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- PDB-1pau: Crystal structure of the complex of apopain with the tetrapeptide... -

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Basic information

Entry
Database: PDB / ID: 1pau
TitleCrystal structure of the complex of apopain with the tetrapeptide aldehyde inhibitor AC-DEVD-CHO
Components
  • (APOPAIN) x 2
  • ACE-ASP-GLU-VAL-ASJ
KeywordsHYDROLASE/HYDROLASE INHIBITOR / CYSTEINE PROTEASE / CASPASE-3 / APOPAIN / CPP32 / YAMA / PROTEASE-INHIBITOR COMPLEX / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


caspase-3 / Stimulation of the cell death response by PAK-2p34 / phospholipase A2 activator activity / anterior neural tube closure / intrinsic apoptotic signaling pathway in response to osmotic stress / leukocyte apoptotic process / positive regulation of pyroptotic inflammatory response / glial cell apoptotic process / NADE modulates death signalling / luteolysis ...caspase-3 / Stimulation of the cell death response by PAK-2p34 / phospholipase A2 activator activity / anterior neural tube closure / intrinsic apoptotic signaling pathway in response to osmotic stress / leukocyte apoptotic process / positive regulation of pyroptotic inflammatory response / glial cell apoptotic process / NADE modulates death signalling / luteolysis / response to cobalt ion / cysteine-type endopeptidase activity involved in apoptotic signaling pathway / death-inducing signaling complex / cyclin-dependent protein serine/threonine kinase inhibitor activity / cellular response to staurosporine / Apoptosis induced DNA fragmentation / cysteine-type endopeptidase activity involved in execution phase of apoptosis / Caspase activation via Dependence Receptors in the absence of ligand / Apoptotic cleavage of cell adhesion proteins / death receptor binding / SMAC, XIAP-regulated apoptotic response / Activation of caspases through apoptosome-mediated cleavage / axonal fasciculation / Signaling by Hippo / cysteine-type endopeptidase activity involved in apoptotic process / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / fibroblast apoptotic process / execution phase of apoptosis / negative regulation of cytokine production / epithelial cell apoptotic process / platelet formation / Other interleukin signaling / positive regulation of amyloid-beta formation / Apoptotic cleavage of cellular proteins / pyroptotic inflammatory response / negative regulation of B cell proliferation / T cell homeostasis / negative regulation of activated T cell proliferation / B cell homeostasis / neurotrophin TRK receptor signaling pathway / protein maturation / negative regulation of cell cycle / response to X-ray / Caspase-mediated cleavage of cytoskeletal proteins / response to amino acid / cell fate commitment / regulation of macroautophagy / response to tumor necrosis factor / Pyroptosis / response to glucose / response to UV / response to glucocorticoid / keratinocyte differentiation / enzyme activator activity / striated muscle cell differentiation / Degradation of the extracellular matrix / intrinsic apoptotic signaling pathway / erythrocyte differentiation / hippocampus development / apoptotic signaling pathway / sensory perception of sound / response to nicotine / protein catabolic process / regulation of protein stability / response to hydrogen peroxide / neuron differentiation / protein processing / response to wounding / positive regulation of neuron apoptotic process / response to estradiol / peptidase activity / heart development / neuron apoptotic process / protease binding / response to lipopolysaccharide / aspartic-type endopeptidase activity / learning or memory / response to hypoxia / response to xenobiotic stimulus / cysteine-type endopeptidase activity / neuronal cell body / apoptotic process / DNA damage response / protein-containing complex binding / proteolysis / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Caspase-like / 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 ...Caspase-like / 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 / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Ac-Asp-Glu-Val-Asp-Aldehyde / Caspase-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsRotonda, J. / Becker, J.W.
Citation
Journal: Nat.Struct.Biol. / Year: 1996
Title: The three-dimensional structure of apopain/CPP32, a key mediator of apoptosis.
Authors: Rotonda, J. / Nicholson, D.W. / Fazil, K.M. / Gallant, M. / Gareau, Y. / Labelle, M. / Peterson, E.P. / Rasper, D.M. / Ruel, R. / Vaillancourt, J.P. / Thornberry, N.A. / Becker, J.W.
#1: Journal: Nature / Year: 1995
Title: Identification and Inhibition of the Ice/Ced-3 Protease Necessary for Mammalian Apoptosis
Authors: Nicholson, D.W. / Ali, A. / Thornberry, N.A. / Vaillancourt, J.P. / Ding, C.K. / Gallant, M. / Gareau, Y. / Griffin, P.R. / Labelle, M. / Lazebnik, Y.A. / Munday, N.A. / Raju, S.M. / ...Authors: Nicholson, D.W. / Ali, A. / Thornberry, N.A. / Vaillancourt, J.P. / Ding, C.K. / Gallant, M. / Gareau, Y. / Griffin, P.R. / Labelle, M. / Lazebnik, Y.A. / Munday, N.A. / Raju, S.M. / Smulson, M.E. / Yamin, T.T. / Yu, V.L. / Miller, D.K.
History
DepositionJun 6, 1996Processing site: BNL
Revision 1.0Jul 7, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 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 1.3Dec 12, 2012Group: Other
Revision 1.4Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.5Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: 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_comp_id / _struct_conn.ptnr2_auth_seq_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: APOPAIN
B: APOPAIN
C: ACE-ASP-GLU-VAL-ASJ


