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Yorodumi- PDB-4nuv: Heterotetramer structure of Region II from Plasmodium vivax Duffy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4nuv | ||||||
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Title | Heterotetramer structure of Region II from Plasmodium vivax Duffy Binding Protein (PvDBP) bound to the ectodomain of the Duffy Antigen Receptor for Chemokines (DARC) | ||||||
Components |
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Keywords | membrane protein / cell invasion / Duffy Binding Like (DBL) Domain Fold / GPCR / Adhesion / Invasion / Red blood cell binding / Chemokine Binding / Duffy Antigen Receptor for Chemokines / Membrane / protein binding | ||||||
Function / homology | Function and homology information regulation of chemokine production / C-C chemokine binding / chemokine-mediated signaling pathway / Peptide ligand-binding receptors / G protein-coupled receptor activity / defense response / recycling endosome / transmembrane signaling receptor activity / signaling receptor activity / early endosome ...regulation of chemokine production / C-C chemokine binding / chemokine-mediated signaling pathway / Peptide ligand-binding receptors / G protein-coupled receptor activity / defense response / recycling endosome / transmembrane signaling receptor activity / signaling receptor activity / early endosome / host cell surface receptor binding / inflammatory response / membrane / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Plasmodium vivax (malaria parasite P. vivax) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Tolia, N.H. | ||||||
Citation | Journal: Plos Pathog. / Year: 2014 Title: Red Blood Cell Invasion by Plasmodium vivax: Structural Basis for DBP Engagement of DARC. Authors: Batchelor, J.D. / Malpede, B.M. / Omattage, N.S. / Dekoster, G.T. / Henzler-Wildman, K.A. / Tolia, N.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4nuv.cif.gz | 376.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nuv.ent.gz | 316.6 KB | Display | PDB format |
PDBx/mmJSON format | 4nuv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nu/4nuv ftp://data.pdbj.org/pub/pdb/validation_reports/nu/4nuv | HTTPS FTP |
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-Related structure data
Related structure data | 4nuuC 3rrcS C: citing same article (ref.) S: Starting model for refinement |
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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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Unit cell |
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-Components
#1: Protein | Mass: 37610.051 Da / Num. of mol.: 2 / Fragment: unp residues 211-525 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax) Strain: Salvador I / Gene: PVDR / Production host: Escherichia coli (E. coli) / References: UniProt: P22290 #2: Protein/peptide | Mass: 3628.606 Da / Num. of mol.: 2 / Fragment: unp residues 14-43 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DARC, ACKR1, FY, GPD / Production host: Escherichia coli (E. coli) / References: UniProt: Q16570 #3: Chemical | #4: 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: 2.35 Å3/Da / Density % sol: 47.59 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 0.1 M HEPES and 20% (w/v) polyethylene glycol 6000, VAPOR DIFFUSION, HANGING DROP, temperature 290K, pH 7.4 |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å |
Detector | Type: NOIR-1 / Detector: CCD / Date: Dec 20, 2011 |
Radiation | Monochromator: Rosenbaum-Rock monochromator 1: high-resolution double-crystal sagittal focusing, Rosenbaum-Rock monochromator 2: double crystal, Rosenbaum-Rock vertical focusing mirror Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→20 Å / Num. all: 23251 / Num. obs: 22139 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.6→2.7 Å / % possible all: 93.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 3RRC Resolution: 2.6→19.904 Å / SU ML: 0.32 / σ(F): 1.99 / Phase error: 25.69 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→19.904 Å
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Refine LS restraints |
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LS refinement shell |
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