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- PDB-4wjg: Structure of T. brucei haptoglobin-hemoglobin receptor binding to... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4wjg | |||||||||||||||
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Title | Structure of T. brucei haptoglobin-hemoglobin receptor binding to human haptoglobin-hemoglobin | |||||||||||||||
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![]() | ENDOCYTOSIS / Trypanosome / Receptor | |||||||||||||||
Function / homology | ![]() negative regulation of hydrogen peroxide catabolic process / negative regulation of oxidoreductase activity / cell wall / nitric oxide transport / hemoglobin binding / immune system process / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / renal absorption ...negative regulation of hydrogen peroxide catabolic process / negative regulation of oxidoreductase activity / cell wall / nitric oxide transport / hemoglobin binding / immune system process / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / renal absorption / organic acid binding / hemoglobin complex / antioxidant activity / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen / blood vessel diameter maintenance / acute-phase response / hydrogen peroxide catabolic process / oxygen carrier activity / Late endosomal microautophagy / Heme signaling / carbon dioxide transport / response to hydrogen peroxide / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / Cytoprotection by HMOX1 / defense response / regulation of blood pressure / oxygen binding / platelet aggregation / Chaperone Mediated Autophagy / peroxidase activity / specific granule lumen / positive regulation of nitric oxide biosynthetic process / tertiary granule lumen / Factors involved in megakaryocyte development and platelet production / ficolin-1-rich granule lumen / blood microparticle / defense response to bacterium / iron ion binding / serine-type endopeptidase activity / heme binding / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / membrane / metal ion binding / cytosol Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Stoedkilde, K. / Torvund-Jensen, M. / Moestrup, S.K. / Andersen, C.B.F. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for trypanosomal haem acquisition and susceptibility to the host innate immune system. Authors: Stdkilde, K. / Torvund-Jensen, M. / Moestrup, S.K. / Andersen, C.B. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 2.3 MB | Display | ![]() |
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PDB format | ![]() | 1.9 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 7 MB | Display | ![]() |
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Full document | ![]() | 7.1 MB | Display | |
Data in XML | ![]() | 223.2 KB | Display | |
Data in CIF | ![]() | 291 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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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
-Hemoglobin subunit ... , 2 types, 12 molecules AFKPUZBGLQV1
#1: Protein | Mass: 15150.353 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Protein | Mass: 15890.198 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Protein , 3 types, 18 molecules CHMRW2DINSX3EJOTY4
#3: Protein | Mass: 35267.066 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) ![]() #4: Protein | Mass: 16877.578 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Details: First NEAT domain Source: (gene. exp.) ![]() Gene: isdH, harA, sasI, SA1552 / Production host: ![]() ![]() #5: Protein | Mass: 36848.648 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Sugars , 2 types, 33 molecules ![](data/chem/img/NAG.gif)
#6: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #9: Sugar | ChemComp-NAG / ![]() Source method: isolated from a genetically manipulated source Formula: C8H15NO6 / Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 2 types, 24 molecules ![](data/chem/img/HEM.gif)
![](data/chem/img/OXY.gif)
![](data/chem/img/OXY.gif)
#7: Chemical | ChemComp-HEM / #8: Chemical | ChemComp-OXY / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.67 Å3/Da / Density % sol: 66.47 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 15% Polyethylene glycol (PEG) 1500, 0.1M Bis-Tris |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 20, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→29 Å / Num. obs: 184077 / % possible obs: 96.5 % / Redundancy: 2.8 % / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 3.1→3.18 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 1.44 / % possible all: 95.3 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 3.1→29 Å
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Refine LS restraints |
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LS refinement shell |
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