[English] 日本語
Yorodumi
- PDB-4lsz: Caspase-7 in Complex with DARPin D7.18 -

+
Open data


ID or keywords:

Loading...

-
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 / cysteine-type endopeptidase activity involved in execution phase of apoptosis / SMAC, XIAP-regulated apoptotic response / Activation of caspases through apoptosome-mediated cleavage / cysteine-type endopeptidase activity involved in apoptotic process / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes ...caspase-7 / lymphocyte apoptotic process / positive regulation of plasma membrane repair / cellular response to staurosporine / cysteine-type endopeptidase activity involved in execution phase of apoptosis / SMAC, XIAP-regulated apoptotic response / Activation of caspases through apoptosome-mediated cleavage / 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 / Apoptotic cleavage of cellular proteins / protein maturation / Caspase-mediated cleavage of cytoskeletal proteins / response to UV / cysteine-type peptidase activity / striated muscle cell differentiation / protein catabolic process / protein processing / positive regulation of neuron apoptotic process / heart development / peptidase activity / cellular response to lipopolysaccharide / neuron apoptotic process / aspartic-type endopeptidase activity / defense response to bacterium / cysteine-type endopeptidase activity / apoptotic process / proteolysis / RNA binding / extracellular space / 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: 2.26 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlc1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more