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- PDB-5c0z: The structure of oxidized rat cytochrome c at 1.13 angstroms reso... -

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Basic information

Entry
Database: PDB / ID: 5c0z
TitleThe structure of oxidized rat cytochrome c at 1.13 angstroms resolution
ComponentsCytochrome c, somatic
KeywordsELECTRON TRANSPORT / cytochrome oxidized rat native
Function / homology
Function and homology information


Release of apoptotic factors from the mitochondria / Formation of apoptosome / Activation of caspases through apoptosome-mediated cleavage / Transcriptional activation of mitochondrial biogenesis / Pyroptosis / Respiratory electron transport / Detoxification of Reactive Oxygen Species / TP53 Regulates Metabolic Genes / response to carbon monoxide / Cytoprotection by HMOX1 ...Release of apoptotic factors from the mitochondria / Formation of apoptosome / Activation of caspases through apoptosome-mediated cleavage / Transcriptional activation of mitochondrial biogenesis / Pyroptosis / Respiratory electron transport / Detoxification of Reactive Oxygen Species / TP53 Regulates Metabolic Genes / response to carbon monoxide / Cytoprotection by HMOX1 / apoptosome / Regulation of the apoptosome activity / negative regulation of hydrogen peroxide biosynthetic process / response to gravity / positive regulation of cellular respiration / glial cell apoptotic process / response to copper ion / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / hydrogen peroxide metabolic process / respirasome / response to ischemia / mitochondrial intermembrane space / response to oxidative stress / electron transfer activity / apoptotic process / heme binding / enzyme binding / mitochondrion / 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
HEXACYANOFERRATE(3-) / HEME C / Cytochrome c, somatic
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1236 Å
AuthorsEdwards, B.F.P. / Mahapatra, G. / Vaishnav, A.A. / Brunzelle, J.S. / Huttemann, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)NIGMS RO1 089900 United States
Citation
Journal: Faseb J. / Year: 2019
Title: Serine-47 phosphorylation of cytochromecin the mammalian brain regulates cytochromecoxidase and caspase-3 activity.
Authors: Kalpage, H.A. / Vaishnav, A. / Liu, J. / Varughese, A. / Wan, J. / Turner, A.A. / Ji, Q. / Zurek, M.P. / Kapralov, A.A. / Kagan, V.E. / Brunzelle, J.S. / Recanati, M.A. / Grossman, L.I. / ...Authors: Kalpage, H.A. / Vaishnav, A. / Liu, J. / Varughese, A. / Wan, J. / Turner, A.A. / Ji, Q. / Zurek, M.P. / Kapralov, A.A. / Kagan, V.E. / Brunzelle, J.S. / Recanati, M.A. / Grossman, L.I. / Sanderson, T.H. / Lee, I. / Salomon, A.R. / Edwards, B.F.P. / Huttemann, M.
#1: Journal: Biochemistry / Year: 2010
Title: Phosphomimetic substitution of cytochrome C tyrosine 48 decreases respiration and binding to cardiolipin and abolishes ability to trigger downstream caspase activation.
Authors: Pecina, P. / Borisenko, G.G. / Belikova, N.A. / Tyurina, Y.Y. / Pecinova, A. / Lee, I. / Samhan-Arias, A.K. / Przyklenk, K. / Kagan, V.E. / Huttemann, M.
History
DepositionJun 12, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Oct 23, 2019Group: Data collection / Database references / Derived calculations
Category: citation / citation_author / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _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_label_asym_id / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome c, somatic
B: Cytochrome c, somatic
C: Cytochrome c, somatic
D: Cytochrome c, somatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,83612
Polymers46,5144
Non-polymers3,3228
Water9,674537
1
A: Cytochrome c, somatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4593
Polymers11,6281
Non-polymers8302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cytochrome c, somatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6714
Polymers11,6281
Non-polymers1,0423
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Cytochrome c, somatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4593
Polymers11,6281
Non-polymers8302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Cytochrome c, somatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2472
Polymers11,6281
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.401, 52.471, 61.647
Angle α, β, γ (deg.)110.04, 92.77, 92.02
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Cytochrome c, somatic /


Mass: 11628.488 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Tissue: somatic / Gene: Cycs / Plasmid: pLW01 / Cell line (production host): C41 (DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: P62898
#2: Chemical
ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical
ChemComp-FC6 / HEXACYANOFERRATE(3-) / FERRI(III)HEXACYANIDE


Mass: 211.949 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6FeN6
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 537 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsMouse Cytochrome c has the same sequence (UNP P62897/CYC_MOUSE) as this entry (UNP P62898/CYC_RAT)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.12 % / Description: 0.4 mm prisms
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 4000, isopropanol, sodium acetate, potassium ferricyanate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.1236→49.22 Å / Num. all: 134553 / Num. obs: 127840 / % possible obs: 87.4 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 14.4
Reflection shellResolution: 1.1236→1.153 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.548 / Mean I/σ(I) obs: 2 / % possible all: 44.66

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
PHENIX1.8.1refinement
Aimlessdata scaling
PHENIX1.8.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZOO

3zoo


Resolution: 1.1236→49.22 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.096 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.033 / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15928 6713 5 %RANDOM
Rwork0.13184 ---
obs0.13321 127840 87.4 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.3 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.968 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å2-0.17 Å20.45 Å2
2---0.24 Å20.31 Å2
3----0.62 Å2
Refinement stepCycle: LAST / Resolution: 1.1236→49.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3228 0 224 537 3989
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0193605
X-RAY DIFFRACTIONr_bond_other_d0.0040.023440
X-RAY DIFFRACTIONr_angle_refined_deg1.9032.0634906
X-RAY DIFFRACTIONr_angle_other_deg1.18237960
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7325424
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.76125136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.43915668
X-RAY DIFFRACTIONr_dihedral_angle_4_deg31.4881510
X-RAY DIFFRACTIONr_chiral_restr0.1240.2467
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.023988
X-RAY DIFFRACTIONr_gen_planes_other0.0160.02806
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.081.3271672
X-RAY DIFFRACTIONr_mcbond_other1.0791.3271671
X-RAY DIFFRACTIONr_mcangle_it1.37822086
X-RAY DIFFRACTIONr_mcangle_other1.37822087
X-RAY DIFFRACTIONr_scbond_it1.5471.5091933
X-RAY DIFFRACTIONr_scbond_other1.5421.5021859
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8542.1232688
X-RAY DIFFRACTIONr_long_range_B_refined3.49312.2324897
X-RAY DIFFRACTIONr_long_range_B_other2.7711.2454574
X-RAY DIFFRACTIONr_rigid_bond_restr2.51337045
X-RAY DIFFRACTIONr_sphericity_free31.9715122
X-RAY DIFFRACTIONr_sphericity_bonded10.54257378
LS refinement shellResolution: 1.1236→1.153 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 240 -
Rwork0.239 4841 -
obs--44.66 %

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