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- PDB-1cy5: CRYSTAL STRUCTURE OF THE APAF-1 CARD -

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Basic information

Entry
Database: PDB / ID: 1cy5
TitleCRYSTAL STRUCTURE OF THE APAF-1 CARD
ComponentsPROTEIN (APOPTOTIC PROTEASE ACTIVATING FACTOR 1)
KeywordsAPOPTOSIS / CASPASE RECRUITMENT DOMAIN / DEATH FOLD / SIX ALPHA-HELIX BUNDLE / GREEK KEY TOPOLOGY
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
BETA-MERCAPTOETHANOL / Apoptotic protease-activating factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD PROGRAM PACKAGE USED (IF ANY) : SHARP STARTING MODEL FOR MOLECULAR REPLACEMENT: NONE / Resolution: 1.3 Å
AuthorsVaughn, D.E. / Joshua-Tor, L.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Crystal structure of Apaf-1 caspase recruitment domain: an alpha-helical Greek key fold for apoptotic signaling.
Authors: Vaughn, D.E. / Rodriguez, J. / Lazebnik, Y. / Joshua-Tor, L.
History
DepositionAug 31, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (APOPTOTIC PROTEASE ACTIVATING FACTOR 1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5057
Polymers11,1001
Non-polymers4056
Water1,910106
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.350, 46.910, 54.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 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) / Production host: Escherichia coli (E. coli) / References: UniProt: O14727
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O

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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: 2.09 Å3/Da / Density % sol: 30 %
Description: RESIDUES 93-97 ARE DISORDERED AND NOT MODELED. SEE JOURNAL REFERENCE FOR PHASING DETAILS
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8
Details: HANGING DROP VAPOR DIFFUSION WITH EQUAL VOLUMES OF PROTEIN AND RESERVOIR SOLUTIONS. PROTEIN SOLUTION: 5-20 MG/ML PROTEIN IN 0.02 MOLAR TRIS (PH 8.0-8.5) , 0.1-0.2 MOLAR SODIUM CHLORIDE. 0. ...Details: HANGING DROP VAPOR DIFFUSION WITH EQUAL VOLUMES OF PROTEIN AND RESERVOIR SOLUTIONS. PROTEIN SOLUTION: 5-20 MG/ML PROTEIN IN 0.02 MOLAR TRIS (PH 8.0-8.5) , 0.1-0.2 MOLAR SODIUM CHLORIDE. 0.005 MOLAR 2-MERCAPTOETHANOL RESERVOIR SOLUTION: 8-20% (W/V) PEG 8000, 0.2 MOLAR TRIS (PH 7.5-8.0), 0.05-0.2 MOLAR ZINC ACETATE., VAPOR DIFFUSION, HANGING DROP, temperature 17K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
Common name: zinc

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1
DetectorType: ADSC / Detector: CCD / Date: Feb 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.3→30 Å / Num. obs: 24113 / % possible obs: 98 % / Observed criterion σ(I): -9 / Redundancy: 6 % / Rsym value: 0.026 / Net I/σ(I): 35
Reflection shellResolution: 1.3→1.35 Å / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 2.3 / % possible all: 96
Reflection
*PLUS
Num. measured all: 145226 / Rmerge(I) obs: 0.026
Reflection shell
*PLUS
% possible obs: 96 %

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Processing

Software
NameClassification
SHARPphasing
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD PROGRAM PACKAGE USED (IF ANY) : SHARP STARTING MODEL FOR MOLECULAR REPLACEMENT: NONE
Resolution: 1.3→6 Å / Num. parameters: 7764 / Num. restraintsaints: 13719 / Cross valid method: FREE-R / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.199 3918 10 %RANDOM
obs0.169 -87 %-
all-39179 --
Refine analyzeOccupancy sum hydrogen: 741 / Occupancy sum non hydrogen: 853
Refinement stepCycle: LAST / Resolution: 1.3→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms745 0 10 106 861
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.005
X-RAY DIFFRACTIONs_angle_d0.019
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.032
X-RAY DIFFRACTIONs_zero_chiral_vol0.021
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.03
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.068
X-RAY DIFFRACTIONs_approx_iso_adps0.095
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.169
Solvent computation
*PLUS
Displacement parameters
*PLUS

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