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- PDB-2y0b: Caspase-3 in Complex with an Inhibitory DARPin-3.4_S76R -

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Basic information

Entry
Database: PDB / ID: 2y0b
TitleCaspase-3 in Complex with an Inhibitory DARPin-3.4_S76R
Components
  • CASPASE-3 SUBUNIT P17Caspase 3
  • CASPASE-3Caspase 3
  • DARPIN-3.4_S76R
KeywordsHYDROLASE/PROTEIN BINDING / HYDROLASE-PROTEIN BINDING COMPLEX / STRUCTURE-ACTIVITY RELATIONSHIP / ANKYRIN REPEAT PROTEIN / RIBOSOME DISPLAY / APOPTOSIS
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 pyroptosis / glial cell apoptotic process / NADE modulates death signalling / response to cobalt ion ...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 pyroptosis / glial cell apoptotic process / NADE modulates death signalling / response to cobalt ion / cysteine-type endopeptidase activity involved in apoptotic signaling pathway / luteolysis / death-inducing signaling complex / cyclin-dependent protein serine/threonine kinase inhibitor activity / cellular response to staurosporine / Apoptosis induced DNA fragmentation / Apoptotic cleavage of cell adhesion proteins / cysteine-type endopeptidase activity involved in execution phase of apoptosis / Caspase activation via Dependence Receptors in the absence of ligand / death receptor binding / SMAC, XIAP-regulated apoptotic response / axonal fasciculation / Activation of caspases through apoptosome-mediated cleavage / 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 / pyroptosis / Apoptotic cleavage of cellular proteins / negative regulation of B cell proliferation / T cell homeostasis / negative regulation of activated T cell proliferation / neurotrophin TRK receptor signaling pathway / B cell homeostasis / protein maturation / negative regulation of cell cycle / response to X-ray / Caspase-mediated cleavage of cytoskeletal proteins / regulation of macroautophagy / response to amino acid / cell fate commitment / Pyroptosis / response to tumor necrosis factor / response to glucose / response to UV / response to glucocorticoid / keratinocyte differentiation / striated muscle cell differentiation / Degradation of the extracellular matrix / intrinsic apoptotic signaling pathway / erythrocyte differentiation / response to nicotine / apoptotic signaling pathway / hippocampus development / sensory perception of sound / 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 / heart development / peptidase activity / neuron apoptotic process / protease binding / response to lipopolysaccharide / response to hypoxia / aspartic-type endopeptidase activity / learning or memory / response to xenobiotic stimulus / positive regulation of apoptotic process / cysteine-type endopeptidase activity / neuronal cell body / apoptotic process / DNA damage response / protein-containing complex binding / proteolysis / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Caspase-like / Rossmann fold - #1460 / Ankyrin repeat-containing domain / 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-like / Rossmann fold - #1460 / Ankyrin repeat-containing domain / 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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBarandun, J. / Schroeder, T. / Mittl, P. / Grutter, M.G.
CitationJournal: Structure / Year: 2013
Title: Specific Inhibition of Caspase-3 by a Competitive Darpin: Molecular Mimicry between Native and Designed Inhibitors.
Authors: Schroeder, T. / Barandun, J. / Flutsch, A. / Briand, C. / Mittl, P. / Grutter, M.G.
History
DepositionDec 1, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 21, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Database references
Revision 1.2Feb 20, 2013Group: Database references
Revision 1.3Feb 20, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc ...entity_src_gen / pdbx_database_proc / pdbx_database_status / struct_biol / struct_conn
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name ..._entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CASPASE-3 SUBUNIT P17
B: CASPASE-3
C: CASPASE-3 SUBUNIT P17
D: CASPASE-3
G: DARPIN-3.4_S76R
H: DARPIN-3.4_S76R
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,50810
Polymers91,0356
Non-polymers4734
Water6,215345
1
A: CASPASE-3 SUBUNIT P17
B: CASPASE-3
G: DARPIN-3.4_S76R
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8726
Polymers45,5183
Non-polymers3553
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6930 Å2
ΔGint-64.3 kcal/mol
Surface area16030 Å2
MethodPISA
2
C: CASPASE-3 SUBUNIT P17
D: CASPASE-3
H: DARPIN-3.4_S76R
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6364
Polymers45,5183
Non-polymers1181
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6320 Å2
ΔGint-43.6 kcal/mol
Surface area15930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.000, 98.000, 192.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D
13G
23H

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A34 - 173
2114C34 - 173
1124B184 - 276
2124D184 - 276
1134G13 - 131
2134H13 - 131

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(0.9986, 0.004602, 0.05336), (0.004083, -0.9999, 0.009821), (0.0534, -0.009589, -0.9985)-1.243, -0.1552, 43.77
2given(0.9964, -0.002202, 0.08481), (-0.001855, -1, -0.004177), (0.08482, 0.004004, -0.9964)-1.631, 0.2944, 42.39
3given(0.998, 0.05068, 0.03861), (0.05124, -0.9986, -0.01372), (0.03786, 0.01567, -0.9992)-0.4001, -2.313, 44.75

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Components

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Protein , 3 types, 6 molecules ACBDGH

#1: Protein CASPASE-3 SUBUNIT P17 / Caspase 3 / CASPASE-3 / CASP-3 / APOPAIN / CYSTEINE PROTEASE CPP32 / CPP-32 / PROTEIN YAMA / SREBP CLEAVAGE ...CASPASE-3 / CASP-3 / APOPAIN / CYSTEINE PROTEASE CPP32 / CPP-32 / PROTEIN YAMA / SREBP CLEAVAGE ACTIVITY 1 / SCA-1


Mass: 16874.174 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Description: T7 PROMOTER EXPRESSION / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P42574, caspase-3
#2: Protein CASPASE-3 / Caspase 3 / CASPASE-3 / CASP-3 / APOPAIN / CYSTEINE PROTEASE CPP32 / CPP-32 / PROTEIN YAMA / SREBP CLEAVAGE ...CASPASE-3 / CASP-3 / APOPAIN / CYSTEINE PROTEASE CPP32 / CPP-32 / PROTEIN YAMA / SREBP CLEAVAGE ACTIVITY 1 / SCA-1


Mass: 13832.739 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Description: T7 PROMOTER EXPRESSION / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P42574, caspase-3
#3: Protein DARPIN-3.4_S76R


Mass: 14810.638 Da / Num. of mol.: 2 / Fragment: N2C, RESIDUES 1-136
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Description: T5 PROMOTER EXPRESSION / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): XL1BLUE

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Non-polymers , 3 types, 349 molecules

#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 345 / 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: 3

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Sample preparation

CrystalDensity Matthews: 3.11 Å3/Da / Density % sol: 60 % / Description: NONE
Crystal growpH: 7.3
Details: 100 MM HEPES, PH 7.3 (RT) 40 % 2-METHYL-2,4-PENTANEDIOL

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.92
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 12, 2010
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.1→49 Å / Num. obs: 62855 / % possible obs: 99.2 % / Observed criterion σ(I): 1.96 / Redundancy: 3.4 % / Biso Wilson estimate: 35.75 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.94
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 1.96 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DKO

2dko


Resolution: 2.1→84.87 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / SU B: 10.59 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21731 3181 5.1 %RANDOM
Rwork0.19183 ---
obs0.19313 59674 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.484 Å2
Baniso -1Baniso -2Baniso -3
1-2.07 Å21.03 Å20 Å2
2--2.07 Å20 Å2
3----3.1 Å2
Refinement stepCycle: LAST / Resolution: 2.1→84.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5608 0 32 345 5985
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0225771
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9411.9587786
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7615.056716
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.34224.214280
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.013151030
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8461538
X-RAY DIFFRACTIONr_chiral_restr0.0630.2862
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024328
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2731.53520
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.54425657
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.83132251
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.3874.52125
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1096medium positional0.190.5
12C1096medium positional0.190.5
21B767medium positional0.150.5
22D767medium positional0.150.5
31G904medium positional0.240.5
32H904medium positional0.240.5
11A1096medium thermal0.242
12C1096medium thermal0.242
21B767medium thermal0.232
22D767medium thermal0.232
31G904medium thermal0.142
32H904medium thermal0.142
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 218 -
Rwork0.327 4368 -
obs--99.48 %
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)
11.6251-0.34760.10452.64370.45892.0268-0.0330.26070.0829-0.4888-0.013-0.1229-0.3060.03770.0460.31830.0694-0.00590.07840.00350.044342.266310.394310.5143
21.4853-0.3412-0.35642.60080.79222.1186-0.08460.213-0.2129-0.2893-0.01810.16-0.0325-0.31980.10270.23020.0575-0.02830.1072-0.03680.075535.9955-1.707513.0078
31.5063-0.39010.26721.85140.07262.208-0.1536-0.1778-0.30.21590.17190.00070.3398-0.1325-0.01830.25210.09790.05310.0840.03020.101941.9149-9.964536.0005
41.39910.02820.37582.50740.75462.4057-0.1998-0.1574-0.0240.13780.10710.20850.0196-0.30870.09260.18020.11610.03010.12570.00870.060635.59132.220433.29
56.48390.1331-2.49955.13534.71689.75620.448-0.15860.0941-0.1097-0.0189-0.404-0.56290.4145-0.42910.26660.02460.09320.152-0.07750.15261.0966-14.8035-6.5563
67.88391.16083.66983.57773.8379.83160.66830.6194-0.51080.0262-0.0297-0.36620.47311.3603-0.63860.31210.1925-0.12150.3685-0.08180.0960.564615.277152.5609
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A34 - 174
2X-RAY DIFFRACTION2B184 - 277
3X-RAY DIFFRACTION3C34 - 174
4X-RAY DIFFRACTION4D185 - 277
5X-RAY DIFFRACTION5G13 - 131
6X-RAY DIFFRACTION6H13 - 132

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