+Open data
-Basic information
Entry | Database: PDB / ID: 5lgd | |||||||||
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Title | The CIDRa domain from MCvar1 PfEMP1 bound to CD36 | |||||||||
Components |
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Keywords | CELL ADHESION / Plasmodium falciparum cytoadhesion scavenger receptor malaria | |||||||||
Function / homology | Function and homology information short-chain fatty acid transmembrane transporter activity / short-chain fatty acid transport / lipoteichoic acid immune receptor activity / oxidised low-density lipoprotein particle clearance / oxidised low-density lipoprotein particle receptor activity / Intracellular metabolism of fatty acids regulates insulin secretion / long-chain fatty acid import across plasma membrane / response to linoleic acid / oleate transmembrane transporter activity / Toll Like Receptor TLR6:TLR2 Cascade ...short-chain fatty acid transmembrane transporter activity / short-chain fatty acid transport / lipoteichoic acid immune receptor activity / oxidised low-density lipoprotein particle clearance / oxidised low-density lipoprotein particle receptor activity / Intracellular metabolism of fatty acids regulates insulin secretion / long-chain fatty acid import across plasma membrane / response to linoleic acid / oleate transmembrane transporter activity / Toll Like Receptor TLR6:TLR2 Cascade / antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent / low-density lipoprotein particle mediated signaling / toll-like receptor TLR6:TLR2 signaling pathway / cellular response to diacyl bacterial lipopeptide / positive regulation of cholesterol storage / long-chain fatty acid import into cell / triglyceride transport / : / response to stilbenoid / Scavenging by Class B Receptors / plasma lipoprotein particle clearance / production of molecular mediator involved in inflammatory response / regulation of action potential / lipid transport across blood-brain barrier / positive regulation of blood microparticle formation / regulation of lipopolysaccharide-mediated signaling pathway / neutrophil degranulation / cholesterol import / cellular response to hydroperoxide / high-density lipoprotein particle binding / low-density lipoprotein particle clearance / low-density lipoprotein particle receptor activity / platelet degranulation / cellular response to oxidised low-density lipoprotein particle stimulus / Cross-presentation of particulate exogenous antigens (phagosomes) / intestinal cholesterol absorption / Toll-like receptor binding / regulation of removal of superoxide radicals / low-density lipoprotein particle binding / platelet alpha granule membrane / positive regulation of macrophage derived foam cell differentiation / amyloid-beta clearance by cellular catabolic process / response to fatty acid / Regulation of TLR by endogenous ligand / lipid storage / positive regulation of phagocytosis, engulfment / scavenger receptor activity / phagocytosis, recognition / regulation of metabolic process / cholesterol transport / transforming growth factor beta binding / MyD88 deficiency (TLR2/4) / apoptotic cell clearance / intestinal absorption / positive regulation of macrophage cytokine production / MyD88-dependent toll-like receptor signaling pathway / IRAK4 deficiency (TLR2/4) / positive regulation of reactive oxygen species biosynthetic process / lipoprotein transport / positive regulation of cell-matrix adhesion / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / long-chain fatty acid transmembrane transporter activity / toll-like receptor signaling pathway / positive regulation of NLRP3 inflammasome complex assembly / phagocytosis, engulfment / negative regulation of protein import into nucleus / response to lipid / regulation of toll-like receptor signaling pathway / thrombospondin receptor activity / plasma membrane => GO:0005886 / lipoprotein particle binding / cGMP-mediated signaling / cellular response to lipoteichoic acid / cellular response to low-density lipoprotein particle stimulus / regulation of protein-containing complex assembly / positive regulation of blood coagulation / long-chain fatty acid transport / specific granule membrane / energy homeostasis / phagocytic vesicle / nitric oxide mediated signal transduction / positive regulation of interleukin-12 production / receptor-mediated endocytosis / fatty acid metabolic process / positive regulation of interleukin-1 beta production / caveola / cell periphery / brush border membrane / lipid metabolic process / receptor internalization / PPARA activates gene expression / Transcriptional regulation of white adipocyte differentiation / cytokine-mediated signaling pathway / positive regulation of interleukin-6 production / sensory perception of taste / cellular response to amyloid-beta / endocytic vesicle membrane / positive regulation of nitric oxide biosynthetic process / positive regulation of peptidyl-tyrosine phosphorylation / blood coagulation Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Plasmodium falciparum (malaria parasite P. falciparum) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å | |||||||||
Authors | Hsieh, F.L. / Higgins, M.K. | |||||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Nat Commun / Year: 2016 Title: The structural basis for CD36 binding by the malaria parasite. Authors: Hsieh, F.L. / Turner, L. / Bolla, J.R. / Robinson, C.V. / Lavstsen, T. / 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 | 5lgd.cif.gz | 254.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lgd.ent.gz | 205.2 KB | Display | PDB format |
PDBx/mmJSON format | 5lgd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lg/5lgd ftp://data.pdbj.org/pub/pdb/validation_reports/lg/5lgd | HTTPS FTP |
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-Related structure data
Related structure data | 4f7bS 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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Unit cell |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 53104.055 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CD36, GP3B, GP4 / Production host: Homo sapiens (human) / References: UniProt: P16671 |
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#2: Protein | Mass: 20915.965 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Gene: MCvar-1 PfEMP1 / Production host: Homo sapiens (human) / References: UniProt: Q25733 |
-Sugars , 2 types, 9 molecules
#3: Polysaccharide | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#4: Sugar | ChemComp-NAG / |
-Non-polymers , 4 types, 161 molecules
#5: Chemical | #6: Chemical | ChemComp-GOL / #7: Chemical | #8: 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: 2.25 Å3/Da / Density % sol: 45.33 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2 M NaCl, 20% (w/v) PEG6000, 0.1 M Tris, pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 18, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.07→63 Å / Num. obs: 40626 / % possible obs: 99.8 % / Redundancy: 3.2 % / Biso Wilson estimate: 34.48 Å2 / Net I/σ(I): 8.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4F7B Resolution: 2.07→62.99 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.924 / SU R Cruickshank DPI: 0.212 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.209 / SU Rfree Blow DPI: 0.179 / SU Rfree Cruickshank DPI: 0.181
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Displacement parameters | Biso mean: 48.28 Å2
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Refine analyze | Luzzati coordinate error obs: 0.374 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.07→62.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.07→2.12 Å / Total num. of bins used: 20
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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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