[English] 日本語
Yorodumi
- PDB-3v6l: Crystal Structure of caspase-6 inactivation mutation -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3v6l
TitleCrystal Structure of caspase-6 inactivation mutation
ComponentsCaspase-6Caspase 6
KeywordsHYDROLASE / Apoptotic protease / caspase domain
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 / pyroptosis ...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 / pyroptosis / Apoptotic cleavage of cellular proteins / 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 apoptotic process / cysteine-type endopeptidase activity / apoptotic process / proteolysis / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
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: 2.2 Å
AuthorsCao, Q. / Wang, X.J. / Liu, D.F. / Li, L.F. / Su, X.D.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Inhibitory mechanism of caspase-6 phosphorylation revealed by crystal structures, molecular dynamics simulations, and biochemical assays
Authors: Cao, Q. / Wang, X.J. / Liu, C.W. / Liu, D.F. / Li, L.F. / Gao, Y.Q. / Su, X.D.
History
DepositionDec 20, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 28, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2012Group: Database references / Structure summary
Revision 1.2Nov 8, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Caspase-6
B: Caspase-6


Theoretical massNumber of molelcules
Total (without water)65,1462
Polymers65,1462
Non-polymers00
Water4,972276
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-18 kcal/mol
Surface area19150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.350, 126.350, 165.820
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11B-411-

HOH

21B-468-

HOH

31B-484-

HOH

41B-498-

HOH

-
Components

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


Mass: 32573.166 Da / Num. of mol.: 2 / Fragment: UNP residues 21-293 / Mutation: S257E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP6 / Production host: Escherichia coli (E. coli) / References: UniProt: P55212, caspase-6
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 276 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsMUTAGENESIS. SUPPRESSION OF CASPASE-6 ACTIVATION.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 58.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: 0.1M MES, 10% PEG3350, 0.2M sodium chloride, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 28, 2011
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 39913 / Num. obs: 39913 / % possible obs: 99.1 % / Biso Wilson estimate: 30.33 Å2
Reflection shellResolution: 2.2→2.3 Å / Num. unique all: 4620 / % possible all: 93.7

-
Processing

Software
NameVersionClassification
XDSdata scaling
PHENIXmodel building
PHENIX(phenix.refine: 1.6.1_357)refinement
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NR2

3nr2


Resolution: 2.2→19.866 Å / Occupancy max: 1 / Occupancy min: 0.46 / FOM work R set: 0.8546 / SU ML: 0.25 / