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- PDB-1om2: SOLUTION NMR STRUCTURE OF THE MITOCHONDRIAL PROTEIN IMPORT RECEPT... -

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Basic information

Entry
Database: PDB / ID: 1om2
TitleSOLUTION 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
  • PROTEIN (MITOCHONDRIAL ALDEHYDE DEHYDROGENASE)
  • PROTEIN (MITOCHONDRIAL IMPORT RECEPTOR SUBUNIT TOM20)
KeywordsRECEPTOR/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


cellular response to resveratrol / Ethanol oxidation / acetaldehyde metabolic process / Metabolism of serotonin / ethanol metabolic process / Mitochondrial protein degradation / regulation of response to oxidative stress / Smooth Muscle Contraction / PINK1-PRKN Mediated Mitophagy / tRNA import into mitochondrion ...cellular response to resveratrol / Ethanol oxidation / acetaldehyde metabolic process / Metabolism of serotonin / ethanol metabolic process / Mitochondrial protein degradation / regulation of response to oxidative stress / Smooth Muscle Contraction / PINK1-PRKN Mediated Mitophagy / tRNA import into mitochondrion / regulation of dopamine biosynthetic process / regulation of serotonin biosynthetic process / phenylacetaldehyde dehydrogenase (NAD+) activity / nitroglycerin metabolic process / aldehyde catabolic process / mitochondrion targeting sequence binding / mitochondrial outer membrane translocase complex / response to 3,3',5-triiodo-L-thyronine / ethanol catabolic process / Ub-specific processing proteases / NADH binding / mitochondria-associated endoplasmic reticulum membrane contact site / migrasome / protein import into mitochondrial matrix / aldehyde dehydrogenase (NAD+) / protein-transporting ATPase activity / cellular detoxification of aldehyde / carboxylesterase activity / behavioral response to ethanol / aldehyde dehydrogenase (NAD+) activity / mitochondrial envelope / protein targeting to mitochondrion / regulation of reactive oxygen species metabolic process / cellular response to fatty acid / intrinsic apoptotic signaling pathway in response to oxidative stress / apoptotic mitochondrial changes / response to muscle activity / response to testosterone / response to hyperoxia / cellular response to hormone stimulus / sperm midpiece / liver development / response to progesterone / response to ischemia / cell periphery / intracellular protein transport / response to nicotine / : / unfolded protein binding / response to estradiol / response to lipopolysaccharide / response to ethanol / mitochondrial outer membrane / mitochondrial matrix / negative regulation of apoptotic process / mitochondrion / identical protein binding
Similarity search - Function
Mitochondrial outer membrane translocase complex, subunit Tom20 domain / Protein import receptor MAS20 / Protein import receptor MAS20, metazoan / Mitochondrial outer membrane translocase complex, Tom20 domain superfamily / MAS20 protein import receptor / Mitochondrial Import Receptor Subunit Tom20; Chain A / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. ...Mitochondrial outer membrane translocase complex, subunit Tom20 domain / Protein import receptor MAS20 / Protein import receptor MAS20, metazoan / Mitochondrial outer membrane translocase complex, Tom20 domain superfamily / MAS20 protein import receptor / Mitochondrial Import Receptor Subunit Tom20; Chain A / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Aldehyde dehydrogenase, mitochondrial / Mitochondrial import receptor subunit TOM20 homolog
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / TORSION ANGLE DYNAMICS, RESTRAINED ENERGY MINIMIZATION WITH AMBER FORCE FIELD
AuthorsAbe, Y. / Shodai, T. / Muto, T. / Mihara, K. / Torii, H. / Nishikawa, S. / Endo, T. / Kohda, D.
CitationJournal: 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
DepositionApr 23, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Feb 2, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (MITOCHONDRIAL IMPORT RECEPTOR SUBUNIT TOM20)
B: PROTEIN (MITOCHONDRIAL ALDEHYDE DEHYDROGENASE)


Theoretical massNumber of molelcules
Total (without water)11,6972
Polymers11,6972
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200LOWEST TARGET FUNCTION
RepresentativeModel #1

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Components

#1: Protein PROTEIN (MITOCHONDRIAL IMPORT RECEPTOR SUBUNIT TOM20)


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: MITOCHONDRIA / Plasmid: PET-21A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: Q62760
#2: Protein/peptide PROTEIN (MITOCHONDRIAL ALDEHYDE DEHYDROGENASE) / ALDH


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+)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HNCA
121HN(CO)CA
131CBCA(CO)NH
141HN(CA)CB
151HBHA(CO)NH
161C(CO)NH-TOCSY HC(CO)NH-TOCSY
171(H)CCH-COSY
181(H)CCH-TOCSY
19115N-RESOLVED NOESY
110115N-RESOLVED TOCSY
1111NOESY
1121TOCSY
1131HNHA
1141{1H}-15N NOE
11513D F1 13C-FILTERED-F3 13C-RESOLVED NOESY
11612D F1/F2 13C-FILTERED NOESY
NMR detailsText: 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.

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Sample preparation

DetailsContents: 90% WATER/10% D2O, 100% D2O
Sample conditionsIonic strength: 0.02M / pH: 6.8 / Pressure: 1 atm / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMX600BrukerDMX6006001
Bruker DMX750BrukerDMX7507502

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Processing

NMR software
NameVersionDeveloperClassification
DYANA 1.5, EMBOSS5GUNTERT & WUTHRICH, NAKAI & NAKAMURArefinement
DYANAstructure solution
EMBOSSstructure solution
RefinementMethod: 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 ensembleConformer selection criteria: LOWEST TARGET FUNCTION / Conformers calculated total number: 200 / Conformers submitted total number: 20

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