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- PDB-3d9t: CIAP1-BIR3 in complex with N-terminal peptide from Caspase-9 (ATPFQE) -

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Basic information

Entry
Database: PDB / ID: 3d9t
TitleCIAP1-BIR3 in complex with N-terminal peptide from Caspase-9 (ATPFQE)
Components
  • Baculoviral IAP repeat-containing protein 2
  • Caspase-9
KeywordsAPOPTOSIS / zinc finger / Cytoplasm / Metal-binding / Polymorphism / Zinc / Zinc-finger / Alternative splicing / Hydrolase / Protease / Thiol protease / Zymogen
Function / homology
Function and homology information


caspase-9 / caspase complex / negative regulation of ripoptosome assembly involved in necroptotic process / FBXO family protein binding / Formation of apoptosome / apoptosome / regulation of RIG-I signaling pathway / positive regulation of protein K48-linked ubiquitination / regulation of non-canonical NF-kappaB signal transduction / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway ...caspase-9 / caspase complex / negative regulation of ripoptosome assembly involved in necroptotic process / FBXO family protein binding / Formation of apoptosome / apoptosome / regulation of RIG-I signaling pathway / positive regulation of protein K48-linked ubiquitination / regulation of non-canonical NF-kappaB signal transduction / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / regulation of necroptotic process / positive regulation of protein K63-linked ubiquitination / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / leukocyte apoptotic process / CD40 receptor complex / glial cell apoptotic process / response to cobalt ion / Caspase activation via Dependence Receptors in the absence of ligand / negative regulation of necroptotic process / XY body / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / 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 / non-canonical NF-kappaB signal transduction / fibroblast apoptotic process / AKT phosphorylates targets in the cytosol / epithelial cell apoptotic process / positive regulation of protein monoubiquitination / TNFR1-induced proapoptotic signaling / platelet formation / RIPK1-mediated regulated necrosis / regulation of reactive oxygen species metabolic process / response to anesthetic / regulation of toll-like receptor signaling pathway / regulation of innate immune response / Apoptotic cleavage of cellular proteins / Constitutive Signaling by AKT1 E17K in Cancer / necroptotic process / regulation of cell differentiation / signal transduction in response to DNA damage / response to cAMP / positive regulation of execution phase of apoptosis / canonical NF-kappaB signal transduction / cellular response to dexamethasone stimulus / intrinsic apoptotic signaling pathway / TICAM1, RIP1-mediated IKK complex recruitment / protein maturation / placenta development / response to ischemia / IKK complex recruitment mediated by RIP1 / ubiquitin binding / positive regulation of protein ubiquitination / tumor necrosis factor-mediated signaling pathway / TNFR1-induced NF-kappa-B signaling pathway / TNFR2 non-canonical NF-kB pathway / kidney development / enzyme activator activity / Regulation of TNFR1 signaling / NOD1/2 Signaling Pathway / RING-type E3 ubiquitin transferase / protein processing / SH3 domain binding / Regulation of necroptotic cell death / cytoplasmic side of plasma membrane / protein polyubiquitination / intrinsic apoptotic signaling pathway in response to DNA damage / ubiquitin-protein transferase activity / cellular response to UV / ubiquitin protein ligase activity / response to estradiol / peptidase activity / positive regulation of neuron apoptotic process / regulation of cell population proliferation / protein-folding chaperone binding / transferase activity / regulation of inflammatory response / neuron apoptotic process / response to ethanol / regulation of apoptotic process / response to lipopolysaccharide / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription coactivator activity / response to hypoxia / cell surface receptor signaling pathway / positive regulation of canonical NF-kappaB signal transduction / regulation of cell cycle / Ub-specific processing proteases / positive regulation of apoptotic process / cysteine-type endopeptidase activity / apoptotic process / DNA damage response / protein kinase binding / negative regulation of apoptotic process / protein-containing complex binding / protein-containing complex / mitochondrion / zinc ion binding / identical protein binding
Similarity search - Function
CASP9, CARD domain / BIRC2/BIRC3, 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 ...CASP9, CARD domain / BIRC2/BIRC3, 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 / Peptidase C14 family / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Caspase-9 / Baculoviral IAP repeat-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsKulathila, R. / Price, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2009
Title: The structure of the BIR3 domain of cIAP1 in complex with the N-terminal peptides of SMAC and caspase-9.
Authors: Kulathila, R. / Vash, B. / Sage, D. / Cornell-Kennon, S. / Wright, K. / Koehn, J. / Stams, T. / Clark, K. / Price, A.
History
DepositionMay 27, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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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 2
B: Baculoviral IAP repeat-containing protein 2
C: Caspase-9
D: Caspase-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8636
Polymers23,7334
Non-polymers1312
Water4,828268
1
A: Baculoviral IAP repeat-containing protein 2
C: Caspase-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9323
Polymers11,8662
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint-4 kcal/mol
Surface area5650 Å2
MethodPISA
2
B: Baculoviral IAP repeat-containing protein 2
D: Caspase-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9323
Polymers11,8662
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area760 Å2
ΔGint-4 kcal/mol
Surface area5990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.268, 68.427, 122.358
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is the heterodimeric complex of CIAP1-BIR3 with N-terminal peptide from Caspase-9 (ATPFQE).

