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- PDB-4lsz: Caspase-7 in Complex with DARPin D7.18 -

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Basic information

Entry
Database: PDB / ID: 4lsz
TitleCaspase-7 in Complex with DARPin D7.18
Components
  • Caspase-7 subunit p10
  • Caspase-7 subunit p20
  • DARPin D7.18
KeywordsHYDROLASE / Complex structure / Caspase-7 / selected and specific DARPin D7.18
Function / homology
Function and homology information


caspase-7 / lymphocyte apoptotic process / positive regulation of plasma membrane repair / cellular response to staurosporine / SMAC, XIAP-regulated apoptotic response / Activation of caspases through apoptosome-mediated cleavage / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / fibroblast apoptotic process / execution phase of apoptosis ...caspase-7 / lymphocyte apoptotic process / positive regulation of plasma membrane repair / cellular response to staurosporine / SMAC, XIAP-regulated apoptotic response / Activation of caspases through apoptosome-mediated cleavage / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / fibroblast apoptotic process / execution phase of apoptosis / Apoptotic cleavage of cellular proteins / Caspase-mediated cleavage of cytoskeletal proteins / response to UV / striated muscle cell differentiation / cysteine-type peptidase activity / protein maturation / protein catabolic process / protein processing / fibrillar center / positive regulation of neuron apoptotic process / peptidase activity / heart development / cellular response to lipopolysaccharide / neuron apoptotic process / aspartic-type endopeptidase activity / defense response to bacterium / cysteine-type endopeptidase activity / apoptotic process / proteolysis / extracellular space / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Caspase-like / 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-like / 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 / Ankyrin repeat-containing domain / 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: 2.26 Å
AuthorsFluetsch, A. / Lukarska, M. / Gruetter, M.G.
CitationJournal: Biochem.J. / Year: 2014
Title: Combined inhibition of caspase 3 and caspase 7 by two highly selective DARPins slows down cellular demise.
Authors: Flutsch, A. / Ackermann, R. / Schroeder, T. / Lukarska, M. / Hausammann, G.J. / Weinert, C. / Briand, C. / Grutter, M.G.
History
DepositionJul 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 9, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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-7 subunit p20
B: Caspase-7 subunit p10
C: Caspase-7 subunit p20
D: Caspase-7 subunit p10
E: DARPin D7.18
F: DARPin D7.18


Theoretical massNumber of molelcules
Total (without water)100,9426
Polymers100,9426
Non-polymers00
Water2,540141
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.840, 82.310, 95.080
Angle α, β, γ (deg.)90.00, 91.86, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
/ NCS ensembles :
ID
1
2
3

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Components

#1: Protein Caspase-7 subunit p20 / CASP-7 / Apoptotic protease Mch-3 / CMH-1 / ICE-like apoptotic protease 3 / ICE-LAP3 / Caspase-7 ...CASP-7 / Apoptotic protease Mch-3 / CMH-1 / ICE-like apoptotic protease 3 / ICE-LAP3 / Caspase-7 subunit p20 / Caspase-7 subunit p11


Mass: 19750.766 Da / Num. of mol.: 2 / Fragment: Caspase-7 subunit p20, UNP residues 24-198
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP7, MCH3 / Production host: Escherichia coli (E. coli) / References: UniProt: P55210, caspase-7
#2: Protein Caspase-7 subunit p10 / CASP-7 / Apoptotic protease Mch-3 / CMH-1 / ICE-like apoptotic protease 3 / ICE-LAP3 / Caspase-7 ...CASP-7 / Apoptotic protease Mch-3 / CMH-1 / ICE-like apoptotic protease 3 / ICE-LAP3 / Caspase-7 subunit p20 / Caspase-7 subunit p11


Mass: 12424.015 Da / Num. of mol.: 2 / Fragment: Caspase-7 subunit p10, UNP residues 207-303
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP7, MCH3 / Production host: Escherichia coli (E. coli) / References: UniProt: P55210, caspase-7
#3: Protein DARPin D7.18


Mass: 18296.254 Da / Num. of mol.: 2 / Fragment: DARPin D7.18
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 46.95 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 0.8M Sodium Formate, 100mM Tris, 13% PEG 4000, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 10, 2011
RadiationMonochromator: X06SA / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.26→50 Å / Num. all: 43329 / Num. obs: 42969 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.26→2.32 Å / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3IBC, 2P2C

3ibc

2p2c


Resolution: 2.26→12.934 Å / SU ML: 0.24 / σ(F): 1.37 / Phase error: 25.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2084 1713 4 %RANDOM by Phenix
Rwork0.1749 ---
obs0.1762 42872 99.53 %-
all-43329 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.26→12.934 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6084 0 0 141 6225
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086221
X-RAY DIFFRACTIONf_angle_d1.068411
X-RAY DIFFRACTIONf_dihedral_angle_d14.1632272
X-RAY DIFFRACTIONf_chiral_restr0.076926
X-RAY DIFFRACTIONf_plane_restr0.0041107
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2601-2.32620.2871400.23113376X-RAY DIFFRACTION99
2.3262-2.40080.29061410.22293395X-RAY DIFFRACTION99
2.4008-2.48610.3031430.21673430X-RAY DIFFRACTION100
2.4861-2.58490.25711420.22473418X-RAY DIFFRACTION100
2.5849-2.70150.25841430.21623435X-RAY DIFFRACTION99
2.7015-2.84250.25321430.21063432X-RAY DIFFRACTION100
2.8425-3.01840.24311430.20383420X-RAY DIFFRACTION100
3.0184-3.24810.24151430.19643427X-RAY DIFFRACTION100
3.2481-3.56870.20851430.17833440X-RAY DIFFRACTION99
3.5687-4.0710.19061440.15183446X-RAY DIFFRACTION100
4.071-5.07690.16571420.13313446X-RAY DIFFRACTION100
5.0769-12.93470.16741460.16163494X-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)
17.5033.8545-1.83384.0662-1.13193.1035-0.07460.39190.3081-0.06670.06390.1157-0.1551-0.03790.03380.40910.0263-0.0620.38660.0160.3168-5.694612.16966.9218
24.17610.4376-0.13841.791-1.16924.6152-0.15730.2521-0.1966-0.0006-0.01140.27730.1696-0.30680.15860.3043-0.0026-0.05680.3933-0.05970.3158-14.06652.89595.8605
35.86332.0323-1.62573.7022-1.42585.1011-0.03810.2624-0.20110.1156-0.0915-0.0336-0.06260.06260.19950.26870.0238-0.07680.3771-0.02260.2802-5.12876.43186.5227
44.81173.3554-5.02993.922-3.00865.4389-0.3536-0.1966-0.5507-0.1753-0.0605-0.06610.39440.4610.4620.40450.07810.01050.4224-0.04720.523-2.9599-4.328910.2934
55.62932.034-2.91112.3596-2.57066.3711-0.184-0.4454-0.3282-0.0665-0.0440.0850.35830.15050.17040.3140.0123-0.05150.32980.01430.3722-6.42064.117119.3946
63.6576-1.6725-4.83727.0250.8666.74010.37720.3350.082-0.1771-0.6948-0.84920.10330.76040.1130.3668-0.0106-0.0340.60120.09680.497111.95957.845311.9707
74.2741-0.04052.78352.1741-3.69518.5453-0.3667-0.7448-0.4073-0.1580.1650.3050.3341-0.47190.23680.36340.02650.01830.4011-0.11050.4325-15.36461.501221.9005
88.79155.1515-0.90616.04750.03872.2267-0.3066-0.14190.5549-0.23250.1430.376-0.2891-0.43070.12240.34090.0643-0.08290.3954-0.00020.3385-12.055916.420519.0026
96.14735.511-5.36958.8213-4.96644.57990.2291-0.1206-0.04160.28390.01390.77310.0251-0.4082-0.18090.32490.0218-0.02810.4572-0.05520.4507-18.77055.171629.0255
104.6129-3.94023.92964.001-3.84627.2765-0.13280.40510.5923-0.6022-0.2015-0.4195-0.33290.61480.3640.3278-0.0803-0.0820.32940.03220.44251.288616.740315.4609
115.3814-3.8685-0.78647.74751.23141.636-0.0381-0.2617-0.00890.002-0.0592-0.2523-0.14980.17630.07790.395-0.0262-0.060.4730.04350.257710.80254.71439.2667
121.7467-0.5216-0.14571.6505-0.34513.098-0.06-0.3649-0.09720.0493-0.1043-0.0335-0.17910.13950.17970.3282-0.0427-0.08940.52670.0410.34229.17225.553144.3169
133.77560.0887-1.56957.31482.31023.1159-0.3066-0.2465-0.5279-0.13880.2406-0.21640.14180.13370.10310.277-0.0271-0.01510.41190.08760.31377.7733-3.754135.4969
145.1471-1.3483-1.89683.50031.30534.8996-0.0063-0.2642-0.15490.16170.0833-0.07630.0938-0.33080.01410.2846-0.0427-0.08580.39960.06740.33940.99722.564834.8679
154.90134.9519-4.51745.0039-4.58434.2933-0.20460.87690.3474-0.7539-0.344-1.18510.11141.33080.58990.7804-0.0228-0.00740.88890.18210.551716.91456.36046.0824
163.60940.7847-4.75723.37440.2176.72520.01850.7194-0.22940.2341-0.08670.7063-0.0992-0.7919-0.06230.34390.0079-0.0010.5330.02670.4527-9.57046.301234.6311
179.6589-0.16736.66332.8912.36419.1869-0.35390.35190.05970.18280.1417-0.08290.17180.73550.23360.3474-0.05570.00480.54590.04630.425517.41940.829224.5374
187.6739-5.6026-5.42095.43445.9468.1529-0.27980.1330.884-0.6260.6342-1.4108-0.63761.0911-0.43820.4131-0.1096-0.08290.54770.03450.458916.229813.178929.3481
198.9565-5.6096-3.28945.94143.55293.72020.11610.19830.26070.0099-0.0389-0.54540.0010.2186-0.16410.3383-0.0885-0.02340.41870.11850.470215.67789.603221.3449
207.0350.1943-0.92986.54261.19794.2381-0.0818-0.3140.49610.0316-0.1940.1762-0.4992-0.1870.28040.33360.0167-0.07630.3978-0.04870.3362-0.394214.452331.2516
214.10371.62131.01253.1607-3.5169.2791-0.1539-0.03252.4512-0.7601-0.13671.1837-0.9419-0.99170.27350.73570.0694-0.17760.5864-0.08941.0322-22.236120.2687-7.6944
225.0333-2.33432.73386.415-1.97653.5657-0.46960.24141.1109-0.1446-0.05460.795-0.82280.29540.52210.5364-0.0168-0.09280.4729-00.5332-17.852913.1693-9.9478
235.8871.49772.4697.0916-0.44723.1768-0.02040.4702-0.0948-0.23140.05870.6186-0.27840.1853-0.01820.48910.0363-0.05480.6082-0.06230.4174-19.60912.2477-13.6833
244.9743-1.0075-1.67737.1796-6.8327.94840.29220.0414-0.74981.0950.60491.2149-0.7898-1.6089-0.40720.66180.0075-0.07430.5703-0.14660.8412-27.4303-8.3543-12.4368
256.562-0.34621.10617.1604-3.52858.7170.0592-0.7961-1.38360.54330.4990.11511.2404-0.5317-0.54130.70850.0601-0.26690.6701-0.12480.8842-20.3978-15.7549-10.9993
264.0927-2.26214.42424.7072-5.03156.7681-0.69760.98031.2497-0.92250.8022-0.0939-0.2857-0.38430.05250.7449-0.0959-0.07170.72190.10160.621318.368618.299655.7356
279.17162.65426.00945.71934.24365.9529-0.25380.31560.6022-0.69320.0514-1.3623-0.43440.35750.20030.7731-0.1681-0.13440.69740.10280.748926.105317.942158.4923
286.89350.08333.28025.66590.27795.8708-0.3901-0.22370.28970.0890.147-0.4272-0.4103-0.34630.21280.4129-0.0109-0.02870.60040.03020.292718.28625.863859.2437
294.0595-1.41332.5057.2120.78025.69470.1763-0.3593-0.30710.0930.0904-0.66930.2492-0.0268-0.26860.4584-0.0351-0.03180.60240.10420.472921.3983-7.55160.3673
302.6524-1.57741.23263.58822.51224.37660.36170.5009-0.9694-0.3060.14460.07291.0550.1601-0.47110.8509-0.1134-0.23860.76770.12670.890618.4895-19.953155.6343
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 58:78)
2X-RAY DIFFRACTION2(chain A and resid 79:128)
3X-RAY DIFFRACTION3(chain A and resid 129:146)
4X-RAY DIFFRACTION4(chain A and resid 147:171)
5X-RAY DIFFRACTION5(chain A and resid 172:197)
6X-RAY DIFFRACTION6(chain B and resid 210:220)
7X-RAY DIFFRACTION7(chain B and resid 221:238)
8X-RAY DIFFRACTION8(chain B and resid 239:262)
9X-RAY DIFFRACTION9(chain B and resid 263:291)
10X-RAY DIFFRACTION10(chain B and resid 292:303)
11X-RAY DIFFRACTION11(chain C and resid 58:91)
12X-RAY DIFFRACTION12(chain C and resid 92:134)
13X-RAY DIFFRACTION13(chain C and resid 135:163)
14X-RAY DIFFRACTION14(chain C and resid 164:192)
15X-RAY DIFFRACTION15(chain C and resid 193:198)
16X-RAY DIFFRACTION16(chain D and resid 209:223)
17X-RAY DIFFRACTION17(chain D and resid 224:238)
18X-RAY DIFFRACTION18(chain D and resid 239:251)
19X-RAY DIFFRACTION19(chain D and resid 252:288)
20X-RAY DIFFRACTION20(chain D and resid 289:303)
21X-RAY DIFFRACTION21(chain E and resid 12:34)
22X-RAY DIFFRACTION22(chain E and resid 35:60)
23X-RAY DIFFRACTION23(chain E and resid 61:122)
24X-RAY DIFFRACTION24(chain E and resid 123:133)
25X-RAY DIFFRACTION25(chain E and resid 134:164)
26X-RAY DIFFRACTION26(chain F and resid 13:22)
27X-RAY DIFFRACTION27(chain F and resid 23:37)
28X-RAY DIFFRACTION28(chain F and resid 38:90)
29X-RAY DIFFRACTION29(chain F and resid 91:135)
30X-RAY DIFFRACTION30(chain F and resid 136:166)

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