[English] 日本語
Yorodumi
- PDB-2xzt: Caspase-3 in Complex with DARPin-3.4_I78S -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2xzt
TitleCaspase-3 in Complex with DARPin-3.4_I78S
Components
  • (CASPASE-3Caspase 3) x 2
  • DARPIN-3.4_I78S
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 / epithelial cell apoptotic process / fibroblast apoptotic process / execution phase of apoptosis / negative regulation of cytokine production / 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 / response to hydrogen peroxide / regulation of protein stability / protein processing / neuron differentiation / 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: 2.7 Å
AuthorsBarandun, J. / Schroeder, T. / Mittl, P. / Grutter, M.G.
CitationJournal: To be Published
Title: Caspase-3 in Complex with Darpin-3.4_I78S
Authors: Schroeder, T. / Barandun, J. / Grutter, M.G.
History
DepositionNov 29, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 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 1.2Dec 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

-
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_I78S
H: DARPIN-3.4_I78S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,1979
Polymers90,8436
Non-polymers3553
Water2,954164
1
C: CASPASE-3
D: CASPASE-3
H: DARPIN-3.4_I78S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6585
Polymers45,4213
Non-polymers2362
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6480 Å2
ΔGint-48.3 kcal/mol
Surface area16480 Å2
MethodPISA
2
A: CASPASE-3
B: CASPASE-3
G: DARPIN-3.4_I78S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5404
Polymers45,4213
Non-polymers1181
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6240 Å2
ΔGint-42 kcal/mol
Surface area16540 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
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(-0.489, -0.8717, 0.03197), (-0.8721, 0.4877, -0.0411), (0.02024, -0.04798, -0.9986)0.2558, -0.6027, -20.46
2given(-0.4796, -0.8769, 0.03066), (-0.8773, 0.4784, -0.03925), (0.01975, -0.04572, -0.9988)-0.08194, -0.5613, -20.43
3given(-0.4144, -0.9094, -0.03505), (-0.9101, 0.4141, 0.01649), (-0.000478, 0.03874, -0.9992)-3.452, -2.321, -16.83

-
Components

#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
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_I78S


Mass: 14714.440 Da / Num. of mol.: 2 / Fragment: N2C
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
#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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O

-
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: 7.8
Details: 100 MM HEPES, PH 7.8 (RT) 70 % 2-METHYL-2,4-PENTANEDIOL

-
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: 2.7→49 Å / Num. obs: 30248 / % possible obs: 99.8 % / Observed criterion σ(I): 2.66 / Redundancy: 4.4 % / Biso Wilson estimate: 33.24 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.55
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.66 / % possible all: 99.9

-
Processing

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

2dko


Resolution: 2.7→49 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.938 / SU B: 24.512 / SU ML: 0.22 / Cross valid method: THROUGHOUT / ESU R: 0.555 / ESU R Free: 0.285 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23051 1530 5.1 %RANDOM
Rwork0.19681 ---
obs0.19853 28718 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.638 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20.18 Å20 Å2
2--0.36 Å20 Å2
3----0.54 Å2
Refinement stepCycle: LAST / Resolution: 2.7→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5602 0 24 164 5790
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0225737
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8841.9567736
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6965.056711
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.81824.296277
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.4151020
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7551536
X-RAY DIFFRACTIONr_chiral_restr0.0560.2857
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024302
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_it0.1711.53513
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.3325640
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.41832224
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.754.52094
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
11A1109medium positional0.220.5
12C1109medium positional0.220.5
21B767medium positional0.260.5
22D767medium positional0.260.5
31G887medium positional0.250.5
32H887medium positional0.250.5
11A1109medium thermal0.12
12C1109medium thermal0.12
21B767medium thermal0.12
22D767medium thermal0.12
31G887medium thermal0.072
32H887medium thermal0.072
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 107 -
Rwork0.325 2067 -
obs--99.95 %
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)
12.64971.3110.69333.09020.04312.378-0.16130.4961-0.1173-0.51370.1321-0.2494-0.06850.15750.02920.3174-0.17620.04940.2193-0.01240.130229.9429-31.1361-22.0089
23.78461.5391.26463.83351.2522.2167-0.06820.38030.0471-0.40380.00250.3401-0.2963-0.11550.06570.2631-0.093-0.03070.16830.02030.106916.3691-31.507-19.3077
32.95140.20990.19721.7647-0.07512.69450.1256-0.0504-0.1730.1538-0.04790.23460.1295-0.3855-0.07770.1908-0.12960.03160.1239-0.00110.195612.2965-40.63993.8772
43.98020.4131.69152.0867-0.00763.40840.0087-0.23810.24250.2019-0.08060.0716-0.2918-0.25980.07190.221-0.07420.03670.0687-0.01920.121519.3339-29.27820.9787
54.8489-0.96084.01948.74525.641414.1115-0.0198-0.0298-0.3256-0.34310.5395-0.4799-0.16120.6851-0.51960.2343-0.11680.02980.1292-0.10220.242717.8388-60.1932-38.7359
63.6675-1.32722.71935.60830.75689.39450.0799-0.1128-0.2907-0.27890.2186-0.22540.69160.7234-0.29850.2424-0.0479-0.04320.18030.05150.141843.3351-44.875520.3114
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