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- PDB-5az8: Crystal structure of MBP-Tom20 fusion protein tethered with ALDH ... -

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Basic information

Entry
Database: PDB / ID: 5az8
TitleCrystal structure of MBP-Tom20 fusion protein tethered with ALDH presequence via a disulfide bond
Components
  • Maltose-binding periplasmic protein,Mitochondrial import receptor subunit TOM20 homolog
  • peptide GPRLSRLLSYAGC
KeywordsSUGAR BINDING PROTEIN / PEPTIDE BINDING PROTEIN / Fusion protein Comlex / TRANSPORT PROTEIN
Function / homology
Function and homology information


Ethanol oxidation / cellular response to resveratrol / Metabolism of serotonin / ethanol metabolic process / Mitochondrial protein degradation / tRNA import into mitochondrion / Smooth Muscle Contraction / regulation of response to oxidative stress / PINK1-PRKN Mediated Mitophagy / mitochondrion targeting sequence binding ...Ethanol oxidation / cellular response to resveratrol / Metabolism of serotonin / ethanol metabolic process / Mitochondrial protein degradation / tRNA import into mitochondrion / Smooth Muscle Contraction / regulation of response to oxidative stress / PINK1-PRKN Mediated Mitophagy / mitochondrion targeting sequence binding / nitroglycerin reductase activity / regulation of dopamine biosynthetic process / regulation of serotonin biosynthetic process / aldehyde catabolic process / mitochondrial outer membrane translocase complex / phenylacetaldehyde dehydrogenase activity / response to 3,3',5-triiodo-L-thyronine / mitochondria-associated endoplasmic reticulum membrane contact site / migrasome / ethanol catabolic process / Ub-specific processing proteases / protein import into mitochondrial matrix / carboxylesterase activity / acetaldehyde metabolic process / NADH binding / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (non-phosphorylating) activity / protein-transporting ATPase activity / aldehyde dehydrogenase (NAD+) / cellular detoxification of aldehyde / behavioral response to ethanol / protein targeting to mitochondrion / aldehyde dehydrogenase (NAD+) activity / 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 / detection of maltose stimulus / response to testosterone / maltose transport complex / maltose binding / maltose transport / maltodextrin transmembrane transport / apoptotic mitochondrial changes / carbohydrate transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / response to hyperoxia / cellular response to hormone stimulus / sperm midpiece / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / liver development / response to progesterone / cell periphery / response to ischemia / intracellular protein transport / response to nicotine / response to organic cyclic compound / unfolded protein binding / response to estradiol / outer membrane-bounded periplasmic space / response to ethanol / mitochondrial outer membrane / response to lipopolysaccharide / periplasmic space / mitochondrial matrix / DNA damage response / negative regulation of apoptotic process / mitochondrion / membrane / identical protein binding
Similarity search - Function
Protein import receptor MAS20 / Protein import receptor MAS20, metazoan / Mitochondrial outer membrane translocase complex, Tom20 domain superfamily / MAS20 protein import receptor / 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 ...Protein import receptor MAS20 / Protein import receptor MAS20, metazoan / Mitochondrial outer membrane translocase complex, Tom20 domain superfamily / MAS20 protein import receptor / 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 / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
alpha-maltose / ACETYLAMINO-ACETIC ACID / Maltose/maltodextrin-binding periplasmic protein / Aldehyde dehydrogenase, mitochondrial / Mitochondrial import receptor subunit TOM20 homolog
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMatsuoka, R. / Kohda, D.
CitationJournal: Protein Sci. / Year: 2016
Title: Rational design of crystal contact-free space in protein crystals for analyzing spatial distribution of motions within protein molecules.
Authors: Matsuoka, R. / Shimada, A. / Komuro, Y. / Sugita, Y. / Kohda, D.
History
DepositionSep 27, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Database references
Revision 1.2Feb 26, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Maltose-binding periplasmic protein,Mitochondrial import receptor subunit TOM20 homolog
B: peptide GPRLSRLLSYAGC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8984
Polymers49,4382
Non-polymers4592
Water7,260403
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-11 kcal/mol
Surface area19370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.013, 69.013, 212.604
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Maltose-binding periplasmic protein,Mitochondrial import receptor subunit TOM20 homolog / MBP / MMBP / Maltodextrin-binding protein / Mitochondrial 20 kDa outer membrane protein / Outer ...MBP / MMBP / Maltodextrin-binding protein / Mitochondrial 20 kDa outer membrane protein / Outer mitochondrial membrane receptor Tom20


Mass: 48044.613 Da / Num. of mol.: 1
Fragment: UNP RESIDUES 27-394,UNP RESIDUES 65-126,UNP RESIDUES 27-394,UNP RESIDUES 65-126
Mutation: A314V
Source method: isolated from a genetically manipulated source
Details: the fusion protein of 1-369 Maltose binding protein, 370-373 Linker and 374-435 Tom20
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) Rattus norvegicus (Norway rat)
Strain: K12 / Gene: malE, b4034, JW3994, Tomm20 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEX9, UniProt: Q62760
#2: Protein/peptide peptide GPRLSRLLSYAGC


Mass: 1393.660 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Rattus norvegicus (Norway rat) / References: UniProt: P11884*PLUS
#3: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#4: Chemical ChemComp-AAC / ACETYLAMINO-ACETIC ACID / Aceturic acid


Mass: 117.103 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H7NO3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 403 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 24% PEG 8000, 20% Glycerol, 0.04M Potassium thiocyanate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 56782 / % possible obs: 98.4 % / Redundancy: 13.8 % / Net I/σ(I): 22.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ANF, 2V1T

1anf

2v1t


Resolution: 1.7→42.11 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.66 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19555 2880 5.1 %RANDOM
Rwork0.16168 ---
obs0.16347 53911 98.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.954 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.7→42.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3465 0 31 403 3899
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.023575
X-RAY DIFFRACTIONr_bond_other_d0.0020.023440
X-RAY DIFFRACTIONr_angle_refined_deg2.011.9824850
X-RAY DIFFRACTIONr_angle_other_deg1.10537952
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5425442
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.87625.935155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.55715605
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.065158
X-RAY DIFFRACTIONr_chiral_restr0.1270.2540
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214026
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02761
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_it2.0132.3041777
X-RAY DIFFRACTIONr_mcbond_other2.0122.3051778
X-RAY DIFFRACTIONr_mcangle_it2.6533.4472216
X-RAY DIFFRACTIONr_mcangle_other2.6523.4472217
X-RAY DIFFRACTIONr_scbond_it4.1722.7881798
X-RAY DIFFRACTIONr_scbond_other4.1722.7881798
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2183.9752635
X-RAY DIFFRACTIONr_long_range_B_refined8.94221.1744536
X-RAY DIFFRACTIONr_long_range_B_other8.75420.5064351
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.212 192 -
Rwork0.185 3979 -
obs--99.62 %

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