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- PDB-1v1m: CROSSTALK BETWEEN COFACTOR BINDING AND THE PHOSPHORYLATION LOOP C... -

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Entry
Database: PDB / ID: 1v1m
TitleCROSSTALK BETWEEN COFACTOR BINDING AND THE PHOSPHORYLATION LOOP CONFORMATION IN THE BCKD MACHINE
Components(2-OXOISOVALERATE DEHYDROGENASE ...) x 2
KeywordsOXIDOREDUCTASE / KETOACID DEHYDROGENASE / BRANCHED-CHAIN / MULTI-ENZYME COMPLEX / ACYLATION / OXIDATIVE DECARBOXYLATION MAPLE SYRUP URINE DISEASE / THIAMINE DIPHOSPHATE / PHOSPHORYLATION / FLAVOPROTEIN
Function / homology
Function and homology information


Loss-of-function mutations in BCKDHA or BCKDHB cause MSUD / 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) / branched-chain 2-oxo acid dehydrogenase activity / branched-chain alpha-ketoacid dehydrogenase complex / BCKDH synthesizes BCAA-CoA from KIC, KMVA, KIV / Loss-of-function mutations in DBT cause MSUD2 / Loss-of-function mutations in DLD cause MSUD3/DLDD / H139Hfs13* PPM1K causes a mild variant of MSUD / Branched-chain ketoacid dehydrogenase kinase deficiency / branched-chain amino acid catabolic process ...Loss-of-function mutations in BCKDHA or BCKDHB cause MSUD / 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) / branched-chain 2-oxo acid dehydrogenase activity / branched-chain alpha-ketoacid dehydrogenase complex / BCKDH synthesizes BCAA-CoA from KIC, KMVA, KIV / Loss-of-function mutations in DBT cause MSUD2 / Loss-of-function mutations in DLD cause MSUD3/DLDD / H139Hfs13* PPM1K causes a mild variant of MSUD / Branched-chain ketoacid dehydrogenase kinase deficiency / branched-chain amino acid catabolic process / Branched-chain amino acid catabolism / carboxy-lyase activity / response to nutrient / lipid metabolic process / mitochondrial matrix / nucleolus / mitochondrion / nucleoplasm / metal ion binding
Similarity search - Function
: / Transketolase, C-terminal domain / Dehydrogenase, E1 component / Dehydrogenase E1 component / Transketolase, C-terminal domain / Rossmann fold - #920 / Transketolase-like, pyrimidine-binding domain / Transketolase, pyrimidine binding domain / Transketolase, pyrimidine binding domain / Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II ...: / Transketolase, C-terminal domain / Dehydrogenase, E1 component / Dehydrogenase E1 component / Transketolase, C-terminal domain / Rossmann fold - #920 / Transketolase-like, pyrimidine-binding domain / Transketolase, pyrimidine binding domain / Transketolase, pyrimidine binding domain / Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II / Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains / Thiamin diphosphate-binding fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BENZAMIDINE / : / : / THIAMINE DIPHOSPHATE / 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial / 2-oxoisovalerate dehydrogenase subunit beta, mitochondrial
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLi, J. / Wynn, R.M. / Machius, M. / Chuang, J.L. / Karthikeyan, S. / Tomchick, D.R. / Chuang, D.T.
Citation
Journal: J.Biol.Chem. / Year: 2004
Title: Cross-Talk between Thiamin Diphosphate Binding and Phosphorylation Loop Conformation in Human Branched-Chain Alpha-Keto Acid Decarboxylase/Dehydrogenase.
Authors: Li, J. / Wynn, R.M. / Machius, M. / Chuang, J.L. / Karthikeyan, S. / Tomchick, D.R. / Chuang, D.T.
#1: Journal: J.Biol.Chem. / Year: 2003
Title: Roles of His291-Alpha and His146-Beta in the Reductive Acylation Reaction Catalyzed by Human Branched-Chain Alpha-Ketoacid Dehydrogenase: Refined Phosphorylation Loop Structure in the Active Site
Authors: Wynn, R. / Machius, M. / Chuang, J. / Li, J. / Tomchick, D. / Chuang, D.
#2: Journal: J.Biol.Chem. / Year: 2003
Title: Roles of Active Site and Novel K+ Ion-Binding Site Residues in Human Mitochondrial Branched-Chain Alpha-Ketoacid Decarboxylase/Dehydrogenase
Authors: Wynn, R.M. / Ho, R. / Chuang, J.L. / Chuang, D.T.
#3: Journal: Structure / Year: 2000
Title: Crystal Structure of Human Branched-Chain Alpha-Ketoacid Dehydrogenase and the Molecular Basis of Multienzyme Complex Deficiency in Maple Syrup Urine Disease
Authors: Aevarsson, A. / Chuang, J.L. / Wynn, R.M. / Turley, S. / Chuang, D.T. / Hol, W.G.J.
History
DepositionApr 20, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 15, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4Sep 25, 2019Group: Data collection / Experimental preparation / Other / Category: exptl_crystal_grow / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.status_code_sf
Revision 2.0Aug 4, 2021Group: 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 / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / 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_atom_id / _atom_site.auth_comp_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 / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 2.1Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2-OXOISOVALERATE DEHYDROGENASE ALPHA SUBUNIT
B: 2-OXOISOVALERATE DEHYDROGENASE BETA SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,40813
Polymers83,3462
Non-polymers1,06111
Water10,323573
1
A: 2-OXOISOVALERATE DEHYDROGENASE ALPHA SUBUNIT
B: 2-OXOISOVALERATE DEHYDROGENASE BETA SUBUNIT
hetero molecules

