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- PDB-1c15: SOLUTION STRUCTURE OF APAF-1 CARD -

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Basic information

Entry
Database: PDB / ID: 1c15
TitleSOLUTION STRUCTURE OF APAF-1 CARD
ComponentsAPOPTOTIC PROTEASE ACTIVATING FACTOR 1
KeywordsAPOPTOSIS / PROGRAMMED CELL DEATH / APAF / CARD / DED / DD / CASPASE RECRUITMENT DOMAIN / HOMOPHILIC INTERACTION
Function / homology
Function and homology information


response to G1 DNA damage checkpoint signaling / : / regulation of apoptotic DNA fragmentation / Formation of apoptosome / apoptosome / Activation of caspases through apoptosome-mediated cleavage / Regulation of the apoptosome activity / 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 / : / regulation of apoptotic DNA fragmentation / Formation of apoptosome / apoptosome / Activation of caspases through apoptosome-mediated cleavage / Regulation of the apoptosome activity / 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 / cellular response to transforming growth factor beta stimulus / forebrain development / heat shock protein binding / cardiac muscle cell apoptotic process / intrinsic apoptotic signaling pathway / response to nutrient / kidney development / neural tube closure / positive regulation of apoptotic signaling pathway / ADP binding / : / nervous system development / secretory granule lumen / regulation of apoptotic process / neuron apoptotic process / ficolin-1-rich granule lumen / cell differentiation / response to hypoxia / positive regulation of apoptotic process / nucleotide binding / Neutrophil degranulation / apoptotic process / 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. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / Winged helix-like DNA-binding domain superfamily / WD40/YVTN repeat-like-containing 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 / torsion angle dynamics
Model type detailsminimized average
AuthorsZhou, P. / Chou, J. / Olea, R.S. / Yuan, J. / Wagner, G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: Solution structure of Apaf-1 CARD and its interaction with caspase-9 CARD: a structural basis for specific adaptor/caspase interaction.
Authors: Zhou, P. / Chou, J. / Olea, R.S. / Yuan, J. / Wagner, G.
History
DepositionJul 20, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 1999Provider: 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: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: APOPTOTIC PROTEASE ACTIVATING FACTOR 1


Theoretical massNumber of molelcules
Total (without water)11,1001
Polymers11,1001
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)16 / 30structures with the lowest energy
RepresentativeModel #16minimized average structure

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Components

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


Mass: 11099.710 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-2T / Production host: Escherichia coli (E. coli) / References: UniProt: O14727

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Number of used crystals: 1
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-SEPARATED NOESY
1223D 13C-SEPARATED NOESY
1332D NOESY
141HMQC-J
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY.

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Sample preparation

Details
Solution-IDContents
11MM 15N LABELED APAF-1 CARD, 20 MM PHOSPHATE BUFFER, 50 MM NACL
21MM 13C LABELED APAF-1 CARD, 20 MM PHOSPHATE BUFFER, 50 MM NACL
31MM NON-LABELED APAF-1 CARD, 20 MM PHOSPHATE BUFFER, 50 MM NACL
41MM 13C,15N LABELED, 80%DEUTERATED APAF-1 CARD, 20 MM PHOSPHATE BUFFER, 50 MM NACL
Sample conditionsIonic strength: 1 / pH: 6.5 / Pressure: AMBIENT / Temperature: 300 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA7501
Bruker DMXBrukerDMX6002
Bruker DMXBrukerDMX5003

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5GUNTERT ET ALstructure solution
X-PLOR3.851BRUNGERrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 30 / Conformers submitted total number: 16

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