[English] 日本語
Yorodumi
- PDB-4ps0: Caspase-8 specific unnatural amino acid peptides -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ps0
TitleCaspase-8 specific unnatural amino acid peptides
Components
  • (BAL)LQ(HYP)(1U8) PEPTIDE
  • Caspase-3
KeywordsHYDROLASE/HYDROLASE INHIBITOR / PROTEASE / 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 / cyclin-dependent protein serine/threonine kinase inhibitor activity / cellular response to staurosporine / 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 / execution phase of apoptosis / negative regulation of cytokine production / epithelial cell apoptotic process / platelet formation / 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 / Caspase-mediated cleavage of cytoskeletal proteins / response to amino acid / 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 / protein catabolic process / regulation of protein stability / response to hydrogen peroxide / neuron differentiation / protein processing / response to wounding / positive regulation of neuron apoptotic process / response to estradiol / peptidase activity / heart development / neuron apoptotic process / protease binding / response to lipopolysaccharide / aspartic-type endopeptidase activity / learning or memory / response to hypoxia / response to xenobiotic stimulus / cysteine-type endopeptidase activity / neuronal cell body / apoptotic process / DNA damage response / protein-containing complex binding / proteolysis / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
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 ...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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsWolan, D.W. / Vickers, C.J. / Gonzalez-Paez, G.E.
CitationJournal: Acs Chem.Biol. / Year: 2014
Title: Selective inhibition of initiator versus executioner caspases using small peptides containing unnatural amino acids.
Authors: Vickers, C.J. / Gonzalez-Paez, G.E. / Litwin, K.M. / Umotoy, J.C. / Coutsias, E.A. / Wolan, D.W.
History
DepositionMar 6, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Caspase-3
B: Caspase-3
C: (BAL)LQ(HYP)(1U8) PEPTIDE
D: (BAL)LQ(HYP)(1U8) PEPTIDE


Theoretical massNumber of molelcules
Total (without water)66,8544
Polymers66,8544
Non-polymers00
Water8,575476
1
A: Caspase-3
C: (BAL)LQ(HYP)(1U8) PEPTIDE


Theoretical massNumber of molelcules
Total (without water)33,4272
Polymers33,4272
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Caspase-3
D: (BAL)LQ(HYP)(1U8) PEPTIDE


Theoretical massNumber of molelcules
Total (without water)33,4272
Polymers33,4272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.198, 69.189, 93.143
Angle α, β, γ (deg.)90.00, 102.01, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Caspase-3 / CASP-3 / Apopain / Cysteine protease CPP32 / CPP-32 / Protein Yama / SREBP cleavage activity 1 / ...CASP-3 / Apopain / Cysteine protease CPP32 / CPP-32 / Protein Yama / SREBP cleavage activity 1 / SCA-1 / Caspase-3 subunit p17 / Caspase-3 subunit p12


Mass: 32722.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP3, CASPASE-3 CPP32, CPP32 / Plasmid: pet23b / Production host: Escherichia coli (E. coli) / Strain (production host): bl21(de3)plyss / References: UniProt: P42574, caspase-3
#2: Protein/peptide (BAL)LQ(HYP)(1U8) PEPTIDE


Mass: 704.767 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 476 / 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: 2.37 Å3/Da / Density % sol: 48.02 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.15 M sodium citrate, pH 5.5, 14% PEG 6000, 0.3% sodium azide, 0.01 M DTT, VAPOR DIFFUSION, SITTING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 3, 2014 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 1.63→50 Å / Num. all: 76222 / Num. obs: 76222 / % possible obs: 98.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1

