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- PDB-1yfc: Solution nmr structure of a yeast iso-1-ferrocytochrome C -

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Basic information

Entry
Database: PDB / ID: 1yfc
TitleSolution nmr structure of a yeast iso-1-ferrocytochrome C
ComponentsYEAST ISO-1-FERROCYTOCHROME C
KeywordsELECTRON TRANSPORT / FERROCYTOCHROME / MITOCHONDRION / RESPIRATORY CHAIN / METHYLATION
Function / homology
Function and homology information


Release of apoptotic factors from the mitochondria / Pyroptosis / Detoxification of Reactive Oxygen Species / Respiratory electron transport / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / respirasome / mitochondrial intermembrane space / electron transfer activity / heme binding ...Release of apoptotic factors from the mitochondria / Pyroptosis / Detoxification of Reactive Oxygen Species / Respiratory electron transport / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / respirasome / mitochondrial intermembrane space / electron transfer activity / heme binding / mitochondrion / metal ion binding
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 isoform 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / distance geometry
AuthorsBaistrocchi, P. / Banci, L. / Bertini, I. / Turano, P. / Bren, K.L. / Gray, H.B.
Citation
Journal: Biochemistry / Year: 1996
Title: Three-dimensional solution structure of Saccharomyces cerevisiae reduced iso-1-cytochrome c.
Authors: Baistrocchi, P. / Banci, L. / Bertini, I. / Turano, P. / Bren, K.L. / Gray, H.B.
#1: Journal: Biochemistry / Year: 1990
Title: Assignment of Proton Resonances, Identification of Secondary Structural Elements, and Analysis of Backbone Chemical Shifts for the C102T Variant of Yeast Iso-1-Cytochrome C and Horse Cytochrome C
Authors: Gao, Y. / Boyd, J. / Williams, R.J. / Pielak, G.J.
#2: Journal: J.Mol.Biol. / Year: 1990
Title: High-Resolution Refinement of Yeast Iso-1-Cytochrome C and Comparisons with Other Eukaryotic Cytochromes C
Authors: Louie, G.V. / Brayer, G.D.
History
DepositionAug 8, 1996Processing site: BNL
Revision 1.0Mar 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / 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_database_status.process_site / _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_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: YEAST ISO-1-FERROCYTOCHROME C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7182
Polymers12,1001
Non-polymers6191
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 500TARGET FUNCTION <= 0.82 A2
Representative

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Components

#1: Protein YEAST ISO-1-FERROCYTOCHROME C


Mass: 12099.850 Da / Num. of mol.: 1 / Mutation: C102S
Source method: isolated from a genetically manipulated source
Details: REDUCED FORM
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: YEAST ISO-1-CYTOCHROME C / Variant: C102S / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P00044
#2: 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 experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121TOCSY
131DQF-COSY

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Sample preparation

Sample conditionspH: 7.0 / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

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

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Processing

NMR software
NameClassification
DIANAstructure solution
DIANArefinement
RefinementMethod: distance geometry / Software ordinal: 1
NMR ensembleConformer selection criteria: TARGET FUNCTION <= 0.82 A2 / Conformers calculated total number: 500 / Conformers submitted total number: 20

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