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- PDB-5c9m: The structure of oxidized rat cytochrome c (T28A) at 1.362 angstr... -

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Basic information

Entry
Database: PDB / ID: 5c9m
TitleThe structure of oxidized rat cytochrome c (T28A) at 1.362 angstroms resolution.
ComponentsCytochrome c, somatic
KeywordsELECTRON TRANSPORT / cytochrome c oxidized rat mutant
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 / Respiratory electron transport / Pyroptosis / Detoxification of Reactive Oxygen Species / TP53 Regulates Metabolic Genes / Cytoprotection by HMOX1 / apoptosome ...Release of apoptotic factors from the mitochondria / Formation of apoptosome / Activation of caspases through apoptosome-mediated cleavage / Transcriptional activation of mitochondrial biogenesis / Respiratory electron transport / Pyroptosis / Detoxification of Reactive Oxygen Species / TP53 Regulates Metabolic Genes / Cytoprotection by HMOX1 / apoptosome / negative regulation of hydrogen peroxide biosynthetic process / positive regulation of cellular respiration / Regulation of the apoptosome activity / hydrogen peroxide metabolic process / glial cell apoptotic process / response to carbon monoxide / mitochondrial electron transport, cytochrome c to oxygen / response to copper ion / mitochondrial electron transport, ubiquinol to cytochrome c / response to gravity / 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: 1.362 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: To Be Published
Title: The structure of oxidized rat cytochrome c (T28A) at 1.362 angstroms resolution.
Authors: Edwards, B.F.P. / Mahapatra, G. / Vaishnav, A.A. / Brunzelle, J.S. / 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 28, 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 1.2Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / struct_conn
Item: _pdbx_audit_support.funding_organization / _struct_conn.pdbx_leaving_atom_flag
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
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)49,71612
Polymers46,3944
Non-polymers3,3228
Water8,503472
1
A: Cytochrome c, somatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4293
Polymers11,5981
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)12,6414
Polymers11,5981
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)12,4293
Polymers11,5981
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)12,2172
Polymers11,5981
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.517, 52.567, 61.771
Angle α, β, γ (deg.)109.86, 92.93, 92.20
Int Tables number1
Space group name H-MP1
DetailsMonomer confirmed by gel filtration

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Components

#1: Protein
Cytochrome c, somatic


Mass: 11598.462 Da / Num. of mol.: 4 / Mutation: T29A
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


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


Mass: 18.015 Da / Num. of mol.: 472 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.7 % / Description: 0.3 x0.1 mm prisms
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20 mg/ml protein, PEG 4000, isopropanol, sodium acetate, potassium ferricyanate
PH range: 6.5-7.0

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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
RadiationMonochromator: diamond laue / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.362→57.962 Å / Num. all: 80448 / Num. obs: 76544 / % possible obs: 92.37 % / Redundancy: 3.9 % / Biso Wilson estimate: 13 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 14.1
Reflection shellResolution: 1.362→1.398 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.2 / % possible all: 66.24

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
PHENIX1.8.1phasing
Aimless0.3.11data scaling
XDSJan. 10, 2014data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5C0Z

5c0z


Resolution: 1.362→57.96 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.969 / SU B: 2.244 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.057 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16982 3901 4.8 %RANDOM
Rwork0.129 ---
obs0.131 76544 92.37 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.413 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20.04 Å20.89 Å2
2---0.51 Å20.85 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.362→57.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3220 0 224 472 3916
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0193552
X-RAY DIFFRACTIONr_bond_other_d0.0030.023380
X-RAY DIFFRACTIONr_angle_refined_deg1.8032.0634826
X-RAY DIFFRACTIONr_angle_other_deg1.05837812
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4975412
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.91725.152132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.07515648
X-RAY DIFFRACTIONr_dihedral_angle_4_deg31.575158
X-RAY DIFFRACTIONr_chiral_restr0.1220.2456
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.023928
X-RAY DIFFRACTIONr_gen_planes_other0.0140.02792
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_it1.4821.8071660
X-RAY DIFFRACTIONr_mcbond_other1.4821.8061659
X-RAY DIFFRACTIONr_mcangle_it1.8242.722068
X-RAY DIFFRACTIONr_mcangle_other1.8242.7212069
X-RAY DIFFRACTIONr_scbond_it2.0422.0631892
X-RAY DIFFRACTIONr_scbond_other2.0332.061818
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.452.9232632
X-RAY DIFFRACTIONr_long_range_B_refined3.72516.1864679
X-RAY DIFFRACTIONr_long_range_B_other3.04615.2914441
X-RAY DIFFRACTIONr_rigid_bond_restr2.51936932
X-RAY DIFFRACTIONr_sphericity_free35.9155137
X-RAY DIFFRACTIONr_sphericity_bonded12.15857187
LS refinement shellResolution: 1.362→1.398 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 202 -
Rwork0.229 4056 -
obs--66.24 %

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