Theoretical massNumber of molelcules
Total (without water)29,0393
Polymers29,0393
Non-polymers00
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5390 Å2
ΔGint-31 kcal/mol
Surface area10940 Å2
MethodPISA
2
A: APOPAIN
B: APOPAIN
C: ACE-ASP-GLU-VAL-ASJ

A: APOPAIN
B: APOPAIN
C: ACE-ASP-GLU-VAL-ASJ

A: APOPAIN
B: APOPAIN
C: ACE-ASP-GLU-VAL-ASJ

A: APOPAIN
B: APOPAIN
C: ACE-ASP-GLU-VAL-ASJ


Theoretical massNumber of molelcules
Total (without water)116,15612
Polymers116,15612
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-x+1,-y+2,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_575x,-y+2,-z1
Buried area33490 Å2
ΔGint-177 kcal/mol
Surface area31800 Å2
MethodPISA
3
A: APOPAIN
B: APOPAIN
C: ACE-ASP-GLU-VAL-ASJ

A: APOPAIN
B: APOPAIN
C: ACE-ASP-GLU-VAL-ASJ


Theoretical massNumber of molelcules
Total (without water)58,0786
Polymers58,0786
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z1
Buried area15180 Å2
ΔGint-83 kcal/mol
Surface area17460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.810, 84.620, 96.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein APOPAIN / CASPASE-3 / CPP32 / YAMA


Mass: 16639.902 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
References: UniProt: P42574, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Protein APOPAIN / CASPASE-3 / CPP32 / YAMA


Mass: 11910.604 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
References: UniProt: P42574, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#3: Protein/peptide ACE-ASP-GLU-VAL-ASJ


Type: Peptide-like / Class: Inhibitor / Mass: 488.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: Ac-Asp-Glu-Val-Asp-Aldehyde
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE INHIBITOR IS COVALENTLY CONNECTED TO CYS OF THE ENZYME TO FORM A HEMITHIOKETAL.
Sequence detailsAMINO ACID RESIDUES ARE NUMBERED TO FACILITATE COMPARISON WITH THE INTERLEUKIN 1-BETA CONVERTING ...AMINO ACID RESIDUES ARE NUMBERED TO FACILITATE COMPARISON WITH THE INTERLEUKIN 1-BETA CONVERTING ENZYME (ICE, PDB ENTRY 1ICE). RESIDUES IN APOPAIN ARE ASSIGNED THE NUMBERS OF THE HOMOLOGOUS RESIDUES IN THE ALIGNED THREE-DIMENSIONAL STRUCTURE OF ICE. APOPAIN SEQUENCE NUMBERS ARE OMITTED WHEN NO ICE-RELATED RESIDUE IS PRESENT IN APOPAIN, AND APOPAIN-SPECIFIC INSERTIONS ARE INDICATED BY THE ADDITION OF LETTERS TO THE ICE SEQUENCE NUMBERS.

