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Yorodumi- PDB-4c9h: Structure of yeast mitochondrial ADP/ATP carrier isoform 2 inhibi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4c9h | ||||||
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Title | Structure of yeast mitochondrial ADP/ATP carrier isoform 2 inhibited by carboxyatractyloside (P212121 crystal form) | ||||||
Components | ADP, ATP CARRIER PROTEIN 2 | ||||||
Keywords | TRANSPORT PROTEIN / MITOCHONDRIAL CARRIER / ADP/ATP CARRIER | ||||||
Function / homology | Function and homology information Transport of nucleosides and free purine and pyrimidine bases across the plasma membrane / ATP:ADP antiporter activity / ADP transport / mitochondrial ADP transmembrane transport / Mitochondrial protein import / mitochondrial ATP transmembrane transport / heme transport / ATP transport / anaerobic respiration / mitochondrial transport ...Transport of nucleosides and free purine and pyrimidine bases across the plasma membrane / ATP:ADP antiporter activity / ADP transport / mitochondrial ADP transmembrane transport / Mitochondrial protein import / mitochondrial ATP transmembrane transport / heme transport / ATP transport / anaerobic respiration / mitochondrial transport / aerobic respiration / transmembrane transport / mitochondrial inner membrane / apoptotic process / mitochondrion / membrane Similarity search - Function | ||||||
Biological species | SACCHAROMYCES CEREVISIAE (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Ruprecht, J.J. / Hellawell, A.M. / Harding, M. / Crichton, P.G. / McCoy, A.J. / Kunji, E.R.S. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2014 Title: Structures of Yeast Mitochondrial Adp/ATP Carriers Support a Domain-Based Alternating-Access Transport Mechanism Authors: Ruprecht, J.J. / Hellawell, A.M. / Harding, M. / Crichton, P.G. / Mccoy, A.J. / Kunji, E.R.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4c9h.cif.gz | 128.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4c9h.ent.gz | 96.7 KB | Display | PDB format |
PDBx/mmJSON format | 4c9h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4c9h_validation.pdf.gz | 2.3 MB | Display | wwPDB validaton report |
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Full document | 4c9h_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 4c9h_validation.xml.gz | 24.8 KB | Display | |
Data in CIF | 4c9h_validation.cif.gz | 30.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c9/4c9h ftp://data.pdbj.org/pub/pdb/validation_reports/c9/4c9h | HTTPS FTP |
-Related structure data
Related structure data | 4c9gSC 4c9jC 4c9qC 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.9944, -0.1053, 0.0018), Vector: |
-Components
#1: Protein | Mass: 34468.164 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Plasmid: PYES3 / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain (production host): WB12 / References: UniProt: P18239 #2: Chemical | #3: Chemical | ChemComp-CDL / #4: Chemical | ChemComp-CM5 / | Nonpolymer details | CARDIOLIPI | |
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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: 2.5 Å3/Da / Density % sol: 50.5 % / Description: NONE |
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Crystal grow | pH: 8.5 Details: 0.1M TRIS PH 8.5, 10MM SODIUM CITRATE, 50MM AMMONIUM SULFATE, 8% T-BUTANOL, 23.5% PEG600. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 27, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→19.84 Å / Num. obs: 11939 / % possible obs: 99.5 % / Observed criterion σ(I): 6 / Redundancy: 3.6 % / Biso Wilson estimate: 47.01 Å2 / Rmerge(I) obs: 0.19 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 3.2→3.46 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.4 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4C9G Resolution: 3.2→19.839 Å / SU ML: 0.44 / σ(F): 1.34 / Phase error: 28.84 / Stereochemistry target values: ML
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Refinement step | Cycle: LAST / Resolution: 3.2→19.839 Å
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Refine LS restraints |
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LS refinement shell |
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