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- PDB-2n3y: NMR structure of the Y48pCMF variant of human cytochrome c in its... -

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Basic information

Entry
Database: PDB / ID: 2n3y
TitleNMR structure of the Y48pCMF variant of human cytochrome c in its reduced state
ComponentsCytochrome c
KeywordsELECTRON TRANSPORT / Cytochrome c / hemeprotein / mitochondria / apoptosis / phosphorylation
Function / homology
Function and homology information


Formation of apoptosome / apoptosome / activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / Release of apoptotic factors from the mitochondria / Respiratory electron transport / cellular respiration / Regulation of the apoptosome activity / Activation of caspases through apoptosome-mediated cleavage / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes ...Formation of apoptosome / apoptosome / activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / Release of apoptotic factors from the mitochondria / Respiratory electron transport / cellular respiration / Regulation of the apoptosome activity / Activation of caspases through apoptosome-mediated cleavage / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / Detoxification of Reactive Oxygen Species / Pyroptosis / respirasome / intrinsic apoptotic signaling pathway / TP53 Regulates Metabolic Genes / Transcriptional activation of mitochondrial biogenesis / mitochondrial intermembrane space / Cytoprotection by HMOX1 / mitochondrial inner membrane / electron transfer activity / heme binding / mitochondrion / metal ion binding / nucleus / 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
Mesoheme / Cytochrome c
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry, molecular dynamics
Model detailsclosest to the average, model1
AuthorsMoreno-Beltran, B. / Del Conte, R. / Diaz-Quintana, A. / De la Rosa, M.A. / Turano, P. / Diaz-Moreno, I.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structural basis of mitochondrial dysfunction in response to cytochrome c phosphorylation at tyrosine 48.
Authors: Moreno-Beltran, B. / Guerra-Castellano, A. / Diaz-Quintana, A. / Del Conte, R. / Garcia-Maurino, S.M. / Diaz-Moreno, S. / Gonzalez-Arzola, K. / Santos-Ocana, C. / Velazquez-Campoy, A. / De ...Authors: Moreno-Beltran, B. / Guerra-Castellano, A. / Diaz-Quintana, A. / Del Conte, R. / Garcia-Maurino, S.M. / Diaz-Moreno, S. / Gonzalez-Arzola, K. / Santos-Ocana, C. / Velazquez-Campoy, A. / De la Rosa, M.A. / Turano, P. / Diaz-Moreno, I.
History
DepositionJun 15, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2017Group: Database references
Revision 1.2Apr 19, 2017Group: Database references
Revision 1.3Apr 26, 2017Group: Database references

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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)12,3032
Polymers11,6831
Non-polymers6211
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200target function
RepresentativeModel #1closest to the average

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Components

#1: Protein Cytochrome c /


Mass: 11682.618 Da / Num. of mol.: 1 / Mutation: Y48pCMFCc
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CYCS, CYC / Plasmid: pCcY48AMBER / Production host: Escherichia coli (E. coli) / References: UniProt: P99999
#2: Chemical ChemComp-MH0 / Mesoheme


Mass: 620.519 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H36FeN4O4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1223D 1H-15N NOESY
1322D 1H-15N HSQC
1412D 1H-13C HSQC
1522D 1H-1H NOESY
1613D CBCA(CO)NH
1713D HNCO
1813D HNCA
1913D HN(CO)CA
11013D HBHA(CO)NH
11113D (H)CCH-TOCSY
11232D 1H-1H COSY
11332D 1H-13C HSQC aromatic
11413D HN(CA)CB
11513D 1H-13C NOESY aliphatic

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Sample preparation

Details
Solution-IDContentsSolvent system
10.7 mM [U-99% 13C; U-99% 15N] cytochrome c, 90% H2O/10% D2O90% H2O/10% D2O
20.7 mM [U-99% 15N] cytochrome c, 90% H2O/10% D2O90% H2O/10% D2O
30.6 mM cytochrome c, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.7 mMcytochrome c-1[U-99% 13C; U-99% 15N]1
0.7 mMcytochrome c-2[U-99% 15N]2
0.6 mMcytochrome c-33
Sample conditionsIonic strength: 0.05 / pH: 6.3 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAvance9501
Bruker AvanceBrukerAvance7002
Bruker AvanceBrukerAvance5003
Bruker AvanceBrukerAvance5004

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
AMBERCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
TOPSPINBruker Biospincollection
TOPSPINBruker Biospinprocessing
TALOSCornilescu, Delaglio and Baxgeometry optimization
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichchemical shift calculation
CARAKeller and Wuthrichdata analysis
CARAKeller and Wuthrichpeak picking
XEASYBartels et al.chemical shift assignment
XEASYBartels et al.chemical shift calculation
XEASYBartels et al.data analysis
XEASYBartels et al.peak picking
XEASYBartels et al.processing
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: distance geometry, molecular dynamics / Software ordinal: 1 / Details: Molecular dynamics performed in solvent
NMR constraintsNOE constraints total: 2176 / NOE intraresidue total count: 362 / NOE long range total count: 392 / NOE medium range total count: 562 / NOE sequential total count: 769 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 71 / Protein psi angle constraints total count: 71
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 3.79 ° / Maximum upper distance constraint violation: 0.29 Å / Torsion angle constraint violation method: TALOS
NMR ensemble rmsDistance rms dev: 0.0059 Å

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