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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: 2.47 Å3/Da / Density % sol: 51 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5
Details: HANGING DROP VAPOR DIFFUSION. 1.5 MICROLITER DROPS OF PROTEIN:INHIBITOR SOLUTION (8.7 MG/ML IN 10 MILLIMOLAR TRIS-HCL PH 8.5, 10 MILLIMOLAR DTT, 3 MILLIMOLAR SODIUM AZIDE) WERE MIXED WITH AN ...Details: HANGING DROP VAPOR DIFFUSION. 1.5 MICROLITER DROPS OF PROTEIN:INHIBITOR SOLUTION (8.7 MG/ML IN 10 MILLIMOLAR TRIS-HCL PH 8.5, 10 MILLIMOLAR DTT, 3 MILLIMOLAR SODIUM AZIDE) WERE MIXED WITH AN EQUAL VOLUME OF RESERVOIR BUFFER (7% PEG-6000 (W/W), 0.10 MOLAR SODIUM CITRATE PH 5.0, 10 MILLIMOLAR DTT, 3 MILLIMOLAR SODIUM AZIDE) AND INCUBATED AT ROOM TEMPERATURE, vapor diffusion - hanging drop
PH range: 5.0-8.0
Crystal grow
*PLUS
pH: 8.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18.7 mg/mlprotein1drop
210 mMTris-HCl1drop
310 mMdithiothreitol1drop
43 mM1dropNaN3
57.5 %(w/w)PEG60001reservoir
60.10 Msodium citrate1reservoir
710 mMdithiothreitol1reservoir
83 mM1reservoirNaN3

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Nov 9, 1995
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→36 Å / Num. obs: 8929 / % possible obs: 87.1 % / Observed criterion σ(I): 0 / Redundancy: 2.33 % / Biso Wilson estimate: 31.34 Å2 / Rmerge(I) obs: 0.0634 / Rsym value: 0.0555 / Net I/σ(I): 17.4
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 2.27 % / Rmerge(I) obs: 0.257 / Mean I/σ(I) obs: 2.59 / Rsym value: 0.262 / % possible all: 87.1
Reflection
*PLUS
Num. measured all: 20801 / Rmerge(I) obs: 0.055
Reflection shell
*PLUS
% possible obs: 87.1 %

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
SAINTdata reduction
SAINTdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PROTEIN COMPONENT OF INTERLEUKIN-1BETA CONVERTING ENZYME (PDB ENTRY 1ICE)

1ice


Resolution: 2.5→20 Å / Cross valid method: FREE-R / σ(F): 2
Details: THERE IS NO ELECTRON DENSITY FOR RESIDUES A 145 - A 149, A 296 - A 297, B 310 - B 319, AND B 402, PRESUMABLY DUE TO DISORDER. MASS SPECTROMETRY INDICATES THAT THESE RESIDUES ARE PRESENT IN ...Details: THERE IS NO ELECTRON DENSITY FOR RESIDUES A 145 - A 149, A 296 - A 297, B 310 - B 319, AND B 402, PRESUMABLY DUE TO DISORDER. MASS SPECTROMETRY INDICATES THAT THESE RESIDUES ARE PRESENT IN THE SPECIES CRYSTALLIZED.
RfactorNum. reflection% reflectionSelection details
Rfree0.275 845 10.6 %RANDOM
Rwork0.195 ---
obs0.195 7987 78 %-
Displacement parametersBiso mean: 23.56 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1905 0 0 34 1939
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.308
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.14
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.091
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.5→2.59 Å
RfactorNum. reflection% reflection
Rfree0.33 38 10.6 %
Rwork0.257 321 -
obs--35.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2APOPAIN.PARAPOPAIN.PRO
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.14
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.091

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