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- PDB-8dzl: Structure of the K39Q mutant of rat somatic Cytochrome c at 1.36A -

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Basic information

Entry
Database: PDB / ID: 8dzl
TitleStructure of the K39Q mutant of rat somatic Cytochrome c at 1.36A
ComponentsCytochrome c, somatic
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 / Respiratory electron transport / Detoxification of Reactive Oxygen Species / Pyroptosis / 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 / Detoxification of Reactive Oxygen Species / Pyroptosis / TP53 Regulates Metabolic Genes / Cytoprotection by HMOX1 / apoptosome / negative regulation of hydrogen peroxide biosynthetic process / positive regulation of cellular respiration / response to carbon monoxide / Regulation of the apoptosome activity / response to gravity / glial cell apoptotic process / response to copper ion / mitochondrial electron transport, cytochrome c to oxygen / hydrogen peroxide metabolic process / mitochondrial electron transport, ubiquinol to cytochrome c / 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
HEME C / Cytochrome c, somatic
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 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
DepositionAug 8, 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 6, 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)48,4598
Polymers45,9854
Non-polymers2,4744
Water8,719484
1
A: Cytochrome c, somatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1152
Polymers11,4961
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome c, somatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1152
Polymers11,4961
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cytochrome c, somatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1152
Polymers11,4961
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cytochrome c, somatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1152
Polymers11,4961
Non-polymers6191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.578, 61.153, 186.065
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
Cytochrome c, somatic


Mass: 11496.242 Da / Num. of mol.: 4 / Mutation: K39Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Cycs / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: P62898
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 484 / 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: 2.04 Å3/Da / Density % sol: 40.78 % / Description: Red crystals: 0.2 x 0.1 rectanglar bricks
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Wizard Cryo 2#30: 40% PEG 600, 100mM Sodium Citrate pH 5.5

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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: Mar 11, 2022
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12713 Å / Relative weight: 1
ReflectionResolution: 1.36→58.1 Å / Num. obs: 83554 / % possible obs: 99.9 % / Redundancy: 12.1 % / Biso Wilson estimate: 14.69 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.026 / Rrim(I) all: 0.092 / Χ2: 0.78 / Net I/σ(I): 13
Reflection shellResolution: 1.36→1.43 Å / Redundancy: 12.5 % / Rmerge(I) obs: 0.797 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 12815 / CC1/2: 0.942 / Rpim(I) all: 0.233 / Rrim(I) all: 0.831 / Χ2: 0.45 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PDB-REDO1.20.1_4487refinement
AutoProcessdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5C0Z

5c0z


Resolution: 1.36→58.1 Å / SU ML: 0.1159 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 17.7865
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1796 4134 4.96 %
Rwork0.1412 79261 -
obs0.1431 83395 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.6 Å2
Refinement stepCycle: LAST / Resolution: 1.36→58.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3228 0 172 484 3884
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01623488
X-RAY DIFFRACTIONf_angle_d1.46654716
X-RAY DIFFRACTIONf_chiral_restr0.0917452
X-RAY DIFFRACTIONf_plane_restr0.0159588
X-RAY DIFFRACTIONf_dihedral_angle_d12.9971472
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.36-1.380.25311330.20682602X-RAY DIFFRACTION99.93
1.38-1.390.2281460.1862642X-RAY DIFFRACTION99.64
1.39-1.410.27271300.17412560X-RAY DIFFRACTION99.78
1.41-1.430.23621200.17232619X-RAY DIFFRACTION99.82
1.43-1.450.23821260.15672631X-RAY DIFFRACTION99.93
1.45-1.470.22351420.15542626X-RAY DIFFRACTION99.82
1.47-1.490.19211350.14572566X-RAY DIFFRACTION99.74
1.49-1.510.19671360.14682611X-RAY DIFFRACTION99.53
1.51-1.530.19731400.1442627X-RAY DIFFRACTION99.64
1.53-1.560.18631320.13342566X-RAY DIFFRACTION99.26
1.56-1.580.18521260.13122650X-RAY DIFFRACTION99.78
1.58-1.610.18531270.12592624X-RAY DIFFRACTION99.78
1.61-1.640.18331510.12362568X-RAY DIFFRACTION99.82
1.64-1.680.18531360.13262647X-RAY DIFFRACTION99.46
1.68-1.710.17881410.13062596X-RAY DIFFRACTION99.82
1.71-1.750.20411470.12372640X-RAY DIFFRACTION99.93
1.75-1.80.16951480.12912609X-RAY DIFFRACTION99.96
1.8-1.850.1741420.1282626X-RAY DIFFRACTION99.96
1.85-1.90.17831180.12932649X-RAY DIFFRACTION99.86
1.9-1.960.15721420.12862634X-RAY DIFFRACTION99.89
1.96-2.030.17831390.12922634X-RAY DIFFRACTION99.82
2.03-2.110.15681430.1272697X-RAY DIFFRACTION100
2.11-2.210.18091530.12942581X-RAY DIFFRACTION99.89
2.21-2.330.20481530.14592658X-RAY DIFFRACTION99.72
2.33-2.470.21461330.15322656X-RAY DIFFRACTION99.64
2.47-2.660.19751270.14642689X-RAY DIFFRACTION99.61
2.66-2.930.19681440.15332665X-RAY DIFFRACTION99.22
2.93-3.350.18981480.15592733X-RAY DIFFRACTION100
3.35-4.230.14991380.12982752X-RAY DIFFRACTION100
4.23-58.10.13971380.14222903X-RAY DIFFRACTION99.54

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