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Yorodumi- PDB-4u0q: Plasmodium falciparum reticulocyte-binding protein homologue 5 (P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4u0q | ||||||
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Title | Plasmodium falciparum reticulocyte-binding protein homologue 5 (PfRH5) bound to basigin | ||||||
Components |
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Keywords | SIGNALING PROTEIN / Malaria Erythrocyte invasion | ||||||
Function / homology | Function and homology information Defective SLC16A1 causes symptomatic deficiency in lactate transport (SDLT) / Proton-coupled monocarboxylate transport / positive regulation of matrix metallopeptidase secretion / acrosomal membrane / response to mercury ion / endothelial tube morphogenesis / neural retina development / photoreceptor cell maintenance / Basigin interactions / Aspirin ADME ...Defective SLC16A1 causes symptomatic deficiency in lactate transport (SDLT) / Proton-coupled monocarboxylate transport / positive regulation of matrix metallopeptidase secretion / acrosomal membrane / response to mercury ion / endothelial tube morphogenesis / neural retina development / photoreceptor cell maintenance / Basigin interactions / Aspirin ADME / odontogenesis of dentin-containing tooth / D-mannose binding / decidualization / photoreceptor outer segment / positive regulation of vascular endothelial growth factor production / Integrin cell surface interactions / response to cAMP / embryo implantation / neutrophil chemotaxis / Degradation of the extracellular matrix / photoreceptor inner segment / positive regulation of endothelial cell migration / protein localization to plasma membrane / sarcolemma / response to peptide hormone / positive regulation of interleukin-6 production / virus receptor activity / melanosome / signaling receptor activity / basolateral plasma membrane / angiogenesis / endosome / cell surface receptor signaling pathway / positive regulation of viral entry into host cell / cadherin binding / Golgi membrane / intracellular membrane-bounded organelle / focal adhesion / endoplasmic reticulum membrane / mitochondrion / extracellular exosome / 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: 3.1 Å | ||||||
Authors | Wright, K.E. / Hjerrild, K.A. / Bartlett, J. / Douglas, A.D. / Jin, J. / Brown, R.E. / Ashfield, R. / Clemmensen, S.B. / de Jongh, W.A. / Draper, S.J. / Higgins, M.K. | ||||||
Citation | Journal: Nature / Year: 2014 Title: Structure of malaria invasion protein RH5 with erythrocyte basigin and blocking antibodies. Authors: Wright, K.E. / Hjerrild, K.A. / Bartlett, J. / Douglas, A.D. / Jin, J. / Brown, R.E. / Illingworth, J.J. / Ashfield, R. / Clemmensen, S.B. / de Jongh, W.A. / Draper, S.J. / 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 | 4u0q.cif.gz | 395.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4u0q.ent.gz | 320.7 KB | Display | PDB format |
PDBx/mmJSON format | 4u0q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4u0q_validation.pdf.gz | 459.3 KB | Display | wwPDB validaton report |
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Full document | 4u0q_full_validation.pdf.gz | 473.3 KB | Display | |
Data in XML | 4u0q_validation.xml.gz | 32 KB | Display | |
Data in CIF | 4u0q_validation.cif.gz | 43.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u0/4u0q ftp://data.pdbj.org/pub/pdb/validation_reports/u0/4u0q | HTTPS FTP |
-Related structure data
Related structure data | 4u0rSC 4u1gC 3b5hS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 63128.816 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Production host: Drosophila melanogaster (fruit fly) / References: UniProt: B2L3N7 #2: Protein | Mass: 29254.938 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BSG, UNQ6505/PRO21383 / Production host: Escherichia coli (E. coli) / References: UniProt: P35613 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.2M lithium sulphate, 20% PEG 4000, 0.1M MES pH 6.0 |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 18, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→67.46 Å / Num. obs: 23402 / % possible obs: 99.8 % / Redundancy: 6.1 % / Biso Wilson estimate: 66.77 Å2 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 3.1→3.27 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.297 / Mean I/σ(I) obs: 2.7 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4U0R, 3B5H Resolution: 3.1→62.4 Å / Cor.coef. Fo:Fc: 0.8838 / Cor.coef. Fo:Fc free: 0.8393 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.424
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Displacement parameters | Biso mean: 50.95 Å2
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Refine analyze | Luzzati coordinate error obs: 0.631 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 3.1→62.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1→3.24 Å / Total num. of bins used: 12
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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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