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Components

#1: Protein Baculoviral IAP repeat-containing protein 2 / Inhibitor of apoptosis protein 2 / HIAP2 / HIAP-2 / C-IAP1 / TNFR2-TRAF-signaling complex protein 2 ...Inhibitor of apoptosis protein 2 / HIAP2 / HIAP-2 / C-IAP1 / TNFR2-TRAF-signaling complex protein 2 / IAP homolog B / RING finger protein 48


Mass: 11174.601 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BIRC2, API1, IAP2, MIHB, RNF48 / Plasmid: pNAT40 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: Q13490
#2: Protein/peptide Caspase-9 / CASP-9 / ICE-like apoptotic protease 6 / ICE-LAP6 / Apoptotic protease Mch-6 / Apoptotic protease- ...CASP-9 / ICE-like apoptotic protease 6 / ICE-LAP6 / Apoptotic protease Mch-6 / Apoptotic protease-activating factor 3 / APAF-3 / Caspase-9 subunit p35 / Caspase-9 subunit p10


Mass: 691.728 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: peptide synthesized based on N-terminal fragment of Caspase-9 (ATPFQE).
References: UniProt: P55211, caspase-9
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 2.67 Å3/Da / Density % sol: 53.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 3.1M NA FORMATE,10% GLYCEROL,1.5MM PEPTIDE, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→61.2 Å / Num. all: 41742 / Num. obs: 40966 / % possible obs: 98 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Biso Wilson estimate: 17.2 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 35.4
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.257 / Mean I/σ(I) obs: 5.5 / Num. unique all: 4030 / % possible all: 98.6

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Processing

Software
NameClassification
CNXrefinement
StructureStudiodata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1NW9

1nw9


Resolution: 1.5→35.04 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 407066.53 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.205 4141 10.1 %RANDOM
Rwork0.183 ---
obs0.186 40966 98 %-
all-41742 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.8947 Å2 / ksol: 0.403914 e/Å3
Displacement parametersBiso mean: 19.6 Å2
Baniso -1Baniso -2Baniso -3
1--1.92 Å20 Å20 Å2
2---1.26 Å20 Å2
3---3.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.17 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 1.5→35.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1639 0 2 268 1909
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d20.1
X-RAY DIFFRACTIONc_improper_angle_d1.09
X-RAY DIFFRACTIONc_mcbond_it1.151.5
X-RAY DIFFRACTIONc_mcangle_it1.692
X-RAY DIFFRACTIONc_scbond_it2.162
X-RAY DIFFRACTIONc_scangle_it3.082.5
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.244 666 10.3 %
Rwork0.204 5773 -
obs-6439 93.8 %

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