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- PDB-1nw9: STRUCTURE OF CASPASE-9 IN AN INHIBITORY COMPLEX WITH XIAP-BIR3 -

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Basic information

Entry
Database: PDB / ID: 1nw9
TitleSTRUCTURE OF CASPASE-9 IN AN INHIBITORY COMPLEX WITH XIAP-BIR3
Components
  • Baculoviral IAP repeat-containing protein 4
  • caspase 9, apoptosis-related cysteine protease
KeywordsAPOPTOSIS / caspase-9 / XIAP / caspase inhibition / caspase activation / dimerization
Function / homology
Function and homology information


caspase-9 / caspase complex / Formation of apoptosome / apoptosome / endopeptidase regulator activity / regulation of apoptosis involved in tissue homeostasis / inhibition of cysteine-type endopeptidase activity / positive regulation of protein linear polyubiquitination / activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / regulation of BMP signaling pathway ...caspase-9 / caspase complex / Formation of apoptosome / apoptosome / endopeptidase regulator activity / regulation of apoptosis involved in tissue homeostasis / inhibition of cysteine-type endopeptidase activity / positive regulation of protein linear polyubiquitination / activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / regulation of BMP signaling pathway / copper ion homeostasis / nucleotide-binding oligomerization domain containing 1 signaling pathway / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / leukocyte apoptotic process / glial cell apoptotic process / response to cobalt ion / cysteine-type endopeptidase activity involved in apoptotic signaling pathway / protein serine/threonine kinase binding / nucleotide-binding oligomerization domain containing 2 signaling pathway / Caspase activation via Dependence Receptors in the absence of ligand / SMAC, XIAP-regulated apoptotic response / 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 / TNFR1-induced proapoptotic signaling / fibroblast apoptotic process / AKT phosphorylates targets in the cytosol / regulation of innate immune response / epithelial cell apoptotic process / RIPK1-mediated regulated necrosis / platelet formation / cysteine-type endopeptidase inhibitor activity / protein K63-linked ubiquitination / Constitutive Signaling by AKT1 E17K in Cancer / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / protein maturation / enzyme activator activity / positive regulation of type I interferon production / negative regulation of tumor necrosis factor-mediated signaling pathway / signal transduction in response to DNA damage / Regulation of PTEN localization / cellular response to dexamethasone stimulus / intrinsic apoptotic signaling pathway / TNFR1-induced NF-kappa-B signaling pathway / positive regulation of protein ubiquitination / kidney development / response to ischemia / Deactivation of the beta-catenin transactivating complex / Regulation of TNFR1 signaling / positive regulation of JNK cascade / RING-type E3 ubiquitin transferase / NOD1/2 Signaling Pathway / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / Regulation of necroptotic cell death / protein processing / Wnt signaling pathway / SH3 domain binding / Regulation of PTEN stability and activity / ubiquitin-protein transferase activity / positive regulation of canonical Wnt signaling pathway / positive regulation of neuron apoptotic process / cellular response to UV / ubiquitin protein ligase activity / intrinsic apoptotic signaling pathway in response to DNA damage / response to estradiol / regulation of cell population proliferation / peptidase activity / regulation of inflammatory response / neuron apoptotic process / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / response to lipopolysaccharide / response to hypoxia / regulation of cell cycle / defense response to bacterium / positive regulation of apoptotic process / cysteine-type endopeptidase activity / apoptotic process / DNA damage response / negative regulation of apoptotic process / protein kinase binding / protein-containing complex / mitochondrion / nucleoplasm / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
CASP9, CARD domain / XIAP/BIRC8, UBA domain / : / BIRC2/3-like, UBA domain / Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A / Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A / Caspase recruitment domain / BIR repeat. / BIR repeat / Inhibitor of Apoptosis domain ...CASP9, CARD domain / XIAP/BIRC8, UBA domain / : / BIRC2/3-like, UBA domain / Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A / Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A / Caspase recruitment domain / BIR repeat. / BIR repeat / Inhibitor of Apoptosis domain / BIR repeat profile. / Baculoviral inhibition of apoptosis protein repeat / 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 / Zinc finger, C3HC4 type (RING finger) / Death-like domain superfamily / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Caspase-9 / E3 ubiquitin-protein ligase XIAP
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsShiozaki, E.N. / Chai, J. / Rigotti, D.J. / Riedl, S.J. / Li, P. / Srinivasula, S.M. / Alnemri, E.S. / Fairman, R. / Shi, Y.
CitationJournal: Mol.Cell / Year: 2003
Title: Mechanism of XIAP-Mediated Inhibition of Caspase-9
Authors: Shiozaki, E.N. / Chai, J. / Rigotti, D.J. / Riedl, S.J. / Li, P. / Srinivasula, S.M. / Alnemri, E.S. / Fairman, R. / Shi, Y.
History
DepositionFeb 5, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 3, 2018Group: Advisory / Data collection / Category: pdbx_unobs_or_zero_occ_atoms
Revision 1.4Feb 14, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Baculoviral IAP repeat-containing protein 4
B: caspase 9, apoptosis-related cysteine protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8673
Polymers41,8012
Non-polymers651
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-13 kcal/mol
Surface area14910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.4, 104.4, 170.3
Angle α, β, γ (deg.)90, 90, 120
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Baculoviral IAP repeat-containing protein 4 / Inhibitor of apoptosis protein 3 / X-linked inhibitor of apoptosis protein / X-linked IAP / IAP- ...Inhibitor of apoptosis protein 3 / X-linked inhibitor of apoptosis protein / X-linked IAP / IAP-like protein / HILP / the BIR3 domain of XIAP


Mass: 11327.616 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BIRC4 OR API3 OR IAP3 OR XIAP / Production host: Escherichia coli (E. coli) / References: UniProt: P98170
#2: Protein caspase 9, apoptosis-related cysteine protease / / catalytic domain of caspase-9


Mass: 30473.621 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P55211
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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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: 3.2 Å3/Da / Density % sol: 61.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Tris, potassium phosphate, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
1100 mMTris1reservoirpH8.0
21.0 Mpotassium monohydrogen phosphate1reservoir
30.2 M1reservoirNaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 1.1 Å
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Nov 28, 2002 / Details: mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.3→99 Å / Num. all: 23206 / Num. obs: 23136 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.3→2.38 Å / % possible all: 100
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 99 Å / Num. measured all: 415375 / Rmerge(I) obs: 0.071
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.525

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.235 1064 RANDOM
Rwork0.23 --
all0.23 22104 -
obs0.23 22104 -
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2589 0 1 0 2590
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d2.09
X-RAY DIFFRACTIONc_bond_d0.012
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rwork: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS

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