane Similarity search - Function | ||||||
Biological species | Plasmodium vivax (malaria parasite P. vivax) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å | ||||||
Authors | Moskovitz, R. / Higgins, M.K. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: Structural basis for DARC binding in reticulocyte invasion by Plasmodium vivax. Authors: Moskovitz, R. / Pholcharee, T. / DonVito, S.M. / Guloglu, B. / Lowe, E. / Mohring, F. / Moon, R.W. / Higgins, M.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8a44.cif.gz | 325.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8a44.ent.gz | 262.4 KB | Display | PDB format |
PDBx/mmJSON format | 8a44.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8a44_validation.pdf.gz | 446.5 KB | Display | wwPDB validaton report |
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Full document | 8a44_full_validation.pdf.gz | 452.6 KB | Display | |
Data in XML | 8a44_validation.xml.gz | 30.2 KB | Display | |
Data in CIF | 8a44_validation.cif.gz | 43.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a4/8a44 ftp://data.pdbj.org/pub/pdb/validation_reports/a4/8a44 | HTTPS FTP |
-Related structure data
Related structure data | 6r2sS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 35105.344 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax) Gene: dbpII / Production host: Homo sapiens (human) / References: UniProt: A0A7M1C9Q0 |
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#2: Protein | Mass: 6512.702 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DARC / Production host: Homo sapiens (human) / References: UniProt: A0A1P8P1S7 |
#3: Antibody | Mass: 24012.893 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
#4: Antibody | Mass: 23221.805 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.14 Å3/Da / Density % sol: 70.3 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: 15% w/v jeffamine D-2003 10% v/v ethanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9999 Å |
Detector | Type: DECTRIS EIGER2 S 4M / Detector: PIXEL / Date: Dec 14, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 |
Reflection | Resolution: 2.49→72 Å / Num. obs: 52982 / % possible obs: 100 % / Redundancy: 1.9 % / CC1/2: 0.993 / Rpim(I) all: 0.07 / Net I/σ(I): 5.7 |
Reflection shell | Resolution: 2.49→2.57 Å / Num. unique obs: 4488 / CC1/2: 0.463 / Rpim(I) all: 0.735 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6R2S Resolution: 2.49→72 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.13 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 170.32 Å2 / Biso mean: 67.6063 Å2 / Biso min: 36.27 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.49→72 Å
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Refinement TLS params. | Method: refined / Origin x: -20.0781 Å / Origin y: 12.5177 Å / Origin z: -44.4272 Å
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Refinement TLS group |
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