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Yorodumi- PDB-1om2: SOLUTION NMR STRUCTURE OF THE MITOCHONDRIAL PROTEIN IMPORT RECEPT... -
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-Basic information
Entry | Database: PDB / ID: 1om2 | ||||||
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Title | SOLUTION NMR STRUCTURE OF THE MITOCHONDRIAL PROTEIN IMPORT RECEPTOR TOM20 FROM RAT IN A COMPLEX WITH A PRESEQUENCE PEPTIDE DERIVED FROM RAT ALDEHYDE DEHYDROGENASE (ALDH) | ||||||
Components |
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Keywords | RECEPTOR/OXIDOREDUCTASE COMPLEX / MITOCHONDRIAL PROTEIN IMPORT ACROSS OUTER MEMBRANE / RECEPTOR FOR PRESEQUENCES / MITOCHONDRIAL TARGETING SIGNAL / PRESEQUENCE PEPTIDE / RECEPTOR-OXIDOREDUCTASE COMPLEX COMPLEX | ||||||
Function / homology | Function and homology information Ethanol oxidation / cellular response to resveratrol / Metabolism of serotonin / ethanol metabolic process / Mitochondrial protein degradation / tRNA import into mitochondrion / Smooth Muscle Contraction / regulation of response to oxidative stress / PINK1-PRKN Mediated Mitophagy / mitochondrion targeting sequence binding ...Ethanol oxidation / cellular response to resveratrol / Metabolism of serotonin / ethanol metabolic process / Mitochondrial protein degradation / tRNA import into mitochondrion / Smooth Muscle Contraction / regulation of response to oxidative stress / PINK1-PRKN Mediated Mitophagy / mitochondrion targeting sequence binding / nitroglycerin reductase activity / regulation of dopamine biosynthetic process / regulation of serotonin biosynthetic process / phenylacetaldehyde dehydrogenase activity / aldehyde catabolic process / mitochondrial outer membrane translocase complex / response to 3,3',5-triiodo-L-thyronine / mitochondria-associated endoplasmic reticulum membrane contact site / migrasome / ethanol catabolic process / Ub-specific processing proteases / protein import into mitochondrial matrix / carboxylesterase activity / acetaldehyde metabolic process / NADH binding / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (non-phosphorylating) activity / protein-transporting ATPase activity / aldehyde dehydrogenase (NAD+) / cellular detoxification of aldehyde / behavioral response to ethanol / protein targeting to mitochondrion / aldehyde dehydrogenase (NAD+) activity / mitochondrial envelope / response to muscle activity / regulation of reactive oxygen species metabolic process / cellular response to fatty acid / intrinsic apoptotic signaling pathway in response to oxidative stress / response to testosterone / apoptotic mitochondrial changes / response to hyperoxia / cellular response to hormone stimulus / sperm midpiece / liver development / response to progesterone / cell periphery / response to ischemia / response to nicotine / intracellular protein transport / response to organic cyclic compound / unfolded protein binding / response to estradiol / response to ethanol / mitochondrial outer membrane / response to lipopolysaccharide / mitochondrial matrix / negative regulation of apoptotic process / mitochondrion / identical protein binding Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | SOLUTION NMR / TORSION ANGLE DYNAMICS, RESTRAINED ENERGY MINIMIZATION WITH AMBER FORCE FIELD | ||||||
Authors | Abe, Y. / Shodai, T. / Muto, T. / Mihara, K. / Torii, H. / Nishikawa, S. / Endo, T. / Kohda, D. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2000 Title: Structural basis of presequence recognition by the mitochondrial protein import receptor Tom20. Authors: Abe, Y. / Shodai, T. / Muto, T. / Mihara, K. / Torii, H. / Nishikawa, S. / Endo, T. / Kohda, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1om2.cif.gz | 654.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1om2.ent.gz | 552.5 KB | Display | PDB format |
PDBx/mmJSON format | 1om2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/om/1om2 ftp://data.pdbj.org/pub/pdb/validation_reports/om/1om2 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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NMR ensembles |
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-Components
#1: Protein | Mass: 10462.907 Da / Num. of mol.: 1 / Fragment: RESIDUES 51-145 Source method: isolated from a genetically manipulated source Details: CYTOSOLIC DOMAIN, LIMITED PROTEOLYZED FRAGMENT / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cellular location: MITOCHONDRIAL OUTER MEMBRANE / Organelle: MITOCHONDRIAMitochondrion / Plasmid: PET-21A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: Q62760 |
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#2: Protein/peptide | Mass: 1234.450 Da / Num. of mol.: 1 / Fragment: RESIDUES 12-22 / Mutation: A21Y / Source method: obtained synthetically Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THIS PEPTIDE IS NATUALLY FOUND IN RATTUS NORVEGICUS (RAT). THE EXPRESSION SYSTEM WAS ESCHERICHIA COLI, STRAIN BL21(DE3), PLASMID PET-17XB. References: UniProt: P11884, aldehyde dehydrogenase (NAD+) |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: THE INTRA-TOM20 PROTEIN NOES WERE OBTAINED AT PH5.4 AND 0.02M CHAPSO ( DETERGENT) IN THE ABSENCE OF THE PEPTIDE USING 3D 15N-RESOLVED AND 3D 13C- RESOLVED NOESY SPECTRA. THE INTRA-PEPTIDE NOES ...Text: THE INTRA-TOM20 PROTEIN NOES WERE OBTAINED AT PH5.4 AND 0.02M CHAPSO ( DETERGENT) IN THE ABSENCE OF THE PEPTIDE USING 3D 15N-RESOLVED AND 3D 13C- RESOLVED NOESY SPECTRA. THE INTRA-PEPTIDE NOES AND INTERMOLECULAR NOES WERE COLLECTED AT PH6.8 IN THE ABSENCE OF CHAPSO USING 2D AND 3D NOESY SPECTRA WITH ISOTOPE FILTERS. THE NOE ASSIGNMENT WAS COMPLETED BY USING SEQUENCE- SPECIFICALLY DEUTERATED DERIVATIVES OF THE PEPTIDE. THESE THREE NOE SETS WERE COMBINED TO CALCULATE THE COMPLEX STRUCTURE OF TOM20 AND THE PRESEQUENCE PEPTIDE. |
-Sample preparation
Details | Contents: 90% WATER/10% D2O, 100% D2O |
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Sample conditions | Ionic strength: 0.02M / pH: 6.8 / Pressure: 1 atm / Temperature: 303 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: TORSION ANGLE DYNAMICS, RESTRAINED ENERGY MINIMIZATION WITH AMBER FORCE FIELD Software ordinal: 1 Details: DEPOSITED COORDINATES WERE CALCULATED BASED ON 1012 NOE-DERIVED DISTANCE, 80 SLOWLY EXCHANGING AMIDE PROTON-DERIVED DISTANCE, AND 39 DIHEDRAL ANGLE RESTRAINTS. NO VIOLATIONS OF DISTANCE ...Details: DEPOSITED COORDINATES WERE CALCULATED BASED ON 1012 NOE-DERIVED DISTANCE, 80 SLOWLY EXCHANGING AMIDE PROTON-DERIVED DISTANCE, AND 39 DIHEDRAL ANGLE RESTRAINTS. NO VIOLATIONS OF DISTANCE RESTRAINTS EXCEED 0.33 ANGSTROMS, AND NO VIOLATIONS OF ANGLE CONSTRAINTS EXCEED 2.8 DEGREES. | ||||||||||||||||
NMR ensemble | Conformer selection criteria: LOWEST TARGET FUNCTION / Conformers calculated total number: 200 / Conformers submitted total number: 20 |