-
Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 477E

477e


Resolution: 1.63→40.042 Å / SU ML: 0.15 / σ(F): 1.34 / Phase error: 18.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1792 3836 5.04 %random
Rwork0.153 ---
obs0.1543 76158 97.75 %-
all-76158 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.63→40.042 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3938 0 0 476 4414
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0164058
X-RAY DIFFRACTIONf_angle_d1.5535471
X-RAY DIFFRACTIONf_dihedral_angle_d11.9621511
X-RAY DIFFRACTIONf_chiral_restr0.091595
X-RAY DIFFRACTIONf_plane_restr0.008707
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6298-1.65040.26381260.24882537X-RAY DIFFRACTION91
1.6504-1.67220.23031270.21992688X-RAY DIFFRACTION98
1.6722-1.69510.28281380.21922649X-RAY DIFFRACTION99
1.6951-1.71930.24971440.21272712X-RAY DIFFRACTION99
1.7193-1.74490.28561350.20092692X-RAY DIFFRACTION98
1.7449-1.77220.21471560.17942655X-RAY DIFFRACTION98
1.7722-1.80130.20481320.17632651X-RAY DIFFRACTION98
1.8013-1.83230.21681350.16862644X-RAY DIFFRACTION97
1.8323-1.86560.21631450.17542595X-RAY DIFFRACTION94
1.8656-1.90150.22431290.18182658X-RAY DIFFRACTION97
1.9015-1.94030.21151460.19432715X-RAY DIFFRACTION98
1.9403-1.98250.19481400.15312664X-RAY DIFFRACTION99
1.9825-2.02860.17511300.14642736X-RAY DIFFRACTION99
2.0286-2.07940.21191370.16242670X-RAY DIFFRACTION98
2.0794-2.13560.18191420.14812697X-RAY DIFFRACTION99
2.1356-2.19840.19531420.14622708X-RAY DIFFRACTION99
2.1984-2.26940.171700.15512651X-RAY DIFFRACTION98
2.2694-2.35050.16031600.14072608X-RAY DIFFRACTION97
2.3505-2.44460.18051310.14262661X-RAY DIFFRACTION97
2.4446-2.55580.16361510.14662713X-RAY DIFFRACTION99
2.5558-2.69050.18271430.1512706X-RAY DIFFRACTION99
2.6905-2.85910.18771690.15612695X-RAY DIFFRACTION99
2.8591-3.07970.18481600.15242679X-RAY DIFFRACTION99
3.0797-3.38950.15951280.14872719X-RAY DIFFRACTION97
3.3895-3.87970.14191490.13592706X-RAY DIFFRACTION98
3.8797-4.88660.14751240.1232756X-RAY DIFFRACTION99
4.8866-40.05390.17691470.16012757X-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)
14.9083-1.0990.46551.9753-0.10251.71690.07080.2002-0.28140.05340.00950.0960.1545-0.0179-0.03060.113-0.020.03120.07490.0020.1176-12.0775-12.7685-33.7671
26.7283-3.18310.62483.727-0.1111.75740.02130.1832-0.1897-0.15570.03280.23520.0562-0.1879-0.01020.1314-0.039-0.0050.1505-0.0020.116-16.6936-5.9275-43.373
35.3458-0.51960.41321.3615-0.2191.12570.00440.0305-0.38110.06660.04360.15620.1824-0.1913-0.04620.1908-0.039-0.01040.1544-0.02270.2344-19.4915-17.1667-34.6989
42.7439-1.05660.52651.6893-0.31661.58440.0139-0.1691-0.23750.15460.05180.11180.1812-0.1902-0.07360.1657-0.03030.00360.15840.01110.2025-16.7509-13.9755-27.0752
51.3776-0.06370.45571.7868-0.5291.7348-0.0071-0.07370.01230.13120.0393-0.0221-0.0312-0.0482-0.03690.09750.00250.02960.13410.00590.119-14.0671-0.6494-26.3547
