[English] 日本語
Yorodumi
- PDB-2xzd: Caspase-3 in Complex with an Inhibitory DARPin-3.4 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2xzd
TitleCaspase-3 in Complex with an Inhibitory DARPin-3.4
Components
  • (CASPASE-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 / phospholipase A2 activator activity / Stimulation of the cell death response by PAK-2p34 / 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 / phospholipase A2 activator activity / Stimulation of the cell death response by PAK-2p34 / 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 / cellular response to staurosporine / cyclin-dependent protein serine/threonine kinase inhibitor activity / death-inducing signaling complex / Apoptosis induced DNA fragmentation / Apoptotic cleavage of cell adhesion proteins / Caspase activation via Dependence Receptors in the absence of ligand / SMAC, XIAP-regulated apoptotic response / Activation of caspases through apoptosome-mediated cleavage / Signaling by Hippo / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / axonal fasciculation / regulation of synaptic vesicle cycle / death receptor binding / fibroblast apoptotic process / epithelial cell apoptotic process / platelet formation / Other interleukin signaling / response to anesthetic / execution phase of apoptosis / negative regulation of cytokine production / positive regulation of amyloid-beta formation / Apoptotic cleavage of cellular proteins / negative regulation of B cell proliferation / pyroptotic inflammatory response / neurotrophin TRK receptor signaling pathway / negative regulation of activated T cell proliferation / response to tumor necrosis factor / negative regulation of cell cycle / T cell homeostasis / B cell homeostasis / Pyroptosis / cell fate commitment / regulation of macroautophagy / Caspase-mediated cleavage of cytoskeletal proteins / response to X-ray / response to amino acid / response to glucose / response to UV / keratinocyte differentiation / Degradation of the extracellular matrix / striated muscle cell differentiation / intrinsic apoptotic signaling pathway / response to glucocorticoid / protein maturation / erythrocyte differentiation / response to nicotine / hippocampus development / apoptotic signaling pathway / enzyme activator activity / protein catabolic process / response to hydrogen peroxide / sensory perception of sound / protein processing / regulation of protein stability / response to wounding / neuron differentiation / response to estradiol / peptidase activity / positive regulation of neuron apoptotic process / heart development / protease binding / neuron apoptotic process / response to lipopolysaccharide / aspartic-type endopeptidase activity / learning or memory / response to hypoxia / postsynaptic density / response to xenobiotic stimulus / cysteine-type endopeptidase activity / neuronal cell body / apoptotic process / DNA damage response / protein-containing complex binding / glutamatergic synapse / proteolysis / nucleoplasm / nucleus / cytoplasm / cytosol
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: 2.1 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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
Protein , 3 types, 6 molecules ACBDGH

#1: Protein 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 / 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

-
Non-polymers , 3 types, 321 molecules

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


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


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


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

-
Details

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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

-
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.

-
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

-
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

+
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://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