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- PDB-2v1t: CRYSTAL STRUCTURE OF RAT TOM20-ALDH PRESEQUENCE COMPLEX -

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Basic information

Entry
Database: PDB / ID: 2v1t
TitleCRYSTAL STRUCTURE OF RAT TOM20-ALDH PRESEQUENCE COMPLEX
Components
  • ALDEHYDE DEHYDROGENASE
  • MITOCHONDRIAL IMPORT RECEPTOR SUBUNIT TOM20 HOMOLOG
KeywordsOXIDOREDUCTASE / OUTER MEMBRANE / TRANSIT PEPTIDE / PHOSPHORYLATION / MITOCHONDRION / TRANSMEMBRANE / PROTEIN TRANSPORT / NAD / MEMBRANE / TRANSPORT
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.92 Å
AuthorsObita, T. / Igura, M. / Ose, T. / Endo, T. / Maenaka, K. / Kohda, D.
CitationJournal: Embo J. / Year: 2007
Title: Tom20 Recognizes Mitochondrial Presequences Through Dynamic Equilibrium Among Multiple Bound States.
Authors: Saitoh, T. / Igura, M. / Obita, T. / Ose, T. / Kojima, R. / Maenaka, K. / Endo, T. / Kohda, D.
History
DepositionMay 29, 2007Deposition site: PDBE / Processing site: PDBE
SupersessionJun 12, 2007ID: 1WT4
Revision 1.0Jun 12, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_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: MITOCHONDRIAL IMPORT RECEPTOR SUBUNIT TOM20 HOMOLOG
C: ALDEHYDE DEHYDROGENASE
D: ALDEHYDE DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)18,7414
Polymers18,7414
Non-polymers00
Water3,027168
1
A: MITOCHONDRIAL IMPORT RECEPTOR SUBUNIT TOM20 HOMOLOG
C: ALDEHYDE DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)9,3712
Polymers9,3712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: MITOCHONDRIAL IMPORT RECEPTOR SUBUNIT TOM20 HOMOLOG
D: ALDEHYDE DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)9,3712
Polymers9,3712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)33.629, 27.639, 70.967
Angle α, β, γ (deg.)90.00, 103.07, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.84362, -0.21182, 0.49339), (-0.16887, -0.97694, -0.13066), (0.50969, 0.02691, -0.85994)-8.88722, 15.64339, 33.57258
2given(0.85938, 0.0057, 0.51131), (0.00778, -0.99997, -0.00192), (0.51128, 0.00563, -0.8594)-10.43461, 12.3425, 34.20483

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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: 8069.077 Da / Num. of mol.: 2 / Fragment: CYTOSOLIC DOMAIN, RESIDUES 59-126
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Plasmid: PGEX-6P-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q62760
#2: Protein/peptide ALDEHYDE DEHYDROGENASE / ALDH CLASS 2 / ALDH1 / ALDH-E2


Mass: 1301.564 Da / Num. of mol.: 2
Fragment: C-TERMINAL HALF OF THE PRESEQUENCE OF MITOCHONDRIAL PRECURSOR, RESIDUES 12-24
Mutation: YES / Source method: obtained synthetically / Source: (synth.) RATTUS NORVEGICUS (Norway rat) / References: UniProt: P11884, aldehyde dehydrogenase (NAD+)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN C, ALA 23 TO GLY ENGINEERED RESIDUE IN CHAIN C, THR 24 TO CY3 ...ENGINEERED RESIDUE IN CHAIN C, ALA 23 TO GLY ENGINEERED RESIDUE IN CHAIN C, THR 24 TO CY3 ENGINEERED RESIDUE IN CHAIN D, ALA 23 TO GLY ENGINEERED RESIDUE IN CHAIN D, THR 24 TO CY3
Has protein modificationY
Sequence detailsGLY A 54 CLONING ARTIFACT PRO A 55 CLONING ARTIFACT LEU A 56 CLONING ARTIFACT GLY A 57 CLONING ...GLY A 54 CLONING ARTIFACT PRO A 55 CLONING ARTIFACT LEU A 56 CLONING ARTIFACT GLY A 57 CLONING ARTIFACT SER A 58 CLONING ARTIFACT MSE A MODIFIED RESIDUE GLY B 54 CLONING ARTIFACT PRO B 55 CLONING ARTIFACT LEU B 56 CLONING ARTIFACT GLY B 57 CLONING ARTIFACT SER B 58 CLONING ARTIFACT MSE B MODIFIED RESIDUE GLY 23 ENGINEERED

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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: 1.7 Å3/Da / Density % sol: 30 %
Crystal growpH: 7 / Details: PEG 6000, AMMONIUM CHLORIDE, PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL40B2 / Wavelength: 0.9838
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 4, 2004 / Details: MIRRORS
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9838 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 9958 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 24.2
Reflection shellResolution: 1.9→1.98 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 8.4 / % possible all: 93.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.92→32.6 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.919 / SU B: 8.919 / SU ML: 0.134 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.242 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24 879 9 %RANDOM
Rwork0.178 ---
obs0.184 8906 97.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.86 Å2
Baniso -1Baniso -2Baniso -3
1-1.12 Å20 Å20.37 Å2
2---0.07 Å20 Å2
3----0.89 Å2
Refinement stepCycle: LAST / Resolution: 1.92→32.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1279 0 0 168 1447
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221298
X-RAY DIFFRACTIONr_bond_other_d0.0010.02878
X-RAY DIFFRACTIONr_angle_refined_deg1.4232.0291749
X-RAY DIFFRACTIONr_angle_other_deg1.0323.0022171
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.085161
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.47926.78656
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.36915231
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.881154
X-RAY DIFFRACTIONr_chiral_restr0.0850.2206
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021416
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02214
X-RAY DIFFRACTIONr_nbd_refined0.220.2338
X-RAY DIFFRACTIONr_nbd_other0.1720.2931
X-RAY DIFFRACTIONr_nbtor_refined0.1650.2647
X-RAY DIFFRACTIONr_nbtor_other0.0980.2629
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2190.2103
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2040.231
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2750.284
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1820.229
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1211.51050
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.11621323
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1243491
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8744.5426
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.92→1.97 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rwork0.219 639
Rfree-0
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8242-0.1870.48220.6178-0.12710.97270.0041-0.0277-0.0274-0.01630.0032-0.01680.0742-0.0001-0.0073-0.0017-0.0129-0.0003-0.0343-0.0028-0.0171-3.4781.74924.753
21.7004-0.0428-0.42180.53550.64021.00810.03320.02480.0467-0.01770.00420.0004-0.09130.0487-0.03750.0085-0.0117-0.0051-0.02840.008-0.02881.12311.669.912
34.63780.17880.0045.53630.40140.71080.1002-0.0602-0.0252-0.138-0.0053-0.2259-0.2-0.0231-0.09490.0387-0.02860.0292-0.01460.0104-0.065-6.456-8.75926.154
42.4819-0.87650.58623.83353.02993.9108-0.13930.06740.17950.39820.28080.24710.08340.3498-0.14150.06790.0140.0116-0.00510.0005-0.0888-2.50621.0318.375
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A54 - 126
2X-RAY DIFFRACTION2B59 - 126
3X-RAY DIFFRACTION3C12 - 24
4X-RAY DIFFRACTION4D12 - 24

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