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- PDB-8dvx: Structure of acetylated Pig somatic Cytochrome c (Aly39) at 1.5A -

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Basic information

Entry
Database: PDB / ID: 8dvx
TitleStructure of acetylated Pig somatic Cytochrome c (Aly39) at 1.5A
ComponentsCytochrome c
KeywordsELECTRON TRANSPORT / complex IV / Complex III / apoptosis / ischemia / skeletal muscle / acetylation / oxidoreductase
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 / Detoxification of Reactive Oxygen Species / Pyroptosis / Regulation of the apoptosome activity / Cytoprotection by HMOX1 / TP53 Regulates Metabolic Genes / Respiratory electron transport ...Release of apoptotic factors from the mitochondria / Formation of apoptosome / Activation of caspases through apoptosome-mediated cleavage / Transcriptional activation of mitochondrial biogenesis / Detoxification of Reactive Oxygen Species / Pyroptosis / Regulation of the apoptosome activity / Cytoprotection by HMOX1 / TP53 Regulates Metabolic Genes / Respiratory electron transport / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / : / mitochondrial intermembrane space / electron transfer activity / heme binding / apoptotic process / metal ion binding
Similarity search - Function
Cytochrome c, class IA/ IB / Cytochrome c / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily
Similarity search - Domain/homology
HEXACYANOFERRATE(3-) / HEME C / Cytochrome c
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsEdwards, B.F.P. / Huettemann, M. / Vaishnav, A. / Brunzelle, J. / Morse, P. / Wan, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)116807 United States
CitationJournal: Nat Commun / Year: 2023
Title: Cytochrome c lysine acetylation regulates cellular respiration and cell death in ischemic skeletal muscle.
Authors: Morse, P.T. / Perez-Mejias, G. / Wan, J. / Turner, A.A. / Marquez, I. / Kalpage, H.A. / Vaishnav, A. / Zurek, M.P. / Huettemann, P.P. / Kim, K. / Arroum, T. / De la Rosa, M.A. / Chowdhury, D. ...Authors: Morse, P.T. / Perez-Mejias, G. / Wan, J. / Turner, A.A. / Marquez, I. / Kalpage, H.A. / Vaishnav, A. / Zurek, M.P. / Huettemann, P.P. / Kim, K. / Arroum, T. / De la Rosa, M.A. / Chowdhury, D.D. / Lee, I. / Brunzelle, J.S. / Sanderson, T.H. / Malek, M.H. / Meierhofer, D. / Edwards, B.F.P. / Diaz-Moreno, I. / Huttemann, M.
History
DepositionJul 30, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Oct 9, 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
B: Cytochrome c
C: Cytochrome c
D: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,50315
Polymers46,5464
Non-polymers3,95811
Water5,495305
1
A: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6794
Polymers11,6361
Non-polymers1,0423
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1036
Polymers11,6361
Non-polymers1,4665
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4673
Polymers11,6361
Non-polymers8302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2552
Polymers11,6361
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.662, 54.559, 61.782
Angle α, β, γ (deg.)65.970, 87.400, 84.070
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
Cytochrome c


Mass: 11636.421 Da / Num. of mol.: 4 / Mutation: K39(Aly) / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P62895
#2: Chemical
ChemComp-HEC / HEME C


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


Mass: 211.949 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6FeN6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 48.9 % / Description: pink/red blocks 0.1-0.2 x 0.1 mm
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5
Details: JBS3A2: 10% PEG 4K, 20% iso propanol, 15% PEG 4K, 2.5 mM Potassium Ferricyanide.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.12713 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 5, 2020
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12713 Å / Relative weight: 1
ReflectionResolution: 1.5→49.61 Å / Num. obs: 110978 / % possible obs: 86.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 16.95 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.047 / Rrim(I) all: 0.091 / Rsym value: 0.065 / Net I/σ(I): 8.8
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.532 / Mean I/σ(I) obs: 2 / Num. unique obs: 7704 / CC1/2: 0.755 / Rpim(I) all: 0.352 / Rrim(I) all: 0.641 / Rsym value: 0.428 / % possible all: 80.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
AutoProcessdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5C0Z

5c0z


Resolution: 1.5→30.38 Å / SU ML: 0.1978 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / ESU R: 0.2 / Phase error: 22.328
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2038 3874 3.49 %
Rwork0.1705 107104 -
obs0.1716 110978 84.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.74 Å2
Refinement stepCycle: LAST / Resolution: 1.5→30.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3268 0 263 305 3836
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01673616
X-RAY DIFFRACTIONf_angle_d1.57764919
X-RAY DIFFRACTIONf_chiral_restr0.0804452
X-RAY DIFFRACTIONf_plane_restr0.015596
X-RAY DIFFRACTIONf_dihedral_angle_d14.704492
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.36181350.30743289X-RAY DIFFRACTION74.6
1.52-1.540.2587970.29613406X-RAY DIFFRACTION74.98
1.54-1.560.3371300.29123517X-RAY DIFFRACTION78.6
1.56-1.580.31481240.27673612X-RAY DIFFRACTION78.55
1.58-1.60.33151280.2693512X-RAY DIFFRACTION78.92
1.6-1.630.32441400.25573598X-RAY DIFFRACTION80.08
1.63-1.650.27661230.24753790X-RAY DIFFRACTION81.73
1.65-1.680.2771410.2373696X-RAY DIFFRACTION83.7
1.68-1.710.27151250.2253918X-RAY DIFFRACTION85.08
1.71-1.740.27511500.21043762X-RAY DIFFRACTION84.9
1.74-1.780.27311480.21113856X-RAY DIFFRACTION85.74
1.78-1.810.20251500.19693897X-RAY DIFFRACTION85.56
1.81-1.850.23651220.19563803X-RAY DIFFRACTION85.59
1.85-1.890.19181390.17793715X-RAY DIFFRACTION81.83
1.89-1.940.24751220.17833458X-RAY DIFFRACTION76.2
1.94-1.990.18441220.16193422X-RAY DIFFRACTION76.28
1.99-2.050.19161550.16414194X-RAY DIFFRACTION91.67
2.05-2.120.17771500.14234074X-RAY DIFFRACTION91.83
2.12-2.190.18811520.15154146X-RAY DIFFRACTION91.37
2.19-2.280.17931590.15594098X-RAY DIFFRACTION91.23
2.28-2.390.20681450.16654070X-RAY DIFFRACTION90.61
2.39-2.510.18761380.16064103X-RAY DIFFRACTION90.93
2.51-2.670.17731520.16174138X-RAY DIFFRACTION90.62
2.67-2.870.18431420.15234026X-RAY DIFFRACTION89.14
2.87-3.160.23181490.1663853X-RAY DIFFRACTION86.18
3.16-3.620.17721160.14933387X-RAY DIFFRACTION75.14
3.62-4.560.19541600.14664360X-RAY DIFFRACTION96.62
4.56-30.380.16371600.15614404X-RAY DIFFRACTION97.69

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