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- PDB-2ar9: Crystal structure of a dimeric caspase-9 -

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Basic information

Entry
Database: PDB / ID: 2ar9
TitleCrystal structure of a dimeric caspase-9
ComponentsCaspase-9
KeywordsHYDROLASE / caspase / caspase activation / initiator caspase / cysteine protease / engineered caspase-9
Function / homology
Function and homology information


caspase-9 / caspase complex / Formation of apoptosome / apoptosome / activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / leukocyte apoptotic process / glial cell apoptotic process / response to cobalt ion / cysteine-type endopeptidase activity involved in apoptotic signaling pathway / Caspase activation via Dependence Receptors in the absence of ligand ...caspase-9 / caspase complex / Formation of apoptosome / apoptosome / activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / leukocyte apoptotic process / glial cell apoptotic process / response to cobalt ion / cysteine-type endopeptidase activity involved in apoptotic signaling pathway / Caspase activation via Dependence Receptors in the absence of ligand / Regulation of the apoptosome activity / Activation of caspases through apoptosome-mediated cleavage / cysteine-type endopeptidase activity involved in apoptotic process / 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 / Constitutive Signaling by AKT1 E17K in Cancer / protein maturation / enzyme activator activity / signal transduction in response to DNA damage / cellular response to dexamethasone stimulus / intrinsic apoptotic signaling pathway / kidney development / response to ischemia / NOD1/2 Signaling Pathway / protein processing / SH3 domain binding / positive regulation of neuron apoptotic process / cellular response to UV / intrinsic apoptotic signaling pathway in response to DNA damage / response to estradiol / peptidase activity / neuron apoptotic process / response to lipopolysaccharide / response to hypoxia / positive regulation of apoptotic process / cysteine-type endopeptidase activity / apoptotic process / DNA damage response / protein kinase binding / protein-containing complex / mitochondrion / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
CASP9, CARD domain / Caspase recruitment domain / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Rossmann fold - #1460 / Peptidase family C14A, His active site / Caspase family histidine active site. / Peptidase C14, caspase non-catalytic subunit p10 / Peptidase family C14A, cysteine active site ...CASP9, CARD domain / Caspase recruitment domain / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Rossmann fold - #1460 / 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
D-MALATE / Caspase-9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsChao, Y. / Shiozaki, E.N. / Srinivassula, S.M. / Rigotti, D.J. / Fairman, R. / Shi, Y.
CitationJournal: PLOS BIOL. / Year: 2005
Title: Engineering a Dimeric Caspase-9: A Re-Evaluation of the Induced Proximity Model for Caspase Activation
Authors: Chao, Y. / Shiozaki, E.N. / Srinivassula, S.M. / Rigotti, D.J. / Fairman, R. / Shi, Y.
History
DepositionAug 19, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Feb 15, 2012Group: Non-polymer description
Revision 1.5Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Caspase-9
B: Caspase-9
C: Caspase-9
D: Caspase-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,3495
Polymers122,2154
Non-polymers1341
Water2,396133
1
A: Caspase-9
B: Caspase-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2423
Polymers61,1082
Non-polymers1341
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-23 kcal/mol
Surface area18910 Å2
MethodPISA
2
C: Caspase-9
D: Caspase-9


Theoretical massNumber of molelcules
Total (without water)61,1082
Polymers61,1082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-21 kcal/mol
Surface area19210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.698, 78.055, 125.963
Angle α, β, γ (deg.)90.00, 112.50, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-674-

HOH

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Components

#1: Protein
Caspase-9 /


Mass: 30553.812 Da / Num. of mol.: 4 / Fragment: residues 140-416 / Mutation: C287S, G402C, C403I, F404V, N405S, F406M / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P55211, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID / Malic acid


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 2.69 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG5000 monomethylether, MES, tacsimate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 1, 2004
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→99 Å / Num. all: 32242 / Num. obs: 31920 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.08 / Rsym value: 0.08
Reflection shellResolution: 2.8→2.9 Å / % possible all: 98.4

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NW9

1nw9


Resolution: 2.8→11 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.288 3141 random
Rwork0.237 --
all0.24 31618 -
obs0.24 31405 -
Refinement stepCycle: LAST / Resolution: 2.8→11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7144 0 9 133 7286
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.405
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2mal.par
X-RAY DIFFRACTION3water.param

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