[English] 日本語
Yorodumi
- PDB-3ax3: Crystal structure of rat TOM20-ALDH presequence complex: a comple... -

+
Open data


ID or keywords:

Loading...

-
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 / 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 / Ub-specific processing proteases / protein import into mitochondrial matrix / 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more