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- PDB-3ax5: Crystal structure of rat TOM20-ALDH presequence complex: A comple... -

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Basic information

Entry
Database: PDB / ID: 3ax5
TitleCrystal structure of rat TOM20-ALDH presequence complex: A complex (form1) 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


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 / : ...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 / : / regulation of dopamine biosynthetic process / regulation of serotonin biosynthetic process / aldehyde catabolic process / mitochondrion targeting sequence binding / 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 / aldehyde dehydrogenase (NAD+) activity / protein targeting to mitochondrion / 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
PHOSPHATE ION / Aldehyde dehydrogenase, mitochondrial / Mitochondrial import receptor subunit TOM20 homolog
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 29, 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 / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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: Aldehyde dehydrogenase, mitochondrial
C: Mitochondrial import receptor subunit TOM20 homolog
D: Aldehyde dehydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6525
Polymers18,5574
Non-polymers951
Water41423
1
A: Mitochondrial import receptor subunit TOM20 homolog
B: Aldehyde dehydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,3743
Polymers9,2792
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area780 Å2
ΔGint-9 kcal/mol
Surface area5500 Å2
MethodPISA
2
C: Mitochondrial import receptor subunit TOM20 homolog
D: Aldehyde dehydrogenase, mitochondrial


Theoretical massNumber of molelcules
Total (without water)9,2792
Polymers9,2792
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-11 kcal/mol
Surface area5580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.745, 77.401, 116.226
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Mitochondrial import receptor subunit TOM20 homolog


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


Mass: 1256.543 Da / Num. of mol.: 2 / 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: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.53 Å3/Da / Density % sol: 51.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M HEPES-NaOH pH7.0, 10% isopropanol, 20% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1951
21
31
41
51
61
71
81
91
101
111
121
131
141
151
161
171
181
191
201
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 29, 2010
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator, liquid nitrogen cooling
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 9917 / % possible obs: 99.9 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 15.924
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allDiffraction-ID% possible all
2.2-2.247.20.5614761100
2.24-2.287.20.5654952100
2.28-2.327.20.4164753100
2.32-2.377.30.4314884100
2.37-2.427.20.3864935100
2.42-2.487.20.3594726100
2.48-2.547.30.2774957100
2.54-2.617.10.2335038100
2.61-2.687.30.2024809100
2.68-2.777.20.20549110100
2.77-2.877.20.18248311100
2.87-2.997.10.15250312100
2.99-3.127.20.12848313100
3.12-3.297.10.11950114100
3.29-3.497.10.09950515100
3.49-3.767.10.8149916100
3.76-4.146.90.06849617100
4.14-4.736.70.0535101899.6
4.73-5.966.90.05252119100
5.96-306.50.0375482099.3

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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

1wt4
PDB Unreleased entry


Resolution: 2.2→28.4 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.926 / SU B: 6.943 / SU ML: 0.178 / Cross valid method: THROUGHOUT / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27554 477 4.8 %RANDOM
Rwork0.22209 ---
obs0.22473 9438 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.74 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å20 Å2
2---0.11 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.2→28.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1266 0 5 23 1294
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0221303
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9022.0211762
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.75163
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.98726.66760
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.70615236
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.402154
X-RAY DIFFRACTIONr_chiral_restr0.1310.2205
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021966
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_it1.141.5815
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.22321305
X-RAY DIFFRACTIONr_scbond_it3.5363488
X-RAY DIFFRACTIONr_scangle_it5.9744.5455
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.198→2.255 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 37 -
Rwork0.235 639 -
obs--96.99 %

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