[English] 日本語
Yorodumi
- PDB-3s70: Crystal structure of active caspase-6 bound with Ac-VEID-CHO solv... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3s70
TitleCrystal structure of active caspase-6 bound with Ac-VEID-CHO solved by As-SAD
Components
  • Caspase-6
  • aldehyde inhibitor Ac-VEID-CHO
KeywordsHYDROLASE/HYDROLASE INHIBITOR / caspase-6 / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


caspase-6 / Breakdown of the nuclear lamina / regulation of programmed cell death / positive regulation of necroptotic process / cellular response to staurosporine / cysteine-type endopeptidase activity involved in execution phase of apoptosis / cysteine-type endopeptidase activity involved in apoptotic process / hepatocyte apoptotic process / TP53 Regulates Transcription of Caspase Activators and Caspases / Apoptotic cleavage of cellular proteins ...caspase-6 / Breakdown of the nuclear lamina / regulation of programmed cell death / positive regulation of necroptotic process / cellular response to staurosporine / cysteine-type endopeptidase activity involved in execution phase of apoptosis / cysteine-type endopeptidase activity involved in apoptotic process / hepatocyte apoptotic process / TP53 Regulates Transcription of Caspase Activators and Caspases / Apoptotic cleavage of cellular proteins / pyroptotic inflammatory response / protein autoprocessing / intrinsic apoptotic signaling pathway by p53 class mediator / Caspase-mediated cleavage of cytoskeletal proteins / cysteine-type peptidase activity / epithelial cell differentiation / activation of innate immune response / positive regulation of neuron apoptotic process / positive regulation of apoptotic process / cysteine-type endopeptidase activity / apoptotic process / proteolysis / nucleoplasm / identical protein binding / 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
N-acetyl-L-valyl-L-alpha-glutamyl-N-[(2S)-1-carboxy-3-oxopropan-2-yl]-L-isoleucinamide / ACETATE ION / CACODYLATE ION / Caspase-6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.625 Å
AuthorsSu, X.-D. / Liu, X. / Wang, X.-J.
CitationJournal: Plos One / Year: 2011
Title: Get phases from arsenic anomalous scattering: de novo SAD phasing of two protein structures crystallized in cacodylate buffer
Authors: Liu, X. / Zhang, H. / Wang, X.-J. / Li, L.-F. / Su, X.-D.
History
DepositionMay 26, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2012Group: Other

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Caspase-6
B: aldehyde inhibitor Ac-VEID-CHO
C: Caspase-6
D: aldehyde inhibitor Ac-VEID-CHO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,25814
Polymers65,0784
Non-polymers1,17910
Water12,016667
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6910 Å2
ΔGint-37 kcal/mol
Surface area19150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.390, 89.450, 61.130
Angle α, β, γ (deg.)90.00, 111.70, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein / Protein/peptide , 2 types, 4 molecules ACBD

#1: Protein Caspase-6 / CASP-6 / Apoptotic protease Mch-2 / Caspase-6 subunit p18 / Caspase-6 subunit p11


Mass: 32054.637 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP6 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA(DE3) / References: UniProt: P55212, caspase-6
#2: Protein/peptide aldehyde inhibitor Ac-VEID-CHO


Type: Polypeptide / Class: Inhibitor / Mass: 484.543 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemically synthesized
References: N-acetyl-L-valyl-L-alpha-glutamyl-N-[(2S)-1-carboxy-3-oxopropan-2-yl]-L-isoleucinamide

-
Non-polymers , 4 types, 677 molecules

#3: Chemical
ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6AsO2
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 667 / 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: 2.16 Å3/Da / Density % sol: 43.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20%(w/v) PEG 8000, 0.2M magnesium acetate, 0.1M sodium cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 22, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.625→25.3 Å / Num. all: 69470 / Num. obs: 68845 / % possible obs: 99.1 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 2 / Biso Wilson estimate: 10.53 Å2

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.625→19.481 Å / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.9054 / SU ML: 0.18 / σ(F): 1.35 / Phase error: 17.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1939 3483 5.06 %
Rwork0.1637 --
obs0.1652 68845 98.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.715 Å2 / ksol: 0.348 e/Å3
Displacement parametersBiso max: 57.07 Å2 / Biso mean: 13.5034 Å2 / Biso min: 2.16 Å2
Baniso -1Baniso -2Baniso -3
1--1.835 Å2-0 Å21.1745 Å2
2--2.249 Å20 Å2
3----0.414 Å2
Refinement stepCycle: LAST / Resolution: 1.625→19.481 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3892 0 29 667 4588
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064069
X-RAY DIFFRACTIONf_angle_d1.0445490
X-RAY DIFFRACTIONf_chiral_restr0.074595
X-RAY DIFFRACTIONf_plane_restr0.004704
X-RAY DIFFRACTIONf_dihedral_angle_d14.211465
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.625-1.64730.25561240.22282628275299
1.6473-1.67080.2231330.20732630276399
1.6708-1.69570.24841460.20192609275599
1.6957-1.72220.23981440.20612640278499
1.7222-1.75040.23131350.1922595273099
1.7504-1.78060.22581290.176526502779100
1.7806-1.81290.19921520.17472594274699
1.8129-1.84780.18381470.162626402787100
1.8478-1.88550.18731290.16292591272099
1.8855-1.92640.20731540.16442615276999
1.9264-1.97120.2111340.16182643277799
1.9712-2.02040.18671320.15142600273299
2.0204-2.0750.16721260.14892635276199
2.075-2.1360.17081230.14342629275299
2.136-2.20480.17491390.14732613275299
2.2048-2.28350.1941590.15292583274299
2.2835-2.37480.18871380.14462623276199
2.3748-2.48270.18551430.14922595273899
2.4827-2.61330.18281530.14982589274299
2.6133-2.77660.2021440.15632637278199
2.7766-2.99030.20771550.15432589274499
2.9903-3.28990.17671300.15182637276799
3.2899-3.7630.18621450.14152574271998
3.763-4.72970.13861290.12542623275298
4.7297-19.48220.15391400.1512600274096
Refinement TLS params.Method: refined / Origin x: -19.7247 Å / Origin y: 48.8324 Å / Origin z: 48.7457 Å
111213212223313233
T0.0216 Å20.002 Å2-0.0036 Å2-0.0215 Å20.0045 Å2--0.0264 Å2
L0.1651 °2-0.0126 °2-0.1024 °2-0.1533 °20.0307 °2--0.2935 °2
S-0.0072 Å °-0.0145 Å °0.0102 Å °0.0011 Å °0.007 Å °0.0037 Å °0.0023 Å °-0.0017 Å °-0.0011 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA31 - 292
2X-RAY DIFFRACTION1allB0 - 4
3X-RAY DIFFRACTION1allC31 - 291
4X-RAY DIFFRACTION1allD0 - 4
5X-RAY DIFFRACTION1allC - A1 - 681
6X-RAY DIFFRACTION1allC1 - 8
7X-RAY DIFFRACTION1allA1
8X-RAY DIFFRACTION1allA1 - 302

+
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