A: 2-OXOISOVALERATE DEHYDROGENASE ALPHA SUBUNIT
B: 2-OXOISOVALERATE DEHYDROGENASE BETA SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,81526
Polymers166,6934
Non-polymers2,12222
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area28330 Å2
ΔGint-209 kcal/mol
Surface area54220 Å2
MethodPQS
Unit cell
Length a, b, c (Å)145.287, 145.287, 69.165
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-2098-

HOH

21B-2219-

HOH

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Components

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2-OXOISOVALERATE DEHYDROGENASE ... , 2 types, 2 molecules AB

#1: Protein 2-OXOISOVALERATE DEHYDROGENASE ALPHA SUBUNIT / MITOCHONDRIAL PRECURSOR / BRANCHED-CHAIN ALPHA-KETO ACID DEHYDROGENASE E1 / COMPONENT ALPHA CHAIN / ...MITOCHONDRIAL PRECURSOR / BRANCHED-CHAIN ALPHA-KETO ACID DEHYDROGENASE E1 / COMPONENT ALPHA CHAIN / BCKDH E1-ALPHA / BCKDE1A


Mass: 45444.023 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PTRC-ALPHA-BETAHIS (C TERMINALLY TAGGED) / Production host: ESCHERICHIA COLI (E. coli)
Strain (production host): BL-21 CELLS WITH OVEREXPRESSING GROEL AND GROES
References: UniProt: P12694, 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring)
#2: Protein 2-OXOISOVALERATE DEHYDROGENASE BETA SUBUNIT / MITOCHONDRIAL PRECURSOR / BRANCHED-CHAIN ALPHA-KETO ACID DEHYDROGENASE E1 / COMPONENT BETA CHAIN / ...MITOCHONDRIAL PRECURSOR / BRANCHED-CHAIN ALPHA-KETO ACID DEHYDROGENASE E1 / COMPONENT BETA CHAIN / BCKDH E1-BETA


Mass: 37902.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PTRC-ALPHA-BETAHIS (C TERMINALLY TAGGED) / Production host: ESCHERICHIA COLI (E. coli)
Strain (production host): BL-21 CELLS WITH OVEREXPRESSING GROEL AND GROES
References: UniProt: P21953, 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring)

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Non-polymers , 7 types, 584 molecules

#3: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#6: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#7: Chemical ChemComp-BEN / BENZAMIDINE


Mass: 120.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N2
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 573 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED MUTATION ASP 340 ALA
Sequence detailsENGINEERED MUTATION UNOBSERVED

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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: 2.5 Å3/Da / Density % sol: 53.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.5
Details: CRYSTALS WERE GROWN AT 20C VIA THE VAPOR DIFFUSION METHOD BY MIXING EQUAL AMOUNTS OF PROTEIN (20-25 MG/ML IN 50 MM HEPES/NAOH, PH 7.5, 250 MM KCL, 0.5 MM PMSF, 1 MM BENZAMIDINE AND 5% (V/V) ...Details: CRYSTALS WERE GROWN AT 20C VIA THE VAPOR DIFFUSION METHOD BY MIXING EQUAL AMOUNTS OF PROTEIN (20-25 MG/ML IN 50 MM HEPES/NAOH, PH 7.5, 250 MM KCL, 0.5 MM PMSF, 1 MM BENZAMIDINE AND 5% (V/V) GLYCEROL) WITH WELL SOLUTION (1.4-1.6 M AMMONIUM SULFATE, 0.1 M NA-CITRATE PH 5.8, 20 MM B-MERCAPTOETHANOL). SERIALLY DILUTED CRUSHED CRYSTALS WERE USED FOR MICRO-SEEDING ONE DAY AFTER THE DROPS WERE SET UP. CRYSTALS APPEARED ONE DAY AFTER SEEDING AND GREW TO A MAXIMUM SIZE OF 120 X 800 UM WITHIN 10 DAYS. CRYSTALS WERE STABILIZED FOR 12 HOURS BY TRANSFER TO FRESH WELL SOLUTION. THEY WERE THEN CRYO-PROTECTED BY STEP-WISE TRANSFER INTO CRYO-BUFFER CONTAINING 1.6 M AMMONIUM SULFATE, 50 MM HEPES, PH 7.5, 100 MM NA-CITRATE, PH 5.8, 100 MM KCL, 50 MM DTT AND UP TO 20% (V/V) GLYCEROL. IT WAS FOUND THAT MN2+ IONS COULD REPLACE THE MG2+ REQUIRED FOR THE BINDING OF THDP TO THE ENZYME.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.00691
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 25, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00691 Å / Relative weight: 1
ReflectionResolution: 2→36.32 Å / Num. obs: 54331 / % possible obs: 95.4 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 16.5
Reflection shellResolution: 2→2.03 Å / Redundancy: 6 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 3.2 / % possible all: 96.8

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OLS

1ols


Resolution: 2→28.87 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.719 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.17 1534 2.8 %RANDOM
Rwork0.129 ---
obs0.13 52774 95.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.34 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2→28.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5600 0 59 573 6232
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0215834
X-RAY DIFFRACTIONr_bond_other_d0.0020.025167
X-RAY DIFFRACTIONr_angle_refined_deg1.71.9527909
X-RAY DIFFRACTIONr_angle_other_deg0.946312035
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2095714
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1160.2834
X-RAY DIFFRACTIONr_gen_planes_refined0.010.026555
X-RAY DIFFRACTIONr_gen_planes_other0.0090.021233
X-RAY DIFFRACTIONr_nbd_refined0.2280.21291
X-RAY DIFFRACTIONr_nbd_other0.2530.26028
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0870.23141
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2427
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0770.25
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1750.242
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2940.2254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2370.252
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9871.53560
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.81225740
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.98732274
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.8944.52169
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: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.278 116
Rwork0.187 3954

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