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- PDB-1cww: SOLUTION STRUCTURE OF THE CASPASE RECRUITMENT DOMAIN (CARD) FROM ... -

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Entry
Database: PDB / ID: 1cww
TitleSOLUTION STRUCTURE OF THE CASPASE RECRUITMENT DOMAIN (CARD) FROM APAF-1
ComponentsAPOPTOTIC PROTEASE ACTIVATING FACTOR 1
KeywordsAPOPTOSIS / HELICAL BUNDLE
Function / homology
Function and homology information


response to G1 DNA damage checkpoint signaling / Formation of apoptosome / regulation of apoptotic DNA fragmentation / apoptosome / activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / 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 / TP53 Regulates Transcription of Caspase Activators and Caspases ...response to G1 DNA damage checkpoint signaling / Formation of apoptosome / regulation of apoptotic DNA fragmentation / apoptosome / activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / 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 / TP53 Regulates Transcription of Caspase Activators and Caspases / Transcriptional Regulation by E2F6 / cysteine-type endopeptidase activator activity involved in apoptotic process / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / forebrain development / positive regulation of apoptotic signaling pathway / cardiac muscle cell apoptotic process / cellular response to transforming growth factor beta stimulus / heat shock protein binding / intrinsic apoptotic signaling pathway / response to nutrient / kidney development / neural tube closure / ADP binding / activation of cysteine-type endopeptidase activity involved in apoptotic process / nervous system development / neuron apoptotic process / secretory granule lumen / regulation of apoptotic process / ficolin-1-rich granule lumen / cell differentiation / response to hypoxia / positive regulation of apoptotic process / nucleotide binding / apoptotic process / Neutrophil degranulation / protein-containing complex / extracellular exosome / extracellular region / ATP binding / identical protein binding / nucleus / cytosol
Similarity search - Function
Apoptotic Protease-Activating Factor 1, CARD domain / : / Apoptotic protease-activating factor 1-like, winged-helix domain / Apoptotic protease-activating factor 1 / APAF-1 helical domain / APAF-1 helical domain / Apoptotic protease-activating factors, helical domain / Death Domain, Fas / Death Domain, Fas / NB-ARC ...Apoptotic Protease-Activating Factor 1, CARD domain / : / Apoptotic protease-activating factor 1-like, winged-helix domain / Apoptotic protease-activating factor 1 / APAF-1 helical domain / APAF-1 helical domain / Apoptotic protease-activating factors, helical domain / Death Domain, Fas / Death Domain, Fas / NB-ARC / NB-ARC domain / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Death-like domain superfamily / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Apoptotic protease-activating factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DISTANCE GEOMETRY TORSION ANGLE DYNAMICS SIMULATED ANNEALING
AuthorsDay, C.L. / Dupont, C. / Lackmann, M. / Vaux, D.L. / Hinds, M.G.
CitationJournal: Cell Death Differ. / Year: 1999
Title: Solution structure and mutagenesis of the caspase recruitment domain (CARD) from Apaf-1.
Authors: Day, C.L. / Dupont, C. / Lackmann, M. / Vaux, D.L. / Hinds, M.G.
History
DepositionAug 26, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4Dec 21, 2022Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: APOPTOTIC PROTEASE ACTIVATING FACTOR 1


Theoretical massNumber of molelcules
Total (without water)11,5111
Polymers11,5111
Non-polymers00
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 / 250STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS,STRUCTURES WITH THE LOWEST ENERGY
RepresentativeModel #1closest to the average

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Components

#1: Protein APOPTOTIC PROTEASE ACTIVATING FACTOR 1 / CARD OF APAF-1


Mass: 11511.163 Da / Num. of mol.: 1 / Fragment: CASPASE RECRUITMENT DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGEX 6P-3 / Production host: Escherichia coli (E. coli) / References: UniProt: O14727

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1223D 15N-SEPARATED NOESY
132HNHA
1433D 13C-SEPARATED NOESY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY

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Sample preparation

Details
Solution-IDContents
1UNLABELLED 1.5MM APAF-1 CARD 20MM SODIUM PHOSPHATE PH 6.7 75MM NACL 2MM DITHIOTHREITOL
2U-15N 1.5MM APAF-1 CARD 20MM SODIUM PHOSPHATE PH 6.7 75MM NACL 2MM DITHIOTHREITOL
3U-15N; U-13C 1.5MM APAF-1 CARD 20MM SODIUM PHOSPHATE PH 6.7 75MM NACL 2MM DITHIOTHREITOL
Sample conditions
Conditions-IDpHTemperature (K)
16.7 30 K
26.7 30 K
36.7 30 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX5001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.1BRUKER (AG)structure solution
XEASY1.3.13BARTELS ET AL.structure solution
DYANA1.5GUNTERT ET AL.structure solution
X-PLOR3.851BRUNGERrefinement
RefinementMethod: DISTANCE GEOMETRY TORSION ANGLE DYNAMICS SIMULATED ANNEALING
Software ordinal: 1
Details: THE STRUCTURES ARE BASED ON A TOTAL OF 2314 NOE-DERIVED DISTANCE CONSTRAINTS, 31 HYDROGEN BOND CONSTRAINTS AND 173 DIHEDRAL ANGLE CONSTRAINTS.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS,STRUCTURES WITH THE LOWEST ENERGY
Conformers calculated total number: 250 / Conformers submitted total number: 20

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