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Yorodumi- PDB-6i4y: X-ray structure of the human mitochondrial PRELID3b-TRIAP1 complex -
+Open data
-Basic information
Entry | Database: PDB / ID: 6i4y | |||||||||
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Title | X-ray structure of the human mitochondrial PRELID3b-TRIAP1 complex | |||||||||
Components |
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Keywords | LIPID TRANSPORT / Mitochondrial lipid transport / Complex / Phospholipid transporter / Apoptosis / Phosphatidylserine / PS transport | |||||||||
Function / homology | Function and homology information regulation of membrane lipid distribution / phosphatidic acid transfer activity / positive regulation of phospholipid transport / intermembrane lipid transfer / phospholipid transport / phospholipid translocation / detection of maltose stimulus / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / maltose transport complex / negative regulation of release of cytochrome c from mitochondria ...regulation of membrane lipid distribution / phosphatidic acid transfer activity / positive regulation of phospholipid transport / intermembrane lipid transfer / phospholipid transport / phospholipid translocation / detection of maltose stimulus / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / maltose transport complex / negative regulation of release of cytochrome c from mitochondria / carbohydrate transport / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / carbohydrate transmembrane transporter activity / DNA damage response, signal transduction by p53 class mediator / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / Mitochondrial protein degradation / mitochondrial intermembrane space / p53 binding / cellular response to UV / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / negative regulation of apoptotic process / apoptotic process / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / nucleoplasm / membrane / nucleus Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 Å | |||||||||
Authors | Miliara, X. / Berry, J.-L. / Morgan, R.M.L. / Matthews, S.J. | |||||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Nat Commun / Year: 2019 Title: Structural determinants of lipid specificity within Ups/PRELI lipid transfer proteins. Authors: Miliara, X. / Tatsuta, T. / Berry, J.L. / Rouse, S.L. / Solak, K. / Chorev, D.S. / Wu, D. / Robinson, C.V. / Matthews, S. / Langer, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6i4y.cif.gz | 131.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6i4y.ent.gz | 98.3 KB | Display | PDB format |
PDBx/mmJSON format | 6i4y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6i4y_validation.pdf.gz | 827.8 KB | Display | wwPDB validaton report |
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Full document | 6i4y_full_validation.pdf.gz | 840.7 KB | Display | |
Data in XML | 6i4y_validation.xml.gz | 24.3 KB | Display | |
Data in CIF | 6i4y_validation.cif.gz | 32.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i4/6i4y ftp://data.pdbj.org/pub/pdb/validation_reports/i4/6i4y | HTTPS FTP |
-Related structure data
Related structure data | 6i3vC 6i3yC 4xzvS 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
#1: Protein | Mass: 48939.320 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human) Gene: malE, NCTC8450_00456, NCTC9775_03059, TRIAP1, 15E1.1, HSPC132 Production host: Escherichia coli (E. coli) / Variant (production host): SHuffle References: UniProt: A0A376KDN7, UniProt: O43715, UniProt: P0AEX9*PLUS |
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#2: Protein | Mass: 23127.324 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PRELID3B, C20orf45, SLMO2, CGI-107 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y3B1 |
#3: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose |
#4: Chemical | ChemComp-NA / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.39 Å3/Da / Density % sol: 63.71 % / Description: multi plate ellipsoid shape |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: Tacsimate (60% v/v) pH 7 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 19, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.91→76.23 Å / Num. obs: 20182 / % possible obs: 99.6 % / Redundancy: 7.3 % / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 2.91→3.014 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4XZV Resolution: 2.91→76.23 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.903 / SU B: 25.368 / SU ML: 0.431 / Cross valid method: THROUGHOUT / ESU R: 1.404 / ESU R Free: 0.429 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 85.688 Å2
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Refinement step | Cycle: 1 / Resolution: 2.91→76.23 Å
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Refine LS restraints |
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