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

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Basic information

Entry
Database: PDB / ID: 2xzd
TitleCaspase-3 in Complex with an Inhibitory DARPin-3.4
Components
  • (CASPASE-3Caspase 3) x 2
  • DARPIN-3.4
KeywordsHYDROLASE/PROTEIN BINDING / HYDROLASE-PROTEIN BINDING COMPLEX / DE NOVO PROTEIN / APOPTOSIS / ANKYRIN REPEAT PROTEIN / RIBOSOME DISPLAY
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
DepositionNov 24, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Database references
Revision 1.2Feb 20, 2013Group: Database references / Structure summary
Revision 1.3Dec 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_conn / 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_conn.pdbx_leaving_atom_flag / _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
B: CASPASE-3
C: CASPASE-3
D: CASPASE-3
G: DARPIN-3.4
H: DARPIN-3.4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,36810
Polymers90,8956
Non-polymers4734
Water5,711317
1
A: CASPASE-3
B: CASPASE-3
G: DARPIN-3.4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6845
Polymers45,4473
Non-polymers2362
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6500 Å2
ΔGint-55.9 kcal/mol
Surface area16160 Å2
MethodPISA
2
C: CASPASE-3
D: CASPASE-3
H: DARPIN-3.4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6845
Polymers45,4473
Non-polymers2362
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6360 Å2
ΔGint-47 kcal/mol
Surface area16210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.000, 98.000, 193.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 3 types, 6 molecules ACBDGH

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


Mass: 16874.174 Da / Num. of mol.: 2 / Fragment: P17 SUBUNIT, RESIDUES 29-175 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P42574, caspase-3
#2: Protein CASPASE-3 / Caspase 3 / CASP-3 / APOPAIN / CYSTEINE PROTEASE CPP32 / CPP-32 PROTEIN YAM / SREBP CLEAVAGE ACTIVITY 1 / SCA-1


Mass: 13832.739 Da / Num. of mol.: 2 / Fragment: P12 SUBUNIT, RESIDUES 176-277
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P42574, caspase-3
#3: Protein DARPIN-3.4


Mass: 14740.521 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: IN-VITRO EVOLVED SEQUENCE / Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): XL1BLUE

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Non-polymers , 3 types, 321 molecules

#4: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 317 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsCHAIN A AND C, ASP 28 TO SER MUTATIONS FROM CLONING STRATEGY.

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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: 1
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: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→49 Å / Num. obs: 63172 / % possible obs: 99.3 % / Observed criterion σ(I): 1.92 / Redundancy: 3.9 % / Biso Wilson estimate: 35.29 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 15.59
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 4.03 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 1.92 / % 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→49 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.959 / SU B: 10.66 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21811 3211 5.1 %RANDOM
Rwork0.18499 ---
obs0.18667 59961 99.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å20.26 Å20 Å2
2--0.53 Å20 Å2
3----0.79 Å2
Refinement stepCycle: LAST / Resolution: 2.1→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5606 0 32 317 5955
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0225748
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1921.9587752
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2545.056711
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.80624.296277
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.918151022
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6651536
X-RAY DIFFRACTIONr_chiral_restr0.0810.2860
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024302
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_it0.541.53513
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.0625642
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.79632235
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9654.52108
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
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 226 -
Rwork0.345 4393 -
obs--99.5 %
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)
11.3022-0.33460.12323.49280.6872.07420.01220.25890.1049-0.7043-0.0481-0.1988-0.4166-0.00050.03590.41990.09230.01670.08610.01940.103242.075410.382610.5587
21.3137-0.5695-0.46582.68461.18232.3517-0.02860.2224-0.1664-0.3396-0.06770.165-0.1283-0.3430.09630.24310.0709-0.03470.1141-0.03570.133235.8737-1.625913.1795
31.3643-0.25270.07062.21390.11862.4572-0.1345-0.1209-0.2440.1680.13440.00450.3662-0.10980.00010.220.06960.03820.0530.01970.152741.6805-9.583636.2574
41.43950.25760.46212.59021.06392.8163-0.1195-0.1237-0.0050.05470.03140.2076-0.0356-0.31650.08820.17640.09950.02640.09410.00570.14335.45942.304533.5186
56.0931-1.5527-4.58855.05185.805611.82440.5919-0.20710.338-0.20960.1632-0.5457-0.71640.5016-0.75510.19750.01920.07630.1024-0.08030.163861.1791-15.156-6.4119
64.49720.63441.08252.58483.00497.83240.24930.0094-0.20820.00120.1076-0.1706-0.04511.0981-0.35690.17430.0656-0.06170.2712-0.05850.055260.680815.757652.6706
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A34 - 174
2X-RAY DIFFRACTION2B184 - 277
3X-RAY DIFFRACTION3C34 - 175
4X-RAY DIFFRACTION4D185 - 277
5X-RAY DIFFRACTION5G13 - 131
6X-RAY DIFFRACTION6H13 - 132

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