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- PDB-1hr9: Yeast Mitochondrial Processing Peptidase beta-E73Q Mutant Complex... -

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Basic information

Entry
Database: PDB / ID: 1hr9
TitleYeast Mitochondrial Processing Peptidase beta-E73Q Mutant Complexed with Malate Dehydrogenase Signal Peptide
Components
  • MALATE DEHYDROGENASE
  • MITOCHONDRIAL PROCESSING PEPTIDASE ALPHA SUBUNIT
  • MITOCHONDRIAL PROCESSING PEPTIDASE BETA SUBUNIT
KeywordsHYDROLASE / HxxEH zinc-binding motif
Function / homology
Function and homology information


: / Citric acid cycle (TCA cycle) / Gluconeogenesis / mitochondrial processing peptidase complex / mitochondrial processing peptidase / protein processing involved in protein targeting to mitochondrion / Respiratory electron transport / malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / malate metabolic process ...: / Citric acid cycle (TCA cycle) / Gluconeogenesis / mitochondrial processing peptidase complex / mitochondrial processing peptidase / protein processing involved in protein targeting to mitochondrion / Respiratory electron transport / malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / malate metabolic process / Mitochondrial protein degradation / endopeptidase activator activity / tricarboxylic acid cycle / aerobic respiration / metalloendopeptidase activity / carbohydrate metabolic process / mitochondrial matrix / mRNA binding / mitochondrion / proteolysis / metal ion binding / cytoplasm
Similarity search - Function
Malate dehydrogenase, type 1 / Malate dehydrogenase, active site / Malate dehydrogenase active site signature. / Cytochrome Bc1 Complex; Chain A, domain 1 / Metalloenzyme, LuxS/M16 peptidase-like / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / L-lactate/malate dehydrogenase / Lactate/malate dehydrogenase, N-terminal / Lactate/malate dehydrogenase, C-terminal ...Malate dehydrogenase, type 1 / Malate dehydrogenase, active site / Malate dehydrogenase active site signature. / Cytochrome Bc1 Complex; Chain A, domain 1 / Metalloenzyme, LuxS/M16 peptidase-like / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / L-lactate/malate dehydrogenase / Lactate/malate dehydrogenase, N-terminal / Lactate/malate dehydrogenase, C-terminal / lactate/malate dehydrogenase, NAD binding domain / lactate/malate dehydrogenase, alpha/beta C-terminal domain / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / Peptidase M16, C-terminal / Peptidase M16 inactive domain / Peptidase M16, N-terminal / Insulinase (Peptidase family M16) / Metalloenzyme, LuxS/M16 peptidase-like / NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Mitochondrial-processing peptidase subunit beta / Mitochondrial-processing peptidase subunit alpha / Malate dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.01 Å
AuthorsTaylor, A.B. / Smith, B.S. / Kitada, S. / Kojima, K. / Miyaura, H. / Otwinowski, Z. / Ito, A. / Deisenhofer, J.
CitationJournal: Structure / Year: 2001
Title: Crystal structures of mitochondrial processing peptidase reveal the mode for specific cleavage of import signal sequences.
Authors: Taylor, A.B. / Smith, B.S. / Kitada, S. / Kojima, K. / Miyaura, H. / Otwinowski, Z. / Ito, A. / Deisenhofer, J.
History
DepositionDec 21, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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_dist_value / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MITOCHONDRIAL PROCESSING PEPTIDASE ALPHA SUBUNIT
B: MITOCHONDRIAL PROCESSING PEPTIDASE BETA SUBUNIT
C: MITOCHONDRIAL PROCESSING PEPTIDASE ALPHA SUBUNIT
D: MITOCHONDRIAL PROCESSING PEPTIDASE BETA SUBUNIT
E: MITOCHONDRIAL PROCESSING PEPTIDASE ALPHA SUBUNIT
F: MITOCHONDRIAL PROCESSING PEPTIDASE BETA SUBUNIT
G: MITOCHONDRIAL PROCESSING PEPTIDASE ALPHA SUBUNIT
H: MITOCHONDRIAL PROCESSING PEPTIDASE BETA SUBUNIT
O: MALATE DEHYDROGENASE
P: MALATE DEHYDROGENASE
Q: MALATE DEHYDROGENASE
R: MALATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)410,05618
Polymers409,31812
Non-polymers7386
Water00
1
A: MITOCHONDRIAL PROCESSING PEPTIDASE ALPHA SUBUNIT
B: MITOCHONDRIAL PROCESSING PEPTIDASE BETA SUBUNIT
O: MALATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,3954
Polymers102,3303
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: MITOCHONDRIAL PROCESSING PEPTIDASE ALPHA SUBUNIT
D: MITOCHONDRIAL PROCESSING PEPTIDASE BETA SUBUNIT
P: MALATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,3954
Polymers102,3303
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: MITOCHONDRIAL PROCESSING PEPTIDASE ALPHA SUBUNIT
F: MITOCHONDRIAL PROCESSING PEPTIDASE BETA SUBUNIT
Q: MALATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,6335
Polymers102,3303
Non-polymers3042
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: MITOCHONDRIAL PROCESSING PEPTIDASE ALPHA SUBUNIT
H: MITOCHONDRIAL PROCESSING PEPTIDASE BETA SUBUNIT
R: MALATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,6335
Polymers102,3303
Non-polymers3042
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)134.370, 178.520, 201.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
MITOCHONDRIAL PROCESSING PEPTIDASE ALPHA SUBUNIT / ALPHA-MPP


