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- PDB-2jti: Solution structure of the yeast iso-1-cytochrome c (T12A) : yeast... -

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Basic information

Entry
Database: PDB / ID: 2jti
TitleSolution structure of the yeast iso-1-cytochrome c (T12A) : yeast cytochrome c peroxidase complex
Components
  • Cytochrome c iso-1
  • Cytochrome c peroxidase, mitochondrial
KeywordsOXIDOREDUCTASE/ELECTRON TRANSPORT / protein/protein / Heme / Hydrogen peroxide / Iron / Metal-binding / Mitochondrion / Oxidoreductase / Peroxidase / Transit peptide / Electron transport / Methylation / Respiratory chain / Transport / OXIDOREDUCTASE-ELECTRON TRANSPORT COMPLEX
Function / homology
Function and homology information


Release of apoptotic factors from the mitochondria / Pyroptosis / Respiratory electron transport / Detoxification of Reactive Oxygen Species / cytochrome-c peroxidase / cytochrome-c peroxidase activity / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / : / response to reactive oxygen species ...Release of apoptotic factors from the mitochondria / Pyroptosis / Respiratory electron transport / Detoxification of Reactive Oxygen Species / cytochrome-c peroxidase / cytochrome-c peroxidase activity / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / : / response to reactive oxygen species / hydrogen peroxide catabolic process / mitochondrial intermembrane space / peroxidase activity / cellular response to oxidative stress / electron transfer activity / mitochondrial matrix / heme binding / mitochondrion / metal ion binding
Similarity search - Function
Cytochrome c, class IA/ IB / Class I peroxidase / Heme-binding peroxidase Ccp1-like / Cytochrome c / Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Cytochrome c-like domain / Peroxidase; domain 1 / Cytochrome Bc1 Complex; Chain D, domain 2 ...Cytochrome c, class IA/ IB / Class I peroxidase / Heme-binding peroxidase Ccp1-like / Cytochrome c / Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Cytochrome c-like domain / Peroxidase; domain 1 / Cytochrome Bc1 Complex; Chain D, domain 2 / Peroxidases heam-ligand binding site / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. / Haem peroxidase / Peroxidase / Peroxidases proximal heme-ligand signature. / Haem peroxidase superfamily / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HEME C / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome c isoform 1 / Cytochrome c peroxidase, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
AuthorsUbbink, M. / Volkov, A.N.
CitationJournal: J.Am.Chem.Soc. / Year: 2010
Title: Shifting the equilibrium between the encounter state and the specific form of a protein complex by interfacial point mutations.
Authors: Volkov, A.N. / Bashir, Q. / Worrall, J.A. / Ullmann, G.M. / Ubbink, M.
History
DepositionAug 1, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / struct_conn / struct_conn_type / 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_nmr_software.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome c peroxidase, mitochondrial
B: Cytochrome c iso-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8044
Polymers45,5692
Non-polymers1,2352
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 120structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Cytochrome c peroxidase, mitochondrial / CCP


Mass: 33525.258 Da / Num. of mol.: 1 / Mutation: N38C,N200C,S263C,T288C,C128A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: DBY939 / Gene: CCP1, CCP, CPO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P00431, cytochrome-c peroxidase
#2: Protein Cytochrome c iso-1


Mass: 12043.809 Da / Num. of mol.: 1 / Mutation: T12A,C102T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: OVIFORMIS / Gene: CYC1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P00044
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D 1H-15N HSQC
NMR detailsText: Four single-cysteine CcP variants have been prepared and labelled with a paramagnetic spin-label. For each variant, two 2D [1H,15N] HSQC spectra were acquired, one of the complex between the ...Text: Four single-cysteine CcP variants have been prepared and labelled with a paramagnetic spin-label. For each variant, two 2D [1H,15N] HSQC spectra were acquired, one of the complex between the spin-labelled protein and 15N Cc and the other of the control sample containing the complex of diamagnetically-labelled CcP with 15N Cc. From these, spin-label induced paramagnetic relaxation enhancements (PREs) of 15N Cc backbone amide resonances were determined and converted into intermolecular distance restraints, which were used for subsequent structure calculation of the protein complex.

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Sample preparation

DetailsContents: 0.3-0.4 mM [U-15N] CC, 0.3-0.4 mM CCP, 93% H2O/7% D2O
Solvent system: 93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.3 mMCC[U-15N]1
0.3 mMCCP1
Sample conditionspH: 6.00 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
AzaraBoucherprocessing
AzaraBoucherpeak picking
ANSIGKraulischemical shift assignment
ANSIGKraulisdata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Coordinates of both proteins were taken from the PDB entry 2pcc. sequences differ slightly from the experiment. structure refinement was based on pre-derived distance restraints for backbone ...Details: Coordinates of both proteins were taken from the PDB entry 2pcc. sequences differ slightly from the experiment. structure refinement was based on pre-derived distance restraints for backbone atoms as a sole input. Only two energy terms, corresponding to restraints and van der waals forces, are specified during the refinement procedure, which consist of two steps. first, a rigid-body docking of the protein molecules is carried out with van der waals parameters for mtsl atoms set to zero. for each run performed, a single cluster of low-energy solutions is consistently produced. during the second step, 30 to 40 best structures are subjected to energy minimization and side-chain dynamics with fixed positions of backbone atoms for both proteins and active van der waals parameters for mtsl. For the refined structures, the entire docking procedure is repeated until no further reduction in energy is observed.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 120 / Conformers submitted total number: 10

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