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- PDB-3ax3: Crystal structure of rat TOM20-ALDH presequence complex: a comple... -

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Basic information

Entry
Database: PDB / ID: 3ax3
TitleCrystal structure of rat TOM20-ALDH presequence complex: a complex (form2) between Tom20 and a disulfide-bridged presequence peptide containing D-Cys and L-Cys at the i and i+3 positions.
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


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 / response to 3,3',5-triiodo-L-thyronine / mitochondrion targeting sequence binding / ethanol catabolic process / mitochondrial outer membrane translocase complex / Ub-specific processing proteases / NADH binding / mitochondria-associated endoplasmic reticulum membrane contact site / migrasome / aldehyde dehydrogenase (NAD+) / protein-transporting ATPase activity / cellular detoxification of aldehyde / carboxylesterase activity / behavioral response to ethanol / aldehyde dehydrogenase (NAD+) activity / mitochondrial envelope / cellular response to fatty acid / regulation of reactive oxygen species metabolic process / intrinsic apoptotic signaling pathway in response to oxidative stress / protein targeting to mitochondrion / response to muscle activity / response to testosterone / protein import into mitochondrial matrix / apoptotic mitochondrial changes / response to hyperoxia / cellular response to hormone stimulus / sperm midpiece / response to progesterone / response to ischemia / cell periphery / response to nicotine / intracellular protein transport / liver development / unfolded protein binding / response to estradiol / response to ethanol / response to lipopolysaccharide / 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, metazoan / Protein import receptor MAS20 / 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, metazoan / Protein import receptor MAS20 / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSaitoh, T. / Maita, Y. / 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 28, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)37,0438
Polymers37,0438
Non-polymers00
Water64936
1
A: Mitochondrial import receptor subunit TOM20 homolog
B: Aldehyde dehydrogenase, mitochondrial


Theoretical massNumber of molelcules
Total (without water)9,2612
Polymers9,2612
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-9 kcal/mol
Surface area4970 Å2
MethodPISA
2
C: Mitochondrial import receptor subunit TOM20 homolog
D: Aldehyde dehydrogenase, mitochondrial


Theoretical massNumber of molelcules
Total (without water)9,2612
Polymers9,2612
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-10 kcal/mol
Surface area4740 Å2
MethodPISA
3
E: Mitochondrial import receptor subunit TOM20 homolog
F: Aldehyde dehydrogenase, mitochondrial


Theoretical massNumber of molelcules
Total (without water)9,2612
Polymers9,2612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-10 kcal/mol
Surface area5120 Å2
MethodPISA
4
G: Mitochondrial import receptor subunit TOM20 homolog
H: Aldehyde dehydrogenase, mitochondrial


Theoretical massNumber of molelcules
Total (without water)9,2612
Polymers9,2612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-10 kcal/mol
Surface area5280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.596, 99.596, 195.180
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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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: 8006.115 Da / Num. of mol.: 4 / Fragment: CYTOSOLIC DOMAIN, UNP RESIDUES 59-126 / Mutation: C100S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Genus: 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: 1254.551 Da / Num. of mol.: 4 / Fragment: C-TERMINAL HALF, UNP RESIDUES 12-20 / Mutation: P13C, S16C / 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.: 36 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.51 Å3/Da / Density % sol: 51.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Tris-HCl pH8.0, 0.2M MgCl2, 30% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 25, 2008
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator, micro-channel, indirect water cooling
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 22101 / % possible obs: 99.7 %
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allDiffraction-ID% possible all
2.1-2.189.20.49622081100
2.18-2.269.90.21321621100
2.26-2.379.90.17722091100
2.37-2.499.90.13721891100
2.49-2.659.80.11321971100
2.65-2.859.80.10421991100
2.85-3.149.80.08922041100
3.14-3.599.60.07222251100
3.59-4.529.40.05222391100
4.52-509.30.0452269197

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Processing

Software
NameVersionClassification
PHASERMRphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WT4, 2V1T

1wt4
PDB Unreleased entry

2v1t


Resolution: 2.1→28.94 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.901 / SU B: 5.173 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28698 1127 5.2 %RANDOM
Rwork0.24301 ---
obs0.2452 20739 99.07 %-
all-20934 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.163 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0.01 Å20 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.1→28.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2452 0 0 36 2488
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0222488
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0062.0183352
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.245304
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.31826.491114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.40615454
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.279158
X-RAY DIFFRACTIONr_chiral_restr0.1430.2394
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211836
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_it1.3561.51556
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.43522484
X-RAY DIFFRACTIONr_scbond_it3.6983932
X-RAY DIFFRACTIONr_scangle_it6.2514.5868
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 82 -
Rwork0.327 1398 -
obs--91.25 %

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