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- PDB-2n9j: Solution structure of oxidized human cytochrome c -

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Basic information

Entry
Database: PDB / ID: 2n9j
TitleSolution structure of oxidized human cytochrome c
ComponentsCytochrome c
KeywordsELECTRON TRANSPORT / cytochrome c / electron transfer
Function / homology
Function and homology information


Formation of apoptosome / apoptosome / activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / Release of apoptotic factors from the mitochondria / Respiratory electron transport / Regulation of the apoptosome activity / Activation of caspases through apoptosome-mediated cleavage / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / cellular respiration ...Formation of apoptosome / apoptosome / activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / Release of apoptotic factors from the mitochondria / Respiratory electron transport / Regulation of the apoptosome activity / Activation of caspases through apoptosome-mediated cleavage / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / cellular respiration / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / Detoxification of Reactive Oxygen Species / : / Pyroptosis / intrinsic apoptotic signaling pathway / TP53 Regulates Metabolic Genes / Transcriptional activation of mitochondrial biogenesis / mitochondrial intermembrane space / Cytoprotection by HMOX1 / mitochondrial inner membrane / electron transfer activity / heme binding / mitochondrion / nucleus / metal ion binding / cytosol
Similarity search - Function
Cytochrome c, class IA/ IB / Cytochrome c / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HEME C / Cytochrome c
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
Model detailslowest energy, model1
AuthorsImai, M. / Saio, T. / Kumeta, H. / Uchida, T. / Inagaki, F. / Ishimori, K.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2016
Title: Investigation of the redox-dependent modulation of structure and dynamics in human cytochrome c.
Authors: Imai, M. / Saio, T. / Kumeta, H. / Uchida, T. / Inagaki, F. / Ishimori, K.
History
DepositionNov 24, 2015Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Feb 17, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / 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_database_status.status_code_nmr_data / _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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_label_atom_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2592
Polymers11,6411
Non-polymers6191
Water00
1


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

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Components

#1: Protein Cytochrome c


Mass: 11640.582 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CYCS, CYC / Production host: Escherichia coli (E. coli) / References: UniProt: P99999
#2: 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 experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC aliphatic
1313D CBCA(CO)NH
1413D C(CO)NH
1513D HNCO
1613D HNCA
1713D HN(CA)CB
1813D HBHA(CO)NH
1913D HN(CO)CA
11013D HN(CA)HA
11113D (H)CCH-TOCSY aliphatic
11213D 1H-15N NOESY
11313D 1H-13C NOESY aliphatic
11412D 1H-13C HSQC aromatic
11513D 1H-13C NOESY aromatic
11612D 1H-13C HSQC aromatic
11713D (H)CCH-TOCSY aromatic
1181(HB)CB(CGCD)HD
1191(HB)CB(CGCDCE)HE

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Sample preparation

DetailsContents: 0.5-1 mM [U-99% 13C; U-99% 15N] Cyt c-1, 50 mM sodium phosphate-2, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMCyt c-1[U-99% 13C; U-99% 15N]0.5-11
50 mMsodium phosphate-21
Sample conditionsIonic strength: 50 / pH: 6.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Agilent INOVAAgilentINOVA8001
Agilent INOVAAgilentINOVA6002
Agilent INOVAAgilentINOVA6003

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Processing

NMR software
NameDeveloperClassification
VnmrJVariancollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TALOS+Yang Shen,Frank Delaglio,Gabriel Cornilescu, Ad baxdata analysis
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
SparkyGoddardrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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