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- PDB-1kmc: Crystal Structure of the Caspase-7 / XIAP-BIR2 Complex -

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Basic information

Entry
Database: PDB / ID: 1kmc
TitleCrystal Structure of the Caspase-7 / XIAP-BIR2 Complex
Components
  • Caspase-7Caspase 7
  • X-LINKED INHIBITOR OF APOPTOSIS PROTEIN
KeywordsAPOPTOSIS/HYDROLASE / COMPLEX / IAP / CASPASE / APOPTOSIS / BIR / APOPTOSIS-HYDROLASE 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. / BIR repeat / Inhibitor of Apoptosis domain / BIR repeat profile. / Baculoviral inhibition of apoptosis protein repeat / Rossmann fold - #1460 / Peptidase family C14A, His active site ...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 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: 2.9 Å
AuthorsRiedl, S.J. / Salvesen, G.S. / Bode, W.
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of the Caspase-7 / XIAP-BIR2 Complex
Authors: Riedl, S.J. / Salvesen, G.S. / Bode, W.
History
DepositionDec 14, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 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 16, 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
B: Caspase-7
C: X-LINKED INHIBITOR OF APOPTOSIS PROTEIN
D: X-LINKED INHIBITOR OF APOPTOSIS PROTEIN


Theoretical massNumber of molelcules
Total (without water)96,3374
Polymers96,3374
Non-polymers00
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7170 Å2
ΔGint-29 kcal/mol
Surface area20240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.13, 88.13, 186.45
Angle α, β, γ (deg.)90, 90, 120
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Caspase-7 / Caspase 7


Mass: 34291.762 Da / Num. of mol.: 2 / Mutation: C285A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / 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 X-LINKED INHIBITOR OF APOPTOSIS PROTEIN / XIAP


Mass: 13876.493 Da / Num. of mol.: 2 / Fragment: XIAP-BIR2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: P98170
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.17 Å3/Da / Density % sol: 43.29 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.3
Details: PEG 3000, Phosphate/citrate, NaCl, pH 4.3, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 25, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 19264 / Num. obs: 18981 / % possible obs: 98.5 % / Redundancy: 4.6 % / Biso Wilson estimate: 71 Å2 / Rmerge(I) obs: 0.074
Reflection shellResolution: 2.9→3.02 Å / Redundancy: 4 % / Rmerge(I) obs: 0.376 / Num. unique all: 1980 / % possible all: 95.2

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Processing

Software
NameClassification
MOLREPphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1I4O

1i4o


Resolution: 2.9→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.275 914 -RANDOM
Rwork0.234 ---
all-19264 --
obs-18981 98.5 %-
Displacement parametersBiso mean: 53.03 Å2
Refinement stepCycle: LAST / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4022 0 0 25 4047
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.32
LS refinement shellResolution: 2.9→2.96 Å
RfactorNum. reflection
Rfree0.359 50
Rwork0.312 -
obs-1011

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