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- PDB-1i51: CRYSTAL STRUCTURE OF CASPASE-7 COMPLEXED WITH XIAP -

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Basic information

Entry
Database: PDB / ID: 1i51
TitleCRYSTAL STRUCTURE OF CASPASE-7 COMPLEXED WITH XIAP
Components
  • CASPASE-7 SUBUNIT P11Caspase 7
  • CASPASE-7 SUBUNIT P20Caspase 7
  • X-LINKED INHIBITOR OF APOPTOSIS PROTEIN
KeywordsHYDROLASE/HYDROLASE INHIBITOR / protease / caspase / IAP / apoptosis / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


caspase-7 / lymphocyte apoptotic process / endopeptidase regulator activity / regulation of apoptosis involved in tissue homeostasis / inhibition of cysteine-type endopeptidase activity / positive regulation of plasma membrane repair / positive regulation of protein linear polyubiquitination / regulation of BMP signaling pathway / copper ion homeostasis / nucleotide-binding oligomerization domain containing 1 signaling pathway ...caspase-7 / lymphocyte apoptotic process / endopeptidase regulator activity / regulation of apoptosis involved in tissue homeostasis / inhibition of cysteine-type endopeptidase activity / positive regulation of plasma membrane repair / positive regulation of protein linear polyubiquitination / 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 / protein serine/threonine kinase binding / cellular response to staurosporine / nucleotide-binding oligomerization domain containing 2 signaling pathway / cysteine-type endopeptidase activity involved in execution phase of apoptosis / 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 / execution phase of apoptosis / regulation of innate immune response / RIPK1-mediated regulated necrosis / cysteine-type endopeptidase inhibitor activity / Apoptotic cleavage of cellular proteins / protein K63-linked ubiquitination / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / protein maturation / positive regulation of type I interferon production / negative regulation of tumor necrosis factor-mediated signaling pathway / Caspase-mediated cleavage of cytoskeletal proteins / cysteine-type peptidase activity / response to UV / striated muscle cell differentiation / Regulation of PTEN localization / TNFR1-induced NF-kappa-B signaling pathway / positive regulation of protein ubiquitination / Deactivation of the beta-catenin transactivating complex / Regulation of TNFR1 signaling / positive regulation of JNK cascade / protein catabolic process / RING-type E3 ubiquitin transferase / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / Regulation of necroptotic cell death / protein processing / Wnt signaling pathway / Regulation of PTEN stability and activity / ubiquitin-protein transferase activity / positive regulation of canonical Wnt signaling pathway / ubiquitin protein ligase activity / regulation of cell population proliferation / heart development / peptidase activity / regulation of inflammatory response / neuron apoptotic process / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / cellular response to lipopolysaccharide / aspartic-type endopeptidase activity / 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 / nucleoplasm / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
XIAP/BIRC8, UBA domain / : / BIRC2/3-like, UBA domain / BIR repeat. / Caspase-like / 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. / Caspase-like / BIR repeat / Inhibitor of Apoptosis domain / BIR repeat profile. / Baculoviral inhibition of apoptosis protein repeat / 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 / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 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: 2.45 Å
AuthorsChai, J. / Shi, Y.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2001
Title: Structural basis of caspase-7 inhibition by XIAP.
Authors: Chai, J. / Shiozaki, E. / Srinivasula, S.M. / Wu, Q. / Datta, P. / Alnemri, E.S. / Shi, Y. / Dataa, P.
History
DepositionFeb 23, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 9, 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-7 SUBUNIT P20
B: CASPASE-7 SUBUNIT P11
C: CASPASE-7 SUBUNIT P20
D: CASPASE-7 SUBUNIT P11
E: X-LINKED INHIBITOR OF APOPTOSIS PROTEIN
F: X-LINKED INHIBITOR OF APOPTOSIS PROTEIN


Theoretical massNumber of molelcules
Total (without water)84,9246
Polymers84,9246
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16380 Å2
ΔGint-97 kcal/mol
Surface area18920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.6, 89.6, 185.5
Angle α, β, γ (deg.)90, 90, 120
Int Tables number154
Space group name H-MP3221
DetailsEach asymmetric unit contains an active biological unit.

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Components

#1: Protein CASPASE-7 SUBUNIT P20 / Caspase 7


Mass: 16635.064 Da / Num. of mol.: 2 / Mutation: D169A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP7 / Plasmid: PET21B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P55210, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Protein CASPASE-7 SUBUNIT P11 / Caspase 7


Mass: 12152.646 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP7 / Plasmid: PET21B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P55210, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#3: Protein X-LINKED INHIBITOR OF APOPTOSIS PROTEIN / XIAP


Mass: 13674.329 Da / Num. of mol.: 2 / Fragment: XIAP-BIR2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: XIAP / Plasmid: PGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P98170

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: ammonium sulfate, PEG4000, Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Details: used macroseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15 mg/mlprotein1drop
225 mMTris1reservoirpH8.0
30.5 Mammonium sulfate1reservoir
415 %PEG40001reservoir
510 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.93 Å
DetectorDetector: CCD / Date: Jan 27, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2.45→99 Å / Num. all: 32034 / Num. obs: 30767 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 60 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 16
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 3 % / Rmerge(I) obs: 0.458 / % possible all: 98.1
Reflection
*PLUS
% possible obs: 96.1 % / Num. measured all: 114661
Reflection shell
*PLUS
% possible obs: 98 %

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1CP3

1cp3


Resolution: 2.45→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.272 1364 random
Rwork0.233 --
all0.235 32034 -
obs0.235 30767 -
Refinement stepCycle: LAST / Resolution: 2.45→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3974 0 0 0 3974
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.328
LS refinement shellResolution: 2.45→2.48 Å / Rfactor Rfree error: 0.012
RfactorNum. reflection% reflection
Rfree0.43 20 -
Rwork0.43 --
obs-515 98 %
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / Num. reflection obs: 27625 / σ(F): 1 / % reflection Rfree: 5 % / Rfactor obs: 0.233 / Rfactor Rwork: 0.236
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.43 / Rfactor Rwork: 0.43

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