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- PDB-2gb8: Solution structure of the complex between yeast iso-1-cytochrome ... -

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Basic information

Entry
Database: PDB / ID: 2gb8
TitleSolution structure of the complex between yeast iso-1-cytochrome c and yeast cytochrome c peroxidase
Components
  • Cytochrome c iso-1
  • Cytochrome c peroxidase
KeywordsOXIDOREDUCTASE/ELECTRON TRANSPORT / protein-protein complex / electron transfer / transient complex / OXIDOREDUCTASE-ELECTRON TRANSPORT COMPLEX
Function / homology
Function and homology information


Release of apoptotic factors from the mitochondria / Pyroptosis / Detoxification of Reactive Oxygen Species / Respiratory electron transport / cytochrome-c peroxidase / cytochrome-c peroxidase activity / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / respirasome / response to reactive oxygen species ...Release of apoptotic factors from the mitochondria / Pyroptosis / Detoxification of Reactive Oxygen Species / Respiratory electron transport / cytochrome-c peroxidase / cytochrome-c peroxidase activity / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / respirasome / response to reactive oxygen species / hydrogen peroxide catabolic process / peroxidase activity / mitochondrial intermembrane space / 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 / rigid-body docking solely on the basis of experimental data; sidechain dynamics.
AuthorsVolkov, A.N. / Worrall, J.A.R. / Ubbink, M.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Solution structure and dynamics of the complex between cytochrome c and cytochrome c peroxidase determined by paramagnetic NMR.
Authors: Volkov, A.N. / Worrall, J.A. / Holtzmann, E. / Ubbink, M.
History
DepositionMar 10, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_conn_type / 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_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
B: Cytochrome c iso-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8344
Polymers45,5992
Non-polymers1,2352
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Cytochrome c peroxidase / / CCP


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


Mass: 12073.835 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: Oviformis / Gene: CYC1 / Plasmid: pBTR1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P00044
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-HEC / HEME C / 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: 1H-15N HSQC
NMR detailsText: Five 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: Five 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: 0.3-0.4mM Cc(Fe3+)-CcP(Fe3+), 1:1 complex; 20mM NaPi, 100mM NaCl pH 6.0
Solvent system: 20mM NaPi, 100mM NaCl pH 6.0
Sample conditionsIonic strength: 120mM / pH: 6.0 / Pressure: ambient / Temperature: 301 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
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
Azara2.7W. Boucherprocessing
ANSIG1.02M. Helgstrand, P.J. Kraulis, P. Allard, T. Harddata analysis
XPLOR-NIH2.13C.D. Schwieters, J.J. Kuszewski, N. Tjandra, G.M. Clorestructure solution
XPLOR-NIH2.13C.D. Schwieters, J.J. Kuszewski, N. Tjandra, G.M. Clorerefinement
RefinementMethod: rigid-body docking solely on the basis of experimental data; sidechain dynamics.
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. Best twenty structures of the final solution show an average rmsd from the lowest energy structure of 0.7 (0.2) Angstrom for the backbone atoms of cytochrome c after superposition of the peroxidase molecules.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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