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- PDB-1i4o: CRYSTAL STRUCTURE OF THE XIAP/CASPASE-7 COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1i4o
TitleCRYSTAL STRUCTURE OF THE XIAP/CASPASE-7 COMPLEX
Components
  • BACULOVIRAL IAP REPEAT-CONTAINING PROTEIN 4
  • CASPASE-7
KeywordsAPOPTOSIS/HYDROLASE / protease-inhibitor / APOPTOSIS-HYDROLASE COMPLEX
Function / homology
Function and homology information


caspase-7 / lymphocyte apoptotic process / regulation of apoptosis involved in tissue homeostasis / positive regulation of plasma membrane repair / positive regulation of protein linear polyubiquitination / copper ion homeostasis / regulation of BMP signaling pathway / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / nucleotide-binding oligomerization domain containing 1 signaling pathway / cellular response to staurosporine ...caspase-7 / lymphocyte apoptotic process / regulation of apoptosis involved in tissue homeostasis / positive regulation of plasma membrane repair / positive regulation of protein linear polyubiquitination / copper ion homeostasis / regulation of BMP signaling pathway / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / nucleotide-binding oligomerization domain containing 1 signaling pathway / cellular response to staurosporine / nucleotide-binding oligomerization domain containing 2 signaling pathway / SMAC, XIAP-regulated apoptotic response / 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 / fibroblast apoptotic process / TNFR1-induced proapoptotic signaling / RIPK1-mediated regulated necrosis / execution phase of apoptosis / regulation of innate immune response / Apoptotic cleavage of cellular proteins / protein K63-linked ubiquitination / positive regulation of type I interferon production / cysteine-type endopeptidase inhibitor activity / negative regulation of tumor necrosis factor-mediated signaling pathway / Caspase-mediated cleavage of cytoskeletal proteins / response to UV / striated muscle cell differentiation / cysteine-type peptidase activity / protein serine/threonine kinase binding / Regulation of PTEN localization / protein maturation / positive regulation of protein ubiquitination / TNFR1-induced NF-kappa-B signaling pathway / positive regulation of JNK cascade / Deactivation of the beta-catenin transactivating complex / Regulation of TNFR1 signaling / protein catabolic process / RING-type E3 ubiquitin transferase / protein processing / Regulation of necroptotic cell death / Wnt signaling pathway / Regulation of PTEN stability and activity / fibrillar center / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / positive regulation of canonical Wnt signaling pathway / peptidase activity / positive regulation of neuron apoptotic process / heart development / cellular response to lipopolysaccharide / regulation of inflammatory response / neuron apoptotic process / response to lipopolysaccharide / regulation of apoptotic process / aspartic-type endopeptidase activity / positive regulation of canonical NF-kappaB signal transduction / regulation of cell cycle / defense response to bacterium / cysteine-type endopeptidase activity / apoptotic process / DNA damage response / negative regulation of apoptotic process / proteolysis / extracellular space / RNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
XIAP/BIRC8, UBA domain / : / BIRC2/3-like, UBA domain / : / BIR repeat. / BIR repeat / Inhibitor of Apoptosis domain / BIR repeat profile. / Baculoviral inhibition of apoptosis protein repeat / Rossmann fold - #1460 ...XIAP/BIRC8, UBA domain / : / BIRC2/3-like, UBA domain / : / BIR repeat. / BIR repeat / Inhibitor of Apoptosis domain / BIR repeat profile. / Baculoviral inhibition of apoptosis protein repeat / Rossmann fold - #1460 / 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Caspase-7 / E3 ubiquitin-protein ligase XIAP
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsHuang, Y. / Park, Y.C. / Rich, R.L. / Segal, D. / Myszka, D.G. / Wu, H.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2001
Title: Structural basis of caspase inhibition by XIAP: differential roles of the linker versus the BIR domain.
Authors: Huang, Y. / Park, Y.C. / Rich, R.L. / Segal, D. / Myszka, D.G. / Wu, H.
History
DepositionFeb 22, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Sep 25, 2013Group: Derived calculations
Revision 1.5Oct 4, 2017Group: Refinement description / Category: software
Revision 1.6Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
A: CASPASE-7
B: CASPASE-7
C: BACULOVIRAL IAP REPEAT-CONTAINING PROTEIN 4
D: BACULOVIRAL IAP REPEAT-CONTAINING PROTEIN 4


Theoretical massNumber of molelcules
Total (without water)96,2734
Polymers96,2734
Non-polymers00
Water3,585199
1
A: CASPASE-7
C: BACULOVIRAL IAP REPEAT-CONTAINING PROTEIN 4


Theoretical massNumber of molelcules
Total (without water)48,1362
Polymers48,1362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-9 kcal/mol
Surface area11920 Å2
MethodPISA
2
B: CASPASE-7
D: BACULOVIRAL IAP REPEAT-CONTAINING PROTEIN 4


Theoretical massNumber of molelcules
Total (without water)48,1362
Polymers48,1362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-10 kcal/mol
Surface area11330 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6770 Å2
ΔGint-39 kcal/mol
Surface area19200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.5, 88.5, 185.4
Angle α, β, γ (deg.)90.0, 90.0, 120.0
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-360-

HOH

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Components

#1: Protein CASPASE-7 / APOPTOTIC PROTEASE MCH-3


Mass: 31885.404 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
References: UniProt: P55210, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Protein BACULOVIRAL IAP REPEAT-CONTAINING PROTEIN 4 / X-LINKED IAP


Mass: 16251.001 Da / Num. of mol.: 2 / Fragment: RESIDUES 120-260
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P98170
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 2.18 Å3/Da / Density % sol: 43.48 %
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17 mg/mlprotein1drop
220 mg/mlTris-HCl1drop
3300 mM1dropNaCl
45 mMdithiothreitol1drop
520-30 %butanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.948
DetectorType: ADSC / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.948 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / % possible obs: 99.3 % / Rmerge(I) obs: 0.052
Reflection shellHighest resolution: 2.4 Å / Rmerge(I) obs: 0.339 / % possible all: 99.5
Reflection shell
*PLUS
% possible obs: 99.5 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1cp3

1cp3


Resolution: 2.4→20 Å / σ(F): 1.5
RfactorNum. reflection% reflection
Rfree0.26 -6 %
Rwork0.224 --
obs-28151 -
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3925 0 0 199 4124
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.009
X-RAY DIFFRACTIONo_angle_deg1.571
Refinement
*PLUS
Highest resolution: 2.4 Å / σ(F): 1.5 / % reflection Rfree: 6 % / Rfactor obs: 0.224 / Rfactor Rfree: 0.26
Solvent computation
*PLUS
Displacement parameters
*PLUS

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