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- PDB-1j3s: Solution Structure of Reduced Recombinant Human Cytochrome c -

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Basic information

Entry
Database: PDB / ID: 1j3s
TitleSolution Structure of Reduced Recombinant Human Cytochrome c
ComponentsCytochrome c
KeywordsELECTRON TRANSPORT / Ferrocytochrome c
Function / homology
Function and homology information


Formation of apoptosome / apoptosome / Release of apoptotic factors from the mitochondria / Respiratory electron transport / Activation of caspases through apoptosome-mediated cleavage / Regulation of the apoptosome activity / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / mitochondrial electron transport, cytochrome c to oxygen / cellular respiration ...Formation of apoptosome / apoptosome / Release of apoptotic factors from the mitochondria / Respiratory electron transport / Activation of caspases through apoptosome-mediated cleavage / Regulation of the apoptosome activity / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / mitochondrial electron transport, cytochrome c to oxygen / cellular respiration / execution phase of apoptosis / 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 / Cytoprotection by HMOX1 / mitochondrial intermembrane space / 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 / Hybrid distance geometry-dynamical simulated annealing method
AuthorsJeng, W.-Y. / Shiu, J.-H. / Tsai, Y.-H. / Chuang, W.-J.
Citation
Journal: To be Published
Title: Solution Structure of Reduced Recombinant Human Cytochrome c
Authors: Jeng, W.-Y. / Shiu, J.-H. / Tsai, Y.-H. / Chuang, W.-J.
#1: Journal: To be Published
Title: Expression and Characterization of Recombinant Human Cytochrome c in E. Coli
Authors: Jeng, W.-Y. / Shiu, J.-H. / Tsai, Y.-H. / Chuang, W.-J.
History
DepositionFeb 12, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 18, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _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_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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 / 100structures with acceptable covalent geometry
RepresentativeModel #1closest to the average

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Components

#1: Protein Cytochrome c / Ferrocytochrome c


Mass: 11640.582 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET-21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): B1-21 (DE3) / References: UniProt: P99999
#2: Chemical ChemComp-HEC / HEME C


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

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
131DQF-COSY
1422D NOESY
1522D TOCSY
1633D 15N-separated NOESY
1743D 15N-separated NOESY
185HNCBCA, CBCA(CO)NH, HBHA(CBCA)NH, HBHA(CBCACO)NH, HNHA
1963D 13C-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
12mM Cytochrome c; 25mM phosphate buffer90% H2O/10% D2O
22mM Cytochrome c; 25mM phosphate buffer100% D2O
32mM Cytochrome c U-15N; 25mM phosphate buffer90% H2O/10% D2O
42mM Cytochrome c U-15N; 25mM phosphate buffer100% D2O
52mM Cytochrome c U-15N, 13C; 25mM phosphate buffer90% H2O/10% D2O
62mM Cytochrome c U-15N, 13C; 25mM phosphate buffer100% D2O
Sample conditionsIonic strength: 125 / pH: 6.5 / Pressure: ambient / Temperature: 300 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.85Brungerrefinement
AURELIA2.5.9Neidigdata analysis
XwinNMR2.6Brukerprocessing
RefinementMethod: Hybrid distance geometry-dynamical simulated annealing method
Software ordinal: 1
Details: The structures are based on a total of 1562 restraints, 1449 are NOE-derived distance constraints, 80 dihedral angle restraints,33 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 100 / Conformers submitted total number: 20

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