[English] 日本語
Yorodumi
- PDB-6ckz: Human caspase-3 in complex with Ac-DW3-KE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ckz
TitleHuman caspase-3 in complex with Ac-DW3-KE
Components
  • ACE-1MH-ASP-B3L-PHE-1U8
  • Caspase-3 subunit p12
  • Caspase-3 subunit p17
KeywordsHYDROLASE/HYDROLASE Inhibitor / caspase-3 / inhibitor / APOPTOSIS / HYDROLASE / HYDROLASE-HYDROLASE Inhibitor complex
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 pyroptotic inflammatory response / glial cell apoptotic process / NADE modulates death signalling / luteolysis ...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 pyroptotic inflammatory response / glial cell apoptotic process / NADE modulates death signalling / luteolysis / response to cobalt ion / cysteine-type endopeptidase activity involved in apoptotic signaling pathway / death-inducing signaling complex / cellular response to staurosporine / cyclin-dependent protein serine/threonine kinase inhibitor activity / Apoptosis induced DNA fragmentation / cysteine-type endopeptidase activity involved in execution phase of apoptosis / Caspase activation via Dependence Receptors in the absence of ligand / Apoptotic cleavage of cell adhesion proteins / death receptor binding / SMAC, XIAP-regulated apoptotic response / Activation of caspases through apoptosome-mediated cleavage / axonal fasciculation / 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 / negative regulation of cytokine production / epithelial cell apoptotic process / platelet formation / execution phase of apoptosis / Other interleukin signaling / positive regulation of amyloid-beta formation / Apoptotic cleavage of cellular proteins / pyroptotic inflammatory response / negative regulation of B cell proliferation / T cell homeostasis / negative regulation of activated T cell proliferation / B cell homeostasis / neurotrophin TRK receptor signaling pathway / protein maturation / negative regulation of cell cycle / response to X-ray / response to amino acid / Caspase-mediated cleavage of cytoskeletal proteins / cell fate commitment / regulation of macroautophagy / response to tumor necrosis factor / Pyroptosis / response to glucose / response to UV / response to glucocorticoid / keratinocyte differentiation / enzyme activator activity / striated muscle cell differentiation / Degradation of the extracellular matrix / intrinsic apoptotic signaling pathway / erythrocyte differentiation / hippocampus development / apoptotic signaling pathway / sensory perception of sound / response to nicotine / regulation of protein stability / protein catabolic process / response to hydrogen peroxide / neuron differentiation / protein processing / response to wounding / positive regulation of neuron apoptotic process / response to estradiol / heart development / peptidase activity / protease binding / neuron apoptotic process / response to lipopolysaccharide / aspartic-type endopeptidase activity / learning or memory / response to hypoxia / response to xenobiotic stimulus / cysteine-type endopeptidase activity / neuronal cell body / DNA damage response / protein-containing complex binding / apoptotic process / proteolysis / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Caspase-like / Rossmann fold - #1460 / 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 ...Caspase-like / Rossmann fold - #1460 / 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 / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
(ACE)(1MH)D(B3L)F(1U8) / Caspase-3
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsSolania, A.T. / Gonzalez-Paez, G.E. / Wolan, D.W.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5R21AI112796 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM118382 United States
CitationJournal: Acs Chem.Biol. / Year: 2019
Title: Selective and Rapid Cell-Permeable Inhibitor of Human Caspase-3.
Authors: Solania, A. / Gonzalez-Paez, G.E. / Wolan, D.W.
History
DepositionMar 1, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 2.0Sep 30, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / pdbx_molecule_features ...atom_site / pdbx_molecule_features / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / pdbx_validate_rmsd_angle / struct_conn / struct_keywords / struct_ref_seq / struct_sheet_range
Item: _atom_site.auth_seq_id / _pdbx_poly_seq_scheme.pdb_seq_num ..._atom_site.auth_seq_id / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_validate_rmsd_angle.auth_seq_id_1 / _pdbx_validate_rmsd_angle.auth_seq_id_2 / _pdbx_validate_rmsd_angle.auth_seq_id_3 / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_keywords.pdbx_keywords / _struct_keywords.text / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.end_auth_seq_id
Revision 2.1Oct 4, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 3.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_rmsd_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Caspase-3 subunit p17
B: Caspase-3 subunit p12
C: ACE-1MH-ASP-B3L-PHE-1U8


Theoretical massNumber of molelcules
Total (without water)33,5843
Polymers33,5843
Non-polymers00
Water3,711206
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: previously determined
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.095, 83.892, 95.863
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

-
Components

#1: Protein Caspase-3 subunit p17 / CASP-3


Mass: 19759.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP3, CPP32 / Production host: Escherichia coli (E. coli) / References: UniProt: P42574, caspase-3
#2: Protein Caspase-3 subunit p12 / CASP-3


Mass: 12981.756 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP3, CPP32 / Production host: Escherichia coli (E. coli) / References: UniProt: P42574, caspase-3
#3: Protein/peptide ACE-1MH-ASP-B3L-PHE-1U8


Type: Peptide-like / Class: CASPASE inhibitor / Mass: 842.934 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: (ACE)(1MH)D(B3L)F(1U8)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.01 Å3/Da / Density % sol: 38.79 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.4
Details: 1:1 dilution with 0.10 M sodium citrate, pH 5.4, 15.2 % PEG6000, 0.010 M DTT, 0.02% NaN3.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 41773 / % possible obs: 95.8 % / Redundancy: 6.3 % / Biso Wilson estimate: 16.46 Å2 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.027 / Rrim(I) all: 0.069 / Rsym value: 0.063 / Net I/av σ(I): 18.2 / Net I/σ(I): 28.2
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.351 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 1635 / CC1/2: 0.889 / Rpim(I) all: 0.228 / Rrim(I) all: 0.509 / Rsym value: 0.452 / % possible all: 75.8

-
Processing

Software
NameVersionClassification
PHENIX(dev_2747: ???)refinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JJE

4jje


Resolution: 1.5→41.946 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1714 2101 5.03 %
Rwork0.1531 --
obs0.1541 41762 95.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→41.946 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1970 0 0 206 2176
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072056
X-RAY DIFFRACTIONf_angle_d1.9852771
X-RAY DIFFRACTIONf_dihedral_angle_d4.1841682
X-RAY DIFFRACTIONf_chiral_restr0.063302
X-RAY DIFFRACTIONf_plane_restr0.005354
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5001-1.5350.25481140.21222074X-RAY DIFFRACTION76
1.535-1.57330.21681310.19482375X-RAY DIFFRACTION88
1.5733-1.61590.2091310.17462662X-RAY DIFFRACTION97
1.6159-1.66340.18971270.1692675X-RAY DIFFRACTION98
1.6634-1.71710.19371520.1632730X-RAY DIFFRACTION99
1.7171-1.77850.16421280.15552673X-RAY DIFFRACTION98
1.7785-1.84970.13771380.14912644X-RAY DIFFRACTION96
1.8497-1.93390.18691430.15692691X-RAY DIFFRACTION99
1.9339-2.03590.18691610.14282699X-RAY DIFFRACTION99
2.0359-2.16340.1791250.14752689X-RAY DIFFRACTION97
2.1634-2.33040.17211330.14372716X-RAY DIFFRACTION98
2.3304-2.56490.17161530.15192723X-RAY DIFFRACTION99
2.5649-2.9360.16211570.15942698X-RAY DIFFRACTION97
2.936-3.69870.15871440.14862786X-RAY DIFFRACTION99
3.6987-41.96240.16631640.14852826X-RAY DIFFRACTION97
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)
10.90970.1424-0.25013.135-1.39612.11080.05210.09960.0804-0.07090.16740.3258-0.1192-0.2362-0.22060.13650.00630.01360.17340.01920.190617.833631.305651.4785
21.5037-0.22490.20862.2774-0.44481.3250.0817-0.1572-0.13770.20490.05340.14490.0964-0.0752-0.14110.2135-0.02730.02010.17510.02890.13823.375416.693569.1338
35.6376-4.7883.84085.1577-5.24546.22950.31070.0397-0.3377-0.2514-0.01780.61710.3297-0.2034-0.27280.2539-0.0745-0.01370.21550.03260.280413.18939.583259.2743
41.0854-0.26280.12471.5134-0.38531.60080.05710.0703-0.1588-0.03880.01520.19430.1846-0.1499-0.07510.1581-0.0273-0.00220.15410.0140.196318.548814.492654.5803
53.8468-0.95781.45951.255-0.28071.80910.09520.1346-0.05840.0468-0.012-0.0540.11230.1435-0.09980.1396-0.0067-0.01240.0865-0.00290.120732.541515.715252.5333
62.0306-0.385-0.01881.3947-0.30240.88840.1202-0.1577-0.13340.1273-0.0362-0.03530.11470.0813-0.06130.1696-0.0183-0.02080.1614-0.00090.159334.304415.619260.3063
72.2666-0.68280.30061.6836-0.93671.94420.0833-0.01650.08640.117-0.038-0.0162-0.1720.069-0.03330.1764-0.02390.00330.1557-0.00930.139935.35728.840659.7036
81.1743-0.63811.00930.9878-0.89591.31360.0722-0.0129-0.05980.09510.00670.0235-0.00520.0055-0.08580.1574-0.0113-0.00650.15300.149536.332321.068458.3273
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 29:51 )A29 - 51
2X-RAY DIFFRACTION2( CHAIN A AND RESID 52:92 )A52 - 92
3X-RAY DIFFRACTION3( CHAIN A AND RESID 93:105 )A93 - 105
4X-RAY DIFFRACTION4( CHAIN A AND RESID 106:154 )A106 - 154
5X-RAY DIFFRACTION5( CHAIN A AND RESID 155:174 )A155 - 174
6X-RAY DIFFRACTION6( CHAIN A AND RESID 201:213 )A201 - 213
7X-RAY DIFFRACTION7( CHAIN A AND RESID 214:246 )A214 - 246
8X-RAY DIFFRACTION8( CHAIN A AND RESID 247:278 )A247 - 278

+
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