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Yorodumi- PDB-5hu6: Structure of the T. brucei haptoglobin-haemoglobin receptor bound... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5hu6 | |||||||||
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Title | Structure of the T. brucei haptoglobin-haemoglobin receptor bound to human haptolgobin-haemoglobin | |||||||||
Components |
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Keywords | TRANSPORT PROTEIN / Trypanosome haptoglobin-haemoglobin | |||||||||
Function / homology | Function and homology information negative regulation of hydrogen peroxide catabolic process / ciliary pocket / negative regulation of oxidoreductase activity / heme transmembrane transporter activity / nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / cellular oxidant detoxification / hemoglobin binding ...negative regulation of hydrogen peroxide catabolic process / ciliary pocket / negative regulation of oxidoreductase activity / heme transmembrane transporter activity / nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / cellular oxidant detoxification / hemoglobin binding / immune system process / renal absorption / hemoglobin complex / antioxidant activity / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen / blood vessel diameter maintenance / receptor-mediated endocytosis / hydrogen peroxide catabolic process / acute-phase response / oxygen carrier activity / Late endosomal microautophagy / Heme signaling / carbon dioxide transport / response to hydrogen peroxide / defense response / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / Cytoprotection by HMOX1 / platelet aggregation / oxygen binding / regulation of blood pressure / Chaperone Mediated Autophagy / specific granule lumen / positive regulation of nitric oxide biosynthetic process / tertiary granule lumen / Factors involved in megakaryocyte development and platelet production / blood microparticle / response to oxidative stress / ficolin-1-rich granule lumen / 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 | Homo sapiens (human) Trypanosoma brucei brucei (eukaryote) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | |||||||||
Authors | Lane-Serff, H. / Higgins, M.K. | |||||||||
Citation | Journal: Elife / Year: 2014 Title: Structural basis for ligand and innate immunity factor uptake by the trypanosome haptoglobin-haemoglobin receptor. Authors: Lane-Serff, H. / MacGregor, P. / Lowe, E.D. / Carrington, M. / 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 | 5hu6.cif.gz | 324.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hu6.ent.gz | 262.9 KB | Display | PDB format |
PDBx/mmJSON format | 5hu6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hu/5hu6 ftp://data.pdbj.org/pub/pdb/validation_reports/hu/5hu6 | HTTPS FTP |
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-Related structure data
Related structure data | 4x0jC 4x0lC 4xolS 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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1 |
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Unit cell |
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-Components
-Hemoglobin subunit ... , 2 types, 2 molecules AB
#1: Protein | Mass: 15150.353 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HBA1, HBA2 / Production host: Homo sapiens (human) / References: UniProt: P69905 |
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#2: Protein | Mass: 15222.419 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HBB / Production host: Homo sapiens (human) / References: UniProt: P68871 |
-Protein , 2 types, 2 molecules CD
#3: Protein | Mass: 28790.809 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HP / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P00738 |
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#4: Protein | Mass: 27930.453 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Gene: HpHbR / Production host: Escherichia coli (E. coli) / References: UniProt: I7B1A7, UniProt: Q581F2*PLUS |
-Sugars , 1 types, 2 molecules
#7: Sugar |
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-Non-polymers , 2 types, 4 molecules
#5: Chemical | #6: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.43 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 12.5% v/v MPD, 0.03 M NaBr, 0.03M NaI, 0.03M NaF, 0.1 M MES/imidazole pH 6.5, 12.5% w/v PEG 1000, 12.5% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.975 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 21, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.975 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→66 Å / Num. obs: 18486 / % possible obs: 99.1 % / Redundancy: 2.7 % / Biso Wilson estimate: 76.4 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 6 |
Reflection shell | Resolution: 2.9→3.06 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 1.9 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4XOL Resolution: 2.9→58.07 Å / Cor.coef. Fo:Fc: 0.9219 / Cor.coef. Fo:Fc free: 0.8765 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.368
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Displacement parameters | Biso mean: 67.95 Å2
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Refine analyze | Luzzati coordinate error obs: 0.441 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.9→58.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.08 Å / Total num. of bins used: 9
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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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