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- PDB-1jxq: Structure of cleaved, CARD domain deleted Caspase-9 -

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Basic information

Entry
Database: PDB / ID: 1jxq
TitleStructure of cleaved, CARD domain deleted Caspase-9
Components
  • Caspase-9
  • benzoxycarbonyl-Val-Ala-Asp-fluoromethyl ketone Inhibitor
KeywordsHYDROLASE/HYDROLASE INHIBITOR / PROTEASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


caspase-9 / caspase complex / Formation of apoptosome / apoptosome / activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / leukocyte apoptotic process / glial cell apoptotic process / response to cobalt ion / cysteine-type endopeptidase activity involved in apoptotic signaling pathway / Caspase activation via Dependence Receptors in the absence of ligand ...caspase-9 / caspase complex / Formation of apoptosome / apoptosome / activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / leukocyte apoptotic process / glial cell apoptotic process / response to cobalt ion / cysteine-type endopeptidase activity involved in apoptotic signaling pathway / Caspase activation via Dependence Receptors in the absence of ligand / 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 / epithelial cell apoptotic process / fibroblast apoptotic process / AKT phosphorylates targets in the cytosol / platelet formation / Constitutive Signaling by AKT1 E17K in Cancer / protein maturation / enzyme activator activity / signal transduction in response to DNA damage / cellular response to dexamethasone stimulus / intrinsic apoptotic signaling pathway / kidney development / response to ischemia / NOD1/2 Signaling Pathway / protein processing / SH3 domain binding / cellular response to UV / positive regulation of neuron apoptotic process / intrinsic apoptotic signaling pathway in response to DNA damage / response to estradiol / peptidase activity / neuron apoptotic process / response to lipopolysaccharide / response to hypoxia / positive regulation of apoptotic process / cysteine-type endopeptidase activity / apoptotic process / DNA damage response / protein kinase binding / protein-containing complex / mitochondrion / nucleus / identical protein binding / cytosol / cytoplasm
Similarity search - Function
CASP9, CARD domain / Caspase recruitment domain / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Rossmann fold - #1460 / Peptidase C14 family / Peptidase family C14A, His active site / Caspase family histidine active site. / Peptidase C14, caspase non-catalytic subunit p10 ...CASP9, CARD domain / Caspase recruitment domain / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / 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 / Death-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsRenatus, M. / Stennicke, H.R. / Scott, F.L. / Liddington, R.C. / Salvesen, G.S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Dimer formation drives the activation of the cell death protease caspase 9.
Authors: Renatus, M. / Stennicke, H.R. / Scott, F.L. / Liddington, R.C. / Salvesen, G.S.
History
DepositionSep 8, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Aug 16, 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Caspase-9
B: Caspase-9
C: Caspase-9
D: Caspase-9
E: benzoxycarbonyl-Val-Ala-Asp-fluoromethyl ketone Inhibitor
F: benzoxycarbonyl-Val-Ala-Asp-fluoromethyl ketone Inhibitor


Theoretical massNumber of molelcules
Total (without water)126,7956
Polymers126,7956
Non-polymers00
Water4,756264
1
A: Caspase-9
B: Caspase-9
E: benzoxycarbonyl-Val-Ala-Asp-fluoromethyl ketone Inhibitor


Theoretical massNumber of molelcules
Total (without water)63,3973
Polymers63,3973
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5190 Å2
ΔGint-21 kcal/mol
Surface area18630 Å2
MethodPISA
2
C: Caspase-9
D: Caspase-9
F: benzoxycarbonyl-Val-Ala-Asp-fluoromethyl ketone Inhibitor


Theoretical massNumber of molelcules
Total (without water)63,3973
Polymers63,3973
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint-20 kcal/mol
Surface area18820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.3, 81.800, 125.400
Angle α, β, γ (deg.)90.00, 111.70, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Caspase-9 / / ICE-LAP6


Mass: 31433.684 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pet23b / Production host: Escherichia coli (E. coli)
References: GenBank: 1336027, UniProt: P55211*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Protein/peptide benzoxycarbonyl-Val-Ala-Asp-fluoromethyl ketone Inhibitor


Mass: 529.943 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: This peptide was chemically synthesized.
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 264 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTO FACILIATE COMPARISON WITH OTHER CASPASES THE CASPASE-1 (INTERLEUKIN 1-BETA CONVERTING ENZYME ...TO FACILIATE COMPARISON WITH OTHER CASPASES THE CASPASE-1 (INTERLEUKIN 1-BETA CONVERTING ENZYME (ICE, PDB ENTRY 1ICE)) NUMBERING SYSTEM HAS BEEN USED. IT IS BASED ON A STRUCTURAL SUPERIMPOSITION OF CASPASE-9 WITH CASPASE-1. RESIDUES IN CASPASE-9 ARE ASSIGNED THE NUMBERS OF THE STRUCTURAL HOMOLOGOUS RESIDUES IN THE ALIGNED THREE-DIMENSIONAL STRUCTURE OF CASPASE-1. CASPASE-9 SEQUENCE NUMBERS ARE OMITTED WHEN NO CASPASE-1-RELATED RESIDUE IS PRESENT IN CASPASE-9, AND CASPASE-9-SPECIFIC INSERTIONS ARE INDICATED BY THE ADDITION OF LETTERS TO THE CASPASE-1 SEQUENCE NUMBERS. THIS NUMBERING SYSTEM HAS ALREADY BEEN USED IN THE PDB ENTRY 1QDU (CASPASE-8) AND 1PAU (CASPASE-3).THE MISSING RESIDUES OF REMARK 465 ARE NUMBERED BASED ON THE SEQRES NUMBER (NOT COORDINATE NUMBER), WITH THE FIRST RESIDUE OF THE SEQRES LABELED AS NUMBER 1 AND SEQUENTIALLY INCREASING TO RESIDUE 284.

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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: 2.719 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Mes pH 6.5, 12% PEG 20,000, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
pH: 8 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
18-10 mg/mlprotein11
210 mMTris11
3100 mM11NaCl
41 mMdithiothreitol11pH8.0
50.1 MMES12pH6.5
612 %PEG2000012

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Data collection

DiffractionMean temperature: 111 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 26, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 33394 / Num. obs: 33394 / % possible obs: 99.4 % / Redundancy: 3 % / Biso Wilson estimate: 30.4 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 14.8
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.283 / Mean I/σ(I) obs: 3.9 / % possible all: 93.2
Reflection
*PLUS
Highest resolution: 2.8 Å / Num. measured all: 112744
Reflection shell
*PLUS
% possible obs: 93.4 %

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Caspase-3 PDB entry 1CP3
Resolution: 2.8→19.91 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: restraint / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.275 1616 4.9 %RANDOM
Rwork0.233 ---
all-33434 --
obs-32867 98.2 %-
Displacement parametersBiso mean: 31.9 Å2
Baniso -1Baniso -2Baniso -3
1-7.75 Å20 Å26.86 Å2
2--1.25 Å20 Å2
3----9.01 Å2
Refinement stepCycle: LAST / Resolution: 2.8→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7332 0 0 264 7596
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_improper_angle_d0.78
Refine LS restraints NCSNCS model details: restraint
LS refinement shellResolution: 2.8→2.96 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.35 286 5.4 %
Rwork0.283 5059 -
obs--96.4 %
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: protein.top
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 20 Å / Num. reflection obs: 31628 / σ(F): 2 / Num. reflection Rfree: 1650 / % reflection Rfree: 4.9 % / Rfactor obs: 0.233 / Rfactor Rfree: 0.276
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 31.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.78
LS refinement shell
*PLUS
Rfactor Rfree: 0.35 / % reflection Rfree: 5.4 % / Rfactor Rwork: 0.283

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