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- PDB-4jje: Caspase-3 specific unnatural amino acid peptides -

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Basic information

Entry
Database: PDB / ID: 4jje
TitleCaspase-3 specific unnatural amino acid peptides
Components
  • Caspase inhibitor
  • Caspase-3
KeywordsHYDROLASE/HYDROLASE INHIBITOR / protease / 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
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 ...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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACE-1MH-ASP-B3L-HLX-1U8 / Caspase-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.481 Å
AuthorsVickers, C.J. / Gonzalez-Paez, G.E. / Wolan, D.W.
CitationJournal: Acs Chem.Biol. / Year: 2013
Title: Selective Detection of Caspase-3 versus Caspase-7 Using Activity-Based Probes with Key Unnatural Amino Acids.
Authors: Vickers, C.J. / Gonzalez-Paez, G.E. / Wolan, D.W.
History
DepositionMar 7, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2014Group: Database references
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conn / struct_ref_seq_dif
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _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 / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Caspase-3
B: Caspase inhibitor


Theoretical massNumber of molelcules
Total (without water)30,4262
Polymers30,4262
Non-polymers00
Water3,855214
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.110, 84.334, 96.088
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 Caspase-3 / CASP-3 / Apopain / Cysteine protease CPP32 / CPP-32 / Protein Yama / SREBP cleavage activity 1 / ...CASP-3 / Apopain / Cysteine protease CPP32 / CPP-32 / Protein Yama / SREBP cleavage activity 1 / SCA-1 / Caspase-3 subunit p17 / Caspase-3 subunit p12


Mass: 29602.684 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP3, Caspase-3 CPP32, CPP32 / Plasmid: pet23b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: P42574, caspase-3
#2: Protein/peptide Caspase inhibitor


Type: Peptide-like / Class: CASPASE inhibitor / Mass: 822.944 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: ACE-1MH-ASP-B3L-HLX-1U8
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE 2,6, DIMETHYLBENZOIC ACID FRAGMENT IN RESIDUE 1U8 OF THE CASPASE INHIBITOR IS REMOVED DURING ...THE 2,6, DIMETHYLBENZOIC ACID FRAGMENT IN RESIDUE 1U8 OF THE CASPASE INHIBITOR IS REMOVED DURING COVALENT ATTACHMENT TO CASPASE

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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: 2.41 Å3/Da / Density % sol: 49.02 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.05M Sodium citrate pH 5.5, 14% PEG 6000, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1.03317 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 12, 2013 / Details: mirrors
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 1.39→42.17 Å / Num. all: 46303 / Num. obs: 46048 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 21.23 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 36.4

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Processing

Software
NameVersionClassification
DENZOdata reduction
SOLVEphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementResolution: 1.481→42.167 Å / SU ML: 0.14 / σ(F): 1.39 / Phase error: 16.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1739 2330 5.06 %
Rwork0.1498 --
obs0.151 46040 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.481→42.167 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1979 0 0 214 2193
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142051
X-RAY DIFFRACTIONf_angle_d1.6242763
X-RAY DIFFRACTIONf_dihedral_angle_d12.92771
X-RAY DIFFRACTIONf_chiral_restr0.111301
X-RAY DIFFRACTIONf_plane_restr0.008362
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4812-1.51140.26381200.24212444X-RAY DIFFRACTION95
1.5114-1.54430.23851260.20742545X-RAY DIFFRACTION99
1.5443-1.58020.22471380.18962522X-RAY DIFFRACTION100
1.5802-1.61970.2061420.17042553X-RAY DIFFRACTION100
1.6197-1.66350.19891460.16192529X-RAY DIFFRACTION100
1.6635-1.71250.20881240.16442574X-RAY DIFFRACTION100
1.7125-1.76780.21821170.15672587X-RAY DIFFRACTION100
1.7678-1.8310.17371310.14022558X-RAY DIFFRACTION100
1.831-1.90430.15381450.13682578X-RAY DIFFRACTION100
1.9043-1.99090.18641440.14312521X-RAY DIFFRACTION100
1.9909-2.09590.18451430.14052575X-RAY DIFFRACTION100
2.0959-2.22720.16061440.14242577X-RAY DIFFRACTION100
2.2272-2.39910.17031380.14382589X-RAY DIFFRACTION100
2.3991-2.64060.1661490.14822586X-RAY DIFFRACTION100
2.6406-3.02260.14391380.15182625X-RAY DIFFRACTION100
3.0226-3.80770.18451440.142617X-RAY DIFFRACTION100
3.8077-42.18410.1651410.1522730X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.43290.0785-0.04290.42150.37510.35430.03370.0990.1222-0.06690.02020.0622-0.0922-0.09620.00010.16740.02080.01890.20730.04820.219418.293131.425251.6044
20.72880.30840.01520.2330.19380.33550.0992-0.1862-0.04450.2070.03280.12230.0364-0.06460.00580.2066-0.0190.00560.16770.03770.146823.767116.53969.3205
30.1664-0.0845-0.0880.3115-0.0070.16860.18540.0044-0.2875-0.15350.04770.61090.2562-0.2595-0.00510.227-0.0721-0.01960.22450.03730.273513.51689.532959.5525
40.33670.1293-0.37660.3248-0.10970.43090.07510.1362-0.1339-0.091-0.02960.17860.1976-0.10080.00050.185-0.0068-0.02160.17180.00810.217219.037614.516554.712
50.09640.0538-0.14930.64040.12330.42520.07950.1106-0.04230.0111-0.0219-0.08760.07560.067300.17460.0024-0.02330.17560.00550.190833.184816.122452.7845
60.67760.1331-0.27890.2278-0.07220.59850.0801-0.05690.01110.0407-0.01260.0108-0.03650.067400.1644-0.0057-0.00890.1743-0.00620.146534.066722.138561.1273
70.2899-0.07620.17420.2392-0.30090.3940.0760.0399-0.04920.04450.01010.0521-0.0312-0.00980.0010.138-0.0013-0.01030.14310.00070.135237.456923.590258.332
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 29 through 51 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 52 through 92 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 93 through 105 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 106 through 154 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 155 through 191 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 192 through 231 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 232 through 278 )A0

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