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- PDB-3ax2: Crystal structure of rat TOM20-ALDH presequence complex: a disulf... -

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Basic information

Entry
Database: PDB / ID: 3ax2
TitleCrystal structure of rat TOM20-ALDH presequence complex: a disulfide-tethered complex with a non-optimized, long linker
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 / Metabolism of serotonin / ethanol metabolic process / tRNA import into mitochondrion / Smooth Muscle Contraction / Mitochondrial protein degradation / regulation of response to oxidative stress / PINK1-PRKN Mediated Mitophagy / : ...cellular response to resveratrol / Ethanol oxidation / Metabolism of serotonin / ethanol metabolic process / tRNA import into mitochondrion / Smooth Muscle Contraction / Mitochondrial protein degradation / regulation of response to oxidative stress / PINK1-PRKN Mediated Mitophagy / : / regulation of dopamine biosynthetic process / regulation of serotonin biosynthetic process / phenylacetaldehyde dehydrogenase (NAD+) activity / mitochondrion targeting sequence binding / aldehyde catabolic process / mitochondrial outer membrane translocase complex / response to 3,3',5-triiodo-L-thyronine / migrasome / ethanol catabolic process / mitochondria-associated endoplasmic reticulum membrane contact site / protein import into mitochondrial matrix / Ub-specific processing proteases / acetaldehyde metabolic process / NADH binding / behavioral response to ethanol / protein-transporting ATPase activity / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (non-phosphorylating) activity / aldehyde dehydrogenase (NAD+) / cellular detoxification of aldehyde / carboxylesterase activity / 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 / response to nicotine / intracellular protein transport / 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, C-terminal / Aldehyde dehydrogenase, N-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 / molecular replacement / Resolution: 1.9 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 1.2Oct 11, 2017Group: Refinement description / Category: software
Revision 1.3Nov 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
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
E: Mitochondrial import receptor subunit TOM20 homolog
F: Aldehyde dehydrogenase, mitochondrial
G: Mitochondrial import receptor subunit TOM20 homolog
H: Aldehyde dehydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,42610
Polymers38,2368
Non-polymers1902
Water3,009167
1
A: Mitochondrial import receptor subunit TOM20 homolog
B: Aldehyde dehydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,6543
Polymers9,5592
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-6 kcal/mol
Surface area5410 Å2
MethodPISA
2
C: Mitochondrial import receptor subunit TOM20 homolog
D: Aldehyde dehydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,6543
Polymers9,5592
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-5 kcal/mol
Surface area5450 Å2
MethodPISA
3
E: Mitochondrial import receptor subunit TOM20 homolog
F: Aldehyde dehydrogenase, mitochondrial


Theoretical massNumber of molelcules
Total (without water)9,5592
Polymers9,5592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-7 kcal/mol
Surface area5030 Å2
MethodPISA
4
G: Mitochondrial import receptor subunit TOM20 homolog
H: Aldehyde dehydrogenase, mitochondrial


Theoretical massNumber of molelcules
Total (without water)9,5592
Polymers9,5592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-7 kcal/mol
Surface area5150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.490, 61.490, 98.341
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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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.: 4 / 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: 1536.782 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 12-20 / 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.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.81 Å3/Da / Density % sol: 56.18 % / Mosaicity: 0.472 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1M sodium acetate pH4.6, 1M ammonium dihydrogen phospjate, 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: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 21, 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: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 32765 / Num. obs: 32732 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rmerge(I) obs: 0.081 / Χ2: 1.026 / Net I/σ(I): 12.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.935.70.58716471.0141100
1.93-1.975.70.44316411.021100
1.97-2.015.70.34516171.0291100
2.01-2.055.70.28216451.0311100
2.05-2.095.70.2316351.0381100
2.09-2.145.70.19216151.0321100
2.14-2.195.80.17616951.0351100
2.19-2.255.80.16315771.0331100
2.25-2.325.80.14616581.0461100
2.32-2.395.80.1316121.0021100
2.39-2.485.80.11916571.0381100
2.48-2.585.80.10716811.0261100
2.58-2.75.80.09616151.0261100
2.7-2.845.80.08716181.0181100
2.84-3.025.80.0816471.0211100
3.02-3.255.80.06916321.0361100
3.25-3.575.80.05916441.0231100
3.57-4.095.80.05416371.0131100
4.09-5.155.70.04916441.0251100
5.15-305.60.04416151.019198.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 30.88 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å26.63 Å
Translation2.5 Å26.63 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WT4

1wt4
PDB Unreleased entry


Resolution: 1.9→27 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.937 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.295 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.2185 1574 5.1 %RANDOM
Rwork0.1876 ---
obs0.1892 31052 94.88 %-
all-32728 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 63.31 Å2 / Biso mean: 24.7696 Å2 / Biso min: 9.93 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å20 Å2
2---0.02 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.9→27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2536 0 10 167 2713
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0222599
X-RAY DIFFRACTIONr_angle_refined_deg2.1932.0173524
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1255329
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.02126.522115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.4515465
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.821158
X-RAY DIFFRACTIONr_chiral_restr0.1640.2407
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211936
X-RAY DIFFRACTIONr_mcbond_it1.4871.51643
X-RAY DIFFRACTIONr_mcangle_it2.4322626
X-RAY DIFFRACTIONr_scbond_it3.9153956
X-RAY DIFFRACTIONr_scangle_it6.3444.5894
LS refinement shellResolution: 1.901→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 106 -
Rwork0.235 2070 -
all-2176 -
obs--92.56 %

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