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- PDB-5wvc: Structure of the CARD-CARD disk -

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Basic information

Entry
Database: PDB / ID: 5wvc
TitleStructure of the CARD-CARD disk
Components
  • Apoptotic protease-activating factor 1
  • Caspase
KeywordsAPOPTOSIS / protein-protein interaction / signaling protein complex
Function / homology
Function and homology information


caspase-9 / response to G1 DNA damage checkpoint signaling / caspase complex / : / regulation of apoptotic DNA fragmentation / Formation of apoptosome / apoptosome / leukocyte apoptotic process / glial cell apoptotic process / response to cobalt ion ...caspase-9 / response to G1 DNA damage checkpoint signaling / caspase complex / : / regulation of apoptotic DNA fragmentation / Formation of apoptosome / apoptosome / leukocyte apoptotic process / glial cell apoptotic process / response to cobalt ion / : / Caspase activation via Dependence Receptors in the absence of ligand / 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 / : / fibroblast apoptotic process / AKT phosphorylates targets in the cytosol / epithelial cell apoptotic process / platelet formation / TP53 Regulates Transcription of Caspase Activators and Caspases / Constitutive Signaling by AKT1 E17K in Cancer / Transcriptional Regulation by E2F6 / cysteine-type endopeptidase activator activity involved in apoptotic process / protein maturation / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / signal transduction in response to DNA damage / forebrain development / cardiac muscle cell apoptotic process / cellular response to transforming growth factor beta stimulus / heat shock protein binding / enzyme activator activity / intrinsic apoptotic signaling pathway / cellular response to dexamethasone stimulus / response to nutrient / kidney development / response to ischemia / neural tube closure / positive regulation of apoptotic signaling pathway / ADP binding / NOD1/2 Signaling Pathway / protein processing / : / SH3 domain binding / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of neuron apoptotic process / cellular response to UV / response to estradiol / peptidase activity / nervous system development / secretory granule lumen / regulation of apoptotic process / neuron apoptotic process / ficolin-1-rich granule lumen / response to lipopolysaccharide / cell differentiation / response to hypoxia / positive regulation of apoptotic process / cysteine-type endopeptidase activity / nucleotide binding / DNA damage response / Neutrophil degranulation / protein kinase binding / apoptotic process / protein-containing complex / mitochondrion / proteolysis / extracellular exosome / extracellular region / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
CASP9, CARD domain / 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 ...CASP9, CARD domain / 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 / Caspase recruitment domain / NB-ARC / NB-ARC domain / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Peptidase family C14A, His active site / Caspase family histidine active site. / Peptidase C14, caspase non-catalytic subunit p10 / Peptidase family C14A, cysteine active site / Caspase family cysteine active site. / Caspase family p10 domain profile. / Peptidase C14A, caspase catalytic domain / Caspase, interleukin-1 beta converting enzyme (ICE) homologues / Peptidase C14, p20 domain / Caspase family p20 domain profile. / : / Caspase domain / Caspase-like domain superfamily / 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
IODIDE ION / cDNA FLJ75893, highly similar to Homo sapiens caspase 9, apoptosis-related cysteine peptidase (CASP9), transcript variant alpha, mRNA / Apoptotic protease-activating factor 1 / Caspase-9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.993 Å
AuthorsLin, S.C. / Lo, Y.C. / Su, T.W.
Funding support Taiwan, 7items
OrganizationGrant numberCountry
Academia SinciaAS-102-TP-B14-1 Taiwan
Academia SinicaAS-102-TP-B14-2 Taiwan
Academia SinicaAS-102-TP-B14 Taiwan
MoST101-2320-B-001-034-MY3 Taiwan
MoST104-2320-B-001-020-MY3 Taiwan
MoST101-2311-B-006-008-MY3 Taiwan
MoST104-2320-B-006-033-MY3 Taiwan
CitationJournal: Structure / Year: 2017
Title: Structural Insights into DD-Fold Assembly and Caspase-9 Activation by the Apaf-1 Apoptosome.
Authors: Su, T.W. / Yang, C.Y. / Kao, W.P. / Kuo, B.J. / Lin, S.M. / Lin, J.Y. / Lo, Y.C. / Lin, S.C.
History
DepositionDec 24, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Apoptotic protease-activating factor 1
D: Caspase
A: Apoptotic protease-activating factor 1
B: Caspase
E: Apoptotic protease-activating factor 1
F: Caspase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,40317
Polymers85,0076
Non-polymers1,39611
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8500 Å2
ΔGint1 kcal/mol
Surface area28030 Å2
Unit cell
Length a, b, c (Å)190.110, 190.110, 68.828
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Apoptotic protease-activating factor 1 / APAF-1


Mass: 10925.555 Da / Num. of mol.: 3 / Fragment: UNP RESIDUES 1-95
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APAF1, KIAA0413 / Production host: Escherichia coli (E. coli) / References: UniProt: O14727
#2: Protein Caspase


Mass: 17409.982 Da / Num. of mol.: 3 / Fragment: UNP RESIDUES 1-128
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: A8K7U6, UniProt: P55211*PLUS
#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: I
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: 4.24 Å3/Da / Density % sol: 70.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.2 M NH4I, 20% PEG 3350

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.993→24.852 Å / Num. obs: 28208 / % possible obs: 97.7 % / Redundancy: 2.6 % / Net I/σ(I): 6.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 2.993→24.852 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.75
RfactorNum. reflection% reflection
Rfree0.2281 2004 7.1 %
Rwork0.1969 --
obs0.1992 28208 97.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.993→24.852 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4794 0 11 0 4805
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034851
X-RAY DIFFRACTIONf_angle_d0.6726505
X-RAY DIFFRACTIONf_dihedral_angle_d13.571918
X-RAY DIFFRACTIONf_chiral_restr0.025731
X-RAY DIFFRACTIONf_plane_restr0.003848
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9933-3.0680.37871360.31951777X-RAY DIFFRACTION93
3.068-3.15080.3551450.30061859X-RAY DIFFRACTION98
3.1508-3.24330.30011420.29311865X-RAY DIFFRACTION98
3.2433-3.34770.31351400.26151881X-RAY DIFFRACTION99
3.3477-3.46710.26491460.23841886X-RAY DIFFRACTION99
3.4671-3.60550.25241460.21991885X-RAY DIFFRACTION99
3.6055-3.76910.28261370.21311852X-RAY DIFFRACTION99
3.7691-3.9670.24391410.2031909X-RAY DIFFRACTION98
3.967-4.21450.20951430.19431857X-RAY DIFFRACTION98
4.2145-4.5380.20951440.16771858X-RAY DIFFRACTION97
4.538-4.99140.20141460.17561874X-RAY DIFFRACTION97
4.9914-5.7060.21531410.1891891X-RAY DIFFRACTION98
5.706-7.16040.25271510.20011911X-RAY DIFFRACTION99
7.1604-24.8530.13721460.13171899X-RAY DIFFRACTION95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.47710.35120.1177.11091.05648.23740.03120.20420.0060.01540.2058-0.1138-0.3303-0.3112-0.26730.4512-0.15470.04640.5783-0.03010.306279.1266-52.4116-11.0212
25.14021.4478-1.2786.3990.57427.46380.0679-0.0308-0.06720.10540.1467-0.32530.4060.2908-0.18510.28070.056-0.02480.65290.00760.372892.8435-73.9771-14.86
34.1284-0.14662.58077.9362.79463.6267-0.08840.4123-0.14950.0859-0.02620.59020.611-0.29980.08860.5465-0.21920.01530.91560.03440.4876.2482-81.791-33.3137
43.431.074-0.38796.52932.05316.36390.0793-0.47330.13990.0265-0.29970.3101-0.14080.25160.20490.4894-0.268-0.01320.7562-0.02340.379465.2068-65.01547.1142
52.6041-1.9294-4.14446.3434-0.45248.11390.1280.3107-0.0681-0.3833-0.190.3233-0.7979-0.62220.12450.5103-0.2093-0.14660.8668-0.07230.615444.5228-57.604-5.4821
68.07472.02950.7415.57221.37015.48460.0475-0.0317-0.0973-0.21870.0544-0.1610.04260.4162-0.10740.4945-0.2902-0.05760.76590.01490.54545.5426-78.8858-20.5605
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and ((resseq 1:95))
2X-RAY DIFFRACTION2chain 'B' and ((resseq 199:300))
3X-RAY DIFFRACTION3chain 'A' and ((resseq 1:95))
4X-RAY DIFFRACTION4chain 'D' and ((resseq 199:301))
5X-RAY DIFFRACTION5chain 'E' and ((resseq 1:94))
6X-RAY DIFFRACTION6chain 'F' and ((resseq 199:301))

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