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- PDB-2ycc: OXIDATION STATE-DEPENDENT CONFORMATIONAL CHANGES IN CYTOCHROME C -

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Basic information

Entry
Database: PDB / ID: 2ycc
TitleOXIDATION STATE-DEPENDENT CONFORMATIONAL CHANGES IN CYTOCHROME C
ComponentsCYTOCHROME C
KeywordsELECTRON TRANSPORT (HEME PROTEIN)
Function / homology
Function and homology information


Release of apoptotic factors from the mitochondria / Pyroptosis / Detoxification of Reactive Oxygen Species / Respiratory electron transport / cardiolipin binding / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / mitochondrial intermembrane space / electron transfer activity / heme binding ...Release of apoptotic factors from the mitochondria / Pyroptosis / Detoxification of Reactive Oxygen Species / Respiratory electron transport / cardiolipin binding / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / 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)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsBerghuis, A.M. / Brayer, G.D.
Citation
Journal: J.Mol.Biol. / Year: 1992
Title: Oxidation state-dependent conformational changes in cytochrome c.
Authors: Berghuis, A.M. / Brayer, G.D.
#1: 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.
#2: Journal: J.Mol.Biol. / Year: 1989
Title: A Polypeptide Chain-Refolding Event Occurs in the Gly82 Variant of Yeast Iso-1-Cytochrome C
Authors: Louie, G.V. / Brayer, G.D.
#3: Journal: J.Mol.Biol. / Year: 1989
Title: Crystallization of Yeast Iso-2-Cytochrome C Using a Novel Hair Seeding Technique
Authors: Leung, C.J. / Nall, B.T. / Brayer, G.D.
#4: Journal: J.Mol.Biol. / Year: 1988
Title: Yeast Iso-1-Cytochrome C. A 2.8 Angstrom Resolution Three-Dimensional Structure Determination
Authors: Louie, G.V. / Hutcheon, W.L.B. / Brayer, G.D.
#5: Journal: Biochemistry / Year: 1988
Title: Role of Phenylalanine-82 in Yeast Iso-1-Cytochrome C and Remote Conformational Changes Induced by a Serine Residue at This Position
Authors: Louie, G.V. / Pielak, G.J. / Smith, M. / Brayer, G.D.
History
DepositionJan 29, 1991Processing site: BNL
Revision 1.0Jul 15, 1992Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 2.0Mar 3, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _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.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Mar 26, 2025Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification
Remark 650HELIX THE END OF THE 50 HELIX (RESIDUE 55) IS DISTORTED.
Remark 700SHEET RESIDUES IN SHEET S1 FORM A HIGHLY DISTORTED BETA TYPE CONFORMATION.

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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)12,8283
Polymers12,1141
Non-polymers7152
Water1,09961
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.470, 36.470, 137.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Atom site foot note1: RESIDUE LYS 72 AND TML 72 FORM EPSILON-N-TRIMETHYLLYSINE. SEE REMARK 8 ABOVE.
2: THE HEME GROUP IS COVALENTLY ATTACHED TO THE PROTEIN VIA THIOETHER BONDS TO THE SG ATOMS OF CYS 14 AND CYS 17.
3: IN ORDER TO CORRECTLY INDICATE IDENTICAL ATOMS BETWEEN THE COORDINATE ENTRIES OF THE REDUCED AND OXIDIZED FORMS OF YEAST ISO-1 CYTOCHROME C (PROTEIN DATA BANK ENTRIES 1YCC AND 2YCC, RESPECTIVELY), ...3: IN ORDER TO CORRECTLY INDICATE IDENTICAL ATOMS BETWEEN THE COORDINATE ENTRIES OF THE REDUCED AND OXIDIZED FORMS OF YEAST ISO-1 CYTOCHROME C (PROTEIN DATA BANK ENTRIES 1YCC AND 2YCC, RESPECTIVELY), THE SIDE-CHAIN ATOM NAMES OF SEVERAL RESIDUES CANNOT FOLLOW IUPAC/IUB SPECIFICATIONS WITH RESPECT TO THE DESIGNATION OF 1 AND 2 FOR BRANCHED SIDE CHAINS. THE AFFECTED RESIDUES ARE GLU -4, GLU 21, ARG 38, GLU 44, TYR 46, ASP 50, GLU 61, TYR 67, PHE 82, AND ASP 90.
Components on special symmetry positions
IDModelComponents
11A-151-

HOH

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Components

#1: Protein CYTOCHROME C


Mass: 12113.876 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P00044
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHIS PROTEIN HAS BEEN STABILIZED FOR ANALYSES BY THE MUTATION OF CYSTEINE 102 TO A THREONINE ...THIS PROTEIN HAS BEEN STABILIZED FOR ANALYSES BY THE MUTATION OF CYSTEINE 102 TO A THREONINE RESIDUE. IN TURN T5 THE H-BOND IS MEDIATED THROUGH A WATER MOLECULE.
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.89 Å3/Da / Density % sol: 34.9 %
Crystal grow
*PLUS
pH: 6.7 / Method: vapor diffusion, hanging drop / Details: took from Sherwood & Brayer from original paper
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12 mg/mlprotein1drop
275 %satammonium sulfate1drop
30.1 Msodium phosphate1drop
490 %satammonium sulfate1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 1.9 Å / Num. measured all: 8632

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.197 / Highest resolution: 1.9 Å
Refinement stepCycle: LAST / Highest resolution: 1.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms848 0 51 61 960
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.022
X-RAY DIFFRACTIONp_angle_d0.046
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 6 Å / Num. reflection obs: 3929 / σ(F): 2 / Rfactor obs: 0.197
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeWeightDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_angle_d0.03
X-RAY DIFFRACTIONx_planar_d0.050.057
X-RAY DIFFRACTIONx_plane_restr0.020.018
X-RAY DIFFRACTIONx_chiral_restr0.150.231

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