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- PDB-3awr: Crystal structure of Rat TOM20-ALDH presequence complex: The inte... -

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Basic information

Entry
Database: PDB / ID: 3awr
TitleCrystal structure of Rat TOM20-ALDH presequence complex: The intermolecular disulfide bond was cleaved in the crystal of a disulfide-tethered complex.
Components
  • Aldehyde dehydrogenase, mitochondrial
  • Mitochondrial import receptor subunit TOM20 homolog
KeywordsMEMBRANE PROTEIN/TRANSPORT PROTEIN / PROTEIN-PROTEIN COMPLEX / MEMBRANE PROTEIN-TRANSPORT PROTEIN complex
Function / homology
Function and homology information


Ethanol oxidation / cellular response to resveratrol / Metabolism of serotonin / ethanol metabolic process / tRNA import into mitochondrion / Mitochondrial protein degradation / Smooth Muscle Contraction / regulation of response to oxidative stress / PINK1-PRKN Mediated Mitophagy / nitroglycerin reductase activity ...Ethanol oxidation / cellular response to resveratrol / Metabolism of serotonin / ethanol metabolic process / tRNA import into mitochondrion / Mitochondrial protein degradation / Smooth Muscle Contraction / regulation of response to oxidative stress / PINK1-PRKN Mediated Mitophagy / nitroglycerin reductase activity / regulation of dopamine biosynthetic process / regulation of serotonin biosynthetic process / mitochondrion targeting sequence binding / aldehyde catabolic process / mitochondrial outer membrane translocase complex / phenylacetaldehyde dehydrogenase (NAD+) activity / response to 3,3',5-triiodo-L-thyronine / migrasome / mitochondria-associated endoplasmic reticulum membrane contact site / ethanol catabolic process / Ub-specific processing proteases / protein import into mitochondrial matrix / carboxylesterase activity / acetaldehyde metabolic process / NADH binding / behavioral response to ethanol / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (non-phosphorylating) activity / protein-transporting ATPase activity / aldehyde dehydrogenase (NAD+) / cellular detoxification of aldehyde / 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 / cell periphery / response to ischemia / response to progesterone / intracellular protein transport / response to nicotine / 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
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, N-terminal / Aldehyde dehydrogenase, C-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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsIgura, M. / Ose, T. / Kohda, D.
CitationJournal: Biochemistry / Year: 2011
Title: Crystallographic snapshots of tom20-mitochondrial presequence interactions with disulfide-stabilized peptides.
Authors: Saitoh, T. / Igura, M. / Miyazaki, Y. / Ose, T. / Maita, N. / Kohda, D.
History
DepositionMar 26, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software
Revision 1.3Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mitochondrial import receptor subunit TOM20 homolog
B: Mitochondrial import receptor subunit TOM20 homolog
C: Aldehyde dehydrogenase, mitochondrial
D: Aldehyde dehydrogenase, mitochondrial


Theoretical massNumber of molelcules
Total (without water)18,6814
Polymers18,6814
Non-polymers00
Water1,27971
1
A: Mitochondrial import receptor subunit TOM20 homolog
C: Aldehyde dehydrogenase, mitochondrial


Theoretical massNumber of molelcules
Total (without water)9,3412
Polymers9,3412
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-9 kcal/mol
Surface area5550 Å2
MethodPISA
2
B: Mitochondrial import receptor subunit TOM20 homolog
D: Aldehyde dehydrogenase, mitochondrial


Theoretical massNumber of molelcules
Total (without water)9,3412
Polymers9,3412
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area780 Å2
ΔGint-8 kcal/mol
Surface area4920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.770, 27.723, 70.812
Angle α, β, γ (deg.)90.00, 102.71, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Mitochondrial import receptor subunit TOM20 homolog / Mitochondrial 20 kDa outer membrane protein / Outer mitochondrial membrane receptor Tom20


Mass: 8022.181 Da / Num. of mol.: 2 / Fragment: CYTOSOLIC DOMAIN, UNP RESIDUES 59-126
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Tomm20 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q62760
#2: Protein/peptide Aldehyde dehydrogenase, mitochondrial / ALDH class 2 / ALDH-E2 / ALDH1


Mass: 1318.549 Da / Num. of mol.: 2
Fragment: C-TERMINAL HALF OF THE PRESEQUENCE, UNP RESIDUES 12-20
Source method: obtained synthetically / Details: The peptide was chemically synthesized. / Source: (synth.) Rattus norvegicus (Norway rat) / References: UniProt: P11884
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.73 Å3/Da / Density % sol: 28.94 % / Mosaicity: 0.914 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.09M MES pH6.0, 0.045M MgCl2, 24% PEG 3350, 10mM DTT , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Jul 12, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→69.01 Å / Num. all: 8876 / Num. obs: 8725 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.089 / Χ2: 1 / Net I/σ(I): 11
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.072.40.2967860.821189.1
2.07-2.152.80.228310.702194.8
2.15-2.253.20.2078611.078199.1
2.25-2.373.50.1758760.9231100
2.37-2.523.70.1328841.0651100
2.52-2.713.70.1178811.0531100
2.71-2.993.70.1018731.0511100
2.99-3.423.70.0759051.0241100
3.42-4.313.70.0638941.0181100
4.31-503.50.0729341.068199.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2V1T

2v1t


Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.917 / SU B: 5.616 / SU ML: 0.157 / Cross valid method: THROUGHOUT / ESU R: 0.279 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25073 405 4.7 %RANDOM
Rwork0.20609 ---
obs0.20813 8221 96.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.663 Å2
Baniso -1Baniso -2Baniso -3
1-1.95 Å20 Å2-0.01 Å2
2---0.84 Å20 Å2
3----1.11 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1234 0 0 71 1305
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221251
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4212.0211693
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9455157
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.59726.66754
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.65215225
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.067154
X-RAY DIFFRACTIONr_chiral_restr0.0960.2199
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021930
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7791.5800
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.53521279
X-RAY DIFFRACTIONr_scbond_it2.2533451
X-RAY DIFFRACTIONr_scangle_it3.7134.5414
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 26 -
Rwork0.247 482 -
all-507 -
obs--81.28 %

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