+Open data
-Basic information
Entry | Database: PDB / ID: 1de4 | ||||||
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Title | HEMOCHROMATOSIS PROTEIN HFE COMPLEXED WITH TRANSFERRIN RECEPTOR | ||||||
Components |
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Keywords | METAL TRANSPORT INHIBITOR/RECEPTOR / HFE / HEREDITARY HEMOCHROMATOSIS / MHC CLASS I / TRANSFERRIN RECEPTOR / METAL TRANSPORT INHIBITOR-RECEPTOR COMPLEX | ||||||
Function / homology | Function and homology information negative regulation of antigen processing and presentation of endogenous peptide antigen via MHC class I / response to iron ion starvation / transferrin receptor activity / negative regulation of T cell cytokine production / hormone biosynthetic process / negative regulation of CD8-positive, alpha-beta T cell activation / negative regulation of mitochondrial fusion / transferrin transport / co-receptor binding / Transferrin endocytosis and recycling ...negative regulation of antigen processing and presentation of endogenous peptide antigen via MHC class I / response to iron ion starvation / transferrin receptor activity / negative regulation of T cell cytokine production / hormone biosynthetic process / negative regulation of CD8-positive, alpha-beta T cell activation / negative regulation of mitochondrial fusion / transferrin transport / co-receptor binding / Transferrin endocytosis and recycling / transferrin receptor binding / positive regulation of isotype switching / regulation of protein localization to cell surface / basal part of cell / Differentiation of keratinocytes in interfollicular epidermis in mammalian skin / positive regulation of signaling receptor activity / response to copper ion / response to iron ion / RND1 GTPase cycle / response to manganese ion / RND2 GTPase cycle / positive regulation of bone resorption / RHOB GTPase cycle / Golgi Associated Vesicle Biogenesis / BMP signaling pathway / RHOC GTPase cycle / RHOJ GTPase cycle / positive regulation of peptide hormone secretion / RHOQ GTPase cycle / positive regulation of SMAD protein signal transduction / CDC42 GTPase cycle / negative regulation of signaling receptor activity / RHOH GTPase cycle / RHOG GTPase cycle / transport across blood-brain barrier / RHOA GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / beta-2-microglobulin binding / negative regulation of ubiquitin-dependent protein catabolic process / response to nutrient / response to retinoic acid / positive regulation of T cell proliferation / clathrin-coated pit / positive regulation of B cell proliferation / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / Hsp70 protein binding / RAC1 GTPase cycle / osteoclast differentiation / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / clathrin-coated endocytic vesicle membrane / negative regulation of receptor binding / DAP12 interactions / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / cellular response to leukemia inhibitory factor / acute-phase response / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / positive regulation of protein-containing complex assembly / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / recycling endosome / receptor internalization / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / positive regulation of protein localization to nucleus / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / cellular response to xenobiotic stimulus / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / Cargo recognition for clathrin-mediated endocytosis / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.8 Å | ||||||
Authors | Bennett, M.J. / Lebron, J.A. / Bjorkman, P.J. | ||||||
Citation | Journal: Nature / Year: 2000 Title: Crystal structure of the hereditary haemochromatosis protein HFE complexed with transferrin receptor. Authors: Bennett, M.J. / Lebron, J.A. / Bjorkman, P.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1de4.cif.gz | 599.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1de4.ent.gz | 493.6 KB | Display | PDB format |
PDBx/mmJSON format | 1de4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1de4_validation.pdf.gz | 471.3 KB | Display | wwPDB validaton report |
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Full document | 1de4_full_validation.pdf.gz | 592.4 KB | Display | |
Data in XML | 1de4_validation.xml.gz | 72.6 KB | Display | |
Data in CIF | 1de4_validation.cif.gz | 107.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/de/1de4 ftp://data.pdbj.org/pub/pdb/validation_reports/de/1de4 | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
-Protein , 3 types, 9 molecules ADGBEHCFI
#1: Protein | Mass: 32339.434 Da / Num. of mol.: 3 / Fragment: ECTODOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PBJ5-GS / Cell (production host): OVARY CELLS / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q30201 #2: Protein | Mass: 11748.160 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell (production host): OVARY CELLS / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P61769 #3: Protein | Mass: 71807.258 Da / Num. of mol.: 3 / Fragment: ECTODOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PACGP67A / Cell (production host): HIGH 5 INSECT CELLS / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P02786 |
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-Sugars , 1 types, 3 molecules
#4: Sugar |
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-Non-polymers , 3 types, 13 molecules
#5: Chemical | #6: Chemical | ChemComp-GOL / | #7: 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: 3.74 Å3/Da / Density % sol: 61 % | ||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 8000, TRIS, TRIMETHYLAMINE HCL, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 7, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→30 Å / Num. all: 122846 / Num. obs: 122846 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 18 |
Reflection shell | Resolution: 2.8→2.85 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.341 / Mean I/σ(I) obs: 3.3 / % possible all: 99.8 |
Reflection | *PLUS |
Reflection shell | *PLUS % possible obs: 99.8 % |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS / Resolution: 2.8→30 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 685830.33 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: SEVERAL SIDECHAINS ARE MODELED AS ALA AS IN UNCOMPLEXED HFE. A POSITIVE DIFFERENCE PEAK NEAR TFR CHAINS C,F,I WHICH LACKED PROTEIN LIGANDS WAS MODELED AS A WATER MOLECULE (WATERS 4,6,8). A ...Details: SEVERAL SIDECHAINS ARE MODELED AS ALA AS IN UNCOMPLEXED HFE. A POSITIVE DIFFERENCE PEAK NEAR TFR CHAINS C,F,I WHICH LACKED PROTEIN LIGANDS WAS MODELED AS A WATER MOLECULE (WATERS 4,6,8). A POSITIVE DIFFERENCE PEAK NEAR THE HFE CHAIN G PLATFORM WAS MODELED AS A GLYCEROL. SEVERAL LOOPS HAVE RESIDUES WITH LOW CORRELATIONS AGAINST THE FINAL MAP: HFE PLATFORM LOOPS FROM STRAND 1 (S1) TO STRAND 2 (S2), S4-ALPHA1 HELIX; HFE ALPHA3 DOMAIN LOOPS S1-S2, S3-S4,S6-S7; BETA-2-MICROGLOBULIN LOOPS S1-S2, S3-S4, S5-S6, C-TERMINUS.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 30.72 Å2 / ksol: 0.303 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 66.3 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→30 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINED | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.5 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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