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- PDB-1hr8: Yeast Mitochondrial Processing Peptidase beta-E73Q Mutant Complex... -

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Basic information

Entry
Database: PDB / ID: 1hr8
TitleYeast Mitochondrial Processing Peptidase beta-E73Q Mutant Complexed with Cytochrome C Oxidase IV Signal Peptide
Components
  • (MITOCHONDRIAL PROCESSING PEPTIDASE ...) x 2
  • CYTOCHROME C OXIDASE POLYPEPTIDE IV
KeywordsHYDROLASE / HxxEH zinc-binding motif
Function / homology
Function and homology information


mitochondrial processing peptidase complex / mitochondrial processing peptidase / protein processing involved in protein targeting to mitochondrion / mitochondrial respiratory chain complex IV assembly / Respiratory electron transport / Mitochondrial protein degradation / respiratory chain complex IV / mitochondrial electron transport, cytochrome c to oxygen / endopeptidase activator activity / proton transmembrane transport ...mitochondrial processing peptidase complex / mitochondrial processing peptidase / protein processing involved in protein targeting to mitochondrion / mitochondrial respiratory chain complex IV assembly / Respiratory electron transport / Mitochondrial protein degradation / respiratory chain complex IV / mitochondrial electron transport, cytochrome c to oxygen / endopeptidase activator activity / proton transmembrane transport / metalloendopeptidase activity / mitochondrial intermembrane space / oxidoreductase activity / mitochondrial inner membrane / mitochondrial matrix / mitochondrion / proteolysis / zinc ion binding / metal ion binding
Similarity search - Function
Cytochrome Bc1 Complex; Chain A, domain 1 / Metalloenzyme, LuxS/M16 peptidase-like / Cytochrome c oxidase subunit Vb, zinc binding region signature. / Cytochrome c oxidase, subunit Vb / Cytochrome c oxidase subunit Vb / Cytochrome c oxidase subunit Vb, zinc binding domain profile. / Cytochrome c oxidase, subunit Vb superfamily / : / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. ...Cytochrome Bc1 Complex; Chain A, domain 1 / Metalloenzyme, LuxS/M16 peptidase-like / Cytochrome c oxidase subunit Vb, zinc binding region signature. / Cytochrome c oxidase, subunit Vb / Cytochrome c oxidase subunit Vb / Cytochrome c oxidase subunit Vb, zinc binding domain profile. / Cytochrome c oxidase, subunit Vb superfamily / : / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / Peptidase M16, C-terminal / Peptidase M16 inactive domain / Peptidase M16, N-terminal / Insulinase (Peptidase family M16) / Metalloenzyme, LuxS/M16 peptidase-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Cytochrome c oxidase subunit 4, mitochondrial / Mitochondrial-processing peptidase subunit beta / Mitochondrial-processing peptidase subunit alpha
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 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: Derived calculations / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _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_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_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: CYTOCHROME C OXIDASE POLYPEPTIDE IV
P: CYTOCHROME C OXIDASE POLYPEPTIDE IV
Q: CYTOCHROME C OXIDASE POLYPEPTIDE IV
R: CYTOCHROME C OXIDASE POLYPEPTIDE IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)417,89418
Polymers417,15512
Non-polymers7386
Water724
1
A: MITOCHONDRIAL PROCESSING PEPTIDASE ALPHA SUBUNIT
B: MITOCHONDRIAL PROCESSING PEPTIDASE BETA SUBUNIT
O: CYTOCHROME C OXIDASE POLYPEPTIDE IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,5935
Polymers104,2893
Non-polymers3042
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: MITOCHONDRIAL PROCESSING PEPTIDASE ALPHA SUBUNIT
D: MITOCHONDRIAL PROCESSING PEPTIDASE BETA SUBUNIT
P: CYTOCHROME C OXIDASE POLYPEPTIDE IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,3544
Polymers104,2893
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
E: MITOCHONDRIAL PROCESSING PEPTIDASE ALPHA SUBUNIT
F: MITOCHONDRIAL PROCESSING PEPTIDASE BETA SUBUNIT
Q: CYTOCHROME C OXIDASE POLYPEPTIDE IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,3544
Polymers104,2893
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
G: MITOCHONDRIAL PROCESSING PEPTIDASE ALPHA SUBUNIT
H: MITOCHONDRIAL PROCESSING PEPTIDASE BETA SUBUNIT
R: CYTOCHROME C OXIDASE POLYPEPTIDE IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,5935
Polymers104,2893
Non-polymers3042
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
C: MITOCHONDRIAL PROCESSING PEPTIDASE ALPHA SUBUNIT
D: MITOCHONDRIAL PROCESSING PEPTIDASE BETA SUBUNIT
P: CYTOCHROME C OXIDASE POLYPEPTIDE IV
hetero molecules

A: MITOCHONDRIAL PROCESSING PEPTIDASE ALPHA SUBUNIT
B: 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: CYTOCHROME C OXIDASE POLYPEPTIDE IV
Q: CYTOCHROME C OXIDASE POLYPEPTIDE IV
R: CYTOCHROME C OXIDASE POLYPEPTIDE IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)417,89418
Polymers417,15512
Non-polymers7386
Water724
TypeNameSymmetry operationNumber
crystal symmetry operation3_645-x+1,y-1/2,-z+1/21
identity operation1_555x,y,z1
Buried area29420 Å2
ΔGint-281 kcal/mol
Surface area138140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.260, 178.120, 202.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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MITOCHONDRIAL PROCESSING PEPTIDASE ... , 2 types, 8 molecules ACEGBDFH

#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

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Protein/peptide , 1 types, 4 molecules OPQR

#3: Protein/peptide
CYTOCHROME C OXIDASE POLYPEPTIDE IV / COX4


Mass: 2862.421 Da / Num. of mol.: 4 / Fragment: RESIDUES 2-25 / Source method: obtained synthetically
Details: The 24 residue peptide of CYTOCHROME C OXIDASE POLYPEPTIDE IV was synthesized using standard solid-phase Fmoc synthesis methodology
References: UniProt: P04037, cytochrome-c oxidase

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Non-polymers , 3 types, 10 molecules

#4: 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
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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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: Jul 2, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.943 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 134234 / Num. obs: 134234 / % possible obs: 99.9 % / Redundancy: 6.1 % / Biso Wilson estimate: 47.1 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 23.4
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.543 / Mean I/σ(I) obs: 3.5 / % possible all: 100
Reflection
*PLUS
Num. measured all: 820094
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

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

1hr6


Resolution: 2.7→48.63 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 6298765.76 / 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
Rfree0.264 2016 1.5 %RANDOM
Rwork0.229 ---
obs0.229 133188 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.8593 Å2 / ksol: 0.323 e/Å3
Displacement parametersBiso mean: 58.7 Å2
Baniso -1Baniso -2Baniso -3
1--9.95 Å20 Å20 Å2
2--1.47 Å20 Å2
3---8.48 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.39 Å
Luzzati d res low-50 Å
Luzzati sigma a0.42 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.7→48.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27952 0 34 4 27990
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
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_d0.53
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: 2.7→2.8 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.328 185 1.4 %
Rwork0.303 13020 -
obs--100 %
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
X-RAY DIFFRACTION4WATER_REP.PARAMWATER_REP.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 1.5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 58.7 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_deg0.53
LS refinement shell
*PLUS
Rfactor Rfree: 0.328 / % reflection Rfree: 1.4 % / Rfactor Rwork: 0.303

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