61.2069-1.01660.38382.68030.0151.98810.02410.12580.0524-0.0740.0221-0.1656-0.02810.1932-0.03710.1421-0.020.01930.18820.00830.1711-4.43142.1262-36.3979
71.656-1.11331.29022.5324-1.43221.87960.02770.13020.0237-0.00050.0067-0.0578-0.04690.0657-0.04720.133-0.01670.02640.17680.00210.1479-10.42993.2141-33.0978
82.98021.3465-1.78432.1679-1.31974.5110.1987-0.40890.29360.2801-0.08920.0589-0.59440.2982-0.13310.20750.0175-0.02510.1517-0.04720.1772-4.083713.9576-11.1861
95.1822.4276-3.27132.8096-1.68884.16850.0524-0.2611-0.06780.3552-0.0283-0.0654-0.10590.0389-0.04950.32150.0115-0.04360.2606-0.040.1629-2.20067.2103-0.9342
101.91440.0052-1.58930.9577-0.11472.89780.0572-0.15860.32710.1719-0.02040.1315-0.494-0.1853-0.04320.3920.0162-0.00690.2889-0.09590.2844-9.057718.524-6.4608
111.60980.513-0.15631.9666-0.53932.3904-0.0421-0.16050.20340.07530.05190.1837-0.3884-0.2158-0.04980.27360.04320.00910.1988-0.05160.2077-11.938115.3937-13.8929
121.3902-0.32240.2842.0573-0.7231.9077-0.0202-0.1593-0.03250.09970.026-0.0099-0.0307-0.0259-0.00170.13620.01130.0090.1606-0.01040.134-10.49821.796-15.3292
131.75660.96190.01843.5666-1.05183.76610.0101-0.067-0.10990.13730.0327-0.267-0.02160.2774-0.02070.17560.0195-0.03540.2326-0.01090.19563.0187-1.3713-13.916
140.47350.0574-0.24512.3702-3.17255.96340.0186-0.1879-0.10720.10080.1010.0690.2253-0.1283-0.12530.24690.01-0.02340.23960.04960.2088-9.1699-10.6341-5.2315
156.5279-0.27722.1685.7352-0.67298.54710.03360.18670.13470.0890.0804-0.296-0.3460.86-0.08690.1891-0.0260.00540.1651-0.03340.14280.87138.8403-24.6263
168.28526.63870.52655.32360.36652.18750.0970.72980.1149-0.3470.10210.2983-0.3325-0.1384-0.18930.20630.0296-0.01750.27620.03640.2408-24.71347.1417-42.3672
175.2628-3.8504-4.01522.82382.93713.06310.0767-0.5322-0.12271.34410.1708-0.62150.81850.6667-0.24150.51010.0537-0.04560.48040.07950.2211-9.6351-5.69953.246
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 34:59 )A34 - 59
2X-RAY DIFFRACTION2( CHAIN A AND RESID 60:80 )A60 - 80
3X-RAY DIFFRACTION3( CHAIN A AND RESID 81:105 )A81 - 105
4X-RAY DIFFRACTION4( CHAIN A AND RESID 106:155 )A106 - 155
5X-RAY DIFFRACTION5( CHAIN A AND RESID 156:213 )A156 - 213
6X-RAY DIFFRACTION6( CHAIN A AND RESID 214:246 )A214 - 246
7X-RAY DIFFRACTION7( CHAIN A AND RESID 247:279 )A247 - 279
8X-RAY DIFFRACTION8( CHAIN B AND RESID 34:59 )B34 - 59
9X-RAY DIFFRACTION9( CHAIN B AND RESID 60:80 )B60 - 80
10X-RAY DIFFRACTION10( CHAIN B AND RESID 81:105 )B81 - 105
11X-RAY DIFFRACTION11( CHAIN B AND RESID 106:154 )B106 - 154
12X-RAY DIFFRACTION12( CHAIN B AND RESID 155:213 )B155 - 213
13X-RAY DIFFRACTION13( CHAIN B AND RESID 214:246 )B214 - 246
14X-RAY DIFFRACTION14( CHAIN B AND RESID 247:267 )B247 - 267
15X-RAY DIFFRACTION15( CHAIN B AND RESID 268:276 )B268 - 276
16X-RAY DIFFRACTION16( CHAIN C AND RESID 402:403 )C402 - 403
17X-RAY DIFFRACTION17( CHAIN D AND RESID 402:403 )D402 - 403

+
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://pdbjlvh1.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