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Yorodumi- PDB-5f0m: Structure of retromer VPS26-VPS35 subunits bound to SNX3 and DMT1... -
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-Basic information
Entry | Database: PDB / ID: 5f0m | ||||||||||||
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Title | Structure of retromer VPS26-VPS35 subunits bound to SNX3 and DMT1 (SeMet labeled) | ||||||||||||
Components |
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Keywords | PROTEIN TRANSPORT / retromer / sorting nexin | ||||||||||||
Function / homology | Function and homology information vanadium ion transmembrane transporter activity / vanadium ion transport / transition metal ion transmembrane transporter activity / paraferritin complex / Defective SLC11A2 causes hypochromic microcytic anemia, with iron overload 1 (AHMIO1) / lead ion transmembrane transporter activity / lead ion transport / negative regulation of early endosome to late endosome transport / nickel cation transmembrane transporter activity / late endosome to Golgi transport ...vanadium ion transmembrane transporter activity / vanadium ion transport / transition metal ion transmembrane transporter activity / paraferritin complex / Defective SLC11A2 causes hypochromic microcytic anemia, with iron overload 1 (AHMIO1) / lead ion transmembrane transporter activity / lead ion transport / negative regulation of early endosome to late endosome transport / nickel cation transmembrane transporter activity / late endosome to Golgi transport / cadmium ion transmembrane transport / nickel cation transport / solute:proton symporter activity / protein to membrane docking / negative regulation of protein transport / positive regulation of locomotion involved in locomotory behavior / neurotransmitter receptor transport, endosome to plasma membrane / mitochondrion-derived vesicle / inorganic cation transmembrane transporter activity / negative regulation of protein localization / regulation of dendritic spine maintenance / Metal ion SLC transporters / membrane invagination / negative regulation of protein homooligomerization / tubular endosome / mitochondrion to lysosome vesicle-mediated transport / zinc ion transmembrane transporter activity / positive regulation of Wnt protein secretion / manganese ion transport / detection of oxygen / regulation of postsynapse assembly / regulation of terminal button organization / cobalt ion transport / retromer, cargo-selective complex / vesicle-mediated transport in synapse / WNT ligand biogenesis and trafficking / cadmium ion transmembrane transporter activity / cobalt ion transmembrane transporter activity / manganese ion transmembrane transporter activity / intralumenal vesicle formation / iron import into cell / iron ion transmembrane transporter activity / retromer complex binding / negative regulation of late endosome to lysosome transport / copper ion transmembrane transporter activity / iron ion transmembrane transport / negative regulation of lysosomal protein catabolic process / positive regulation of dopamine receptor signaling pathway / positive regulation of dopamine biosynthetic process / ferrous iron transmembrane transporter activity / retromer complex / mitochondrial fragmentation involved in apoptotic process / phosphatidylinositol-5-phosphate binding / protein localization to endosome / neurotransmitter receptor transport, endosome to postsynaptic membrane / dopaminergic synapse / voluntary musculoskeletal movement / copper ion transport / negative regulation of viral entry into host cell / basal part of cell / regulation of protein metabolic process / regulation of synapse maturation / transcytosis / endocytic recycling / early phagosome / phosphatidylinositol-3-phosphate binding / regulation of Wnt signaling pathway / retrograde transport, endosome to Golgi / positive regulation of protein localization to cell periphery / regulation of mitochondrion organization / phosphatidylinositol-4-phosphate binding / phosphatidylinositol-3,5-bisphosphate binding / response to iron ion / vacuole / dendrite morphogenesis / negative regulation of phagocytosis / clathrin-coated vesicle / heme biosynthetic process / positive regulation of mitochondrial fission / lysosome organization / cadmium ion binding / regulation of presynapse assembly / D1 dopamine receptor binding / regulation of macroautophagy / erythrocyte development / negative regulation of protein catabolic process / brush border membrane / Iron uptake and transport / response to bacterium / intracellular protein transport / negative regulation of inflammatory response / protein destabilization / trans-Golgi network / modulation of chemical synaptic transmission / regulation of protein stability / recycling endosome / activation of cysteine-type endopeptidase activity involved in apoptotic process / Wnt signaling pathway / multicellular organismal-level iron ion homeostasis / positive regulation of neuron projection development Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||||||||
Authors | Lucas, M. / Gershlick, D. / Vidaurrazaga, A. / Rojas, A.L. / Bonifacino, J.S. / Hierro, A. | ||||||||||||
Funding support | Spain, 3items
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Citation | Journal: Cell / Year: 2016 Title: Structural Mechanism for Cargo Recognition by the Retromer Complex. Authors: Lucas, M. / Gershlick, D.C. / Vidaurrazaga, A. / Rojas, A.L. / Bonifacino, J.S. / Hierro, A. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5f0m.cif.gz | 204.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5f0m.ent.gz | 159.8 KB | Display | PDB format |
PDBx/mmJSON format | 5f0m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5f0m_validation.pdf.gz | 490.2 KB | Display | wwPDB validaton report |
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Full document | 5f0m_full_validation.pdf.gz | 494.9 KB | Display | |
Data in XML | 5f0m_validation.xml.gz | 31.7 KB | Display | |
Data in CIF | 5f0m_validation.cif.gz | 43.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f0/5f0m ftp://data.pdbj.org/pub/pdb/validation_reports/f0/5f0m | HTTPS FTP |
-Related structure data
Related structure data | 5f0jC 5f0kC 5f0lSC 5f0pC C: citing same article (ref.) 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
-Vacuolar protein sorting-associated protein ... , 2 types, 2 molecules AB
#1: Protein | Mass: 53288.270 Da / Num. of mol.: 1 / Fragment: Residues 14-470 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: VPS35, MEM3, TCCCTA00141 / Plasmid: pGST-Parallel2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q96QK1 |
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#2: Protein | Mass: 37913.312 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: VPS26A, VPS26 / Plasmid: pET-Sumo3 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: O75436 |
-Protein / Protein/peptide , 2 types, 2 molecules CD
#3: Protein | Mass: 19193.814 Da / Num. of mol.: 1 / Fragment: Residues 14-470 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SNX3 / Plasmid: pHis-MBP-Parallel2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O60493 |
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#4: Protein/peptide | Mass: 2218.311 Da / Num. of mol.: 1 / Fragment: UNP residues 549-560 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SLC11A2, DCT1, DMT1, NRAMP2, OK/SW-cl.20 / Plasmid: pET-Sumo3 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P49281 |
-Non-polymers , 3 types, 23 molecules
#5: Chemical | ChemComp-SO4 / #6: Chemical | ChemComp-GOL / #7: Chemical | ChemComp-EDO / |
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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: 3.5 Å3/Da / Density % sol: 64.82 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.8 M AmSO4, 0.1 M MES pH 6.0, 5% Glycerol |
-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: May 4, 2015 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.975 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.1→56.89 Å / Num. obs: 55451 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 79.095 Å2 / Rmerge F obs: 0.996 / Rmerge(I) obs: 0.105 / Rrim(I) all: 0.124 / Χ2: 0.999 / Net I/σ(I): 8.57 / Num. measured all: 195953 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5F0L Resolution: 3.1→56.89 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.869 / WRfactor Rfree: 0.2377 / WRfactor Rwork: 0.1906 / FOM work R set: 0.8002 / SU B: 21.512 / SU ML: 0.354 / SU Rfree: 0.4388 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.439 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 198.09 Å2 / Biso mean: 83.908 Å2 / Biso min: 35.18 Å2
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Refinement step | Cycle: final / Resolution: 3.1→56.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.102→3.183 Å / Total num. of bins used: 20
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