Mass: 52532.387 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: PTRC99A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P11914, mitochondrial processing peptidase
#2: Protein
MITOCHONDRIAL PROCESSING PEPTIDASE BETA SUBUNIT / BETA-MPP


Mass: 48894.039 Da / Num. of mol.: 4 / Mutation: E73Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: PTRC99A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P10507, mitochondrial processing peptidase
#3: Protein/peptide
MALATE DEHYDROGENASE / MDH1


Mass: 903.105 Da / Num. of mol.: 4 / Fragment: RESIDUES 2-9 / Source method: obtained synthetically
Details: The 8 resdiue peptide of malate dehydrogenase was synthesized using standard solid-phase Fmoc synthesis methodology
References: UniProt: P17505, malate dehydrogenase
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM

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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: 3 Å3/Da / Density % sol: 59 %
Crystal grow
*PLUS
Temperature: 21 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18-14 mg/mlprotein1drop
250 mMHEPES1drop
330 %(v/v)glycerol1drop
40.2 mMn-dodecylmaltoside1drop
55-9 %(w/v)PEG100001reservoir
635 %(v/v)ethylene glycol1reservoir
76 %(v/v)MPD1reservoir
825 mMsodium citrate1reservoir
92 %(w/v)benzamidine1reservoir
100.2 mMn-dodecylmaltoside1reservoir
112 mMsodium azide1reservoir

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.943 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 30, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.943 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 90666 / Num. obs: 90666 / % possible obs: 93.5 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 13.6
Reflection shellResolution: 3→3.11 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 2.3 / % possible all: 95.9
Reflection
*PLUS
Num. measured all: 418644
Reflection shell
*PLUS
% possible obs: 95.9 %

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Processing

Software
NameClassification
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementStarting model: PDB ID 1HR6

1hr6


Resolution: 3.01→47.55 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 3743721.21 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Maximum Likelihood Function
RfactorNum. reflection% reflectionSelection details
Rfree0.256 2035 2.2 %RANDOM
Rwork0.217 ---
obs0.217 90644 93.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 28.5779 Å2 / ksol: 0.316 e/Å3
Displacement parametersBiso mean: 68.4 Å2
Baniso -1Baniso -2Baniso -3
1--17.83 Å20 Å20 Å2
2--8.49 Å20 Å2
3---9.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.39 Å
Luzzati d res low-50 Å
Luzzati sigma a0.51 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 3.01→47.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27891 0 34 0 27925
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.55
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINED
LS refinement shellResolution: 3.01→3.11 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.416 215 2.5 %
Rwork0.365 8334 -
obs--88.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ZINC.PARAMZINC.TOP
X-RAY DIFFRACTION3HEPES_XPLOR.PARAMHEPES_XPLOR.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 2.2 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 68.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.55
LS refinement shell
*PLUS
Rfactor Rfree: 0.416 / % reflection Rfree: 2.5 % / Rfactor Rwork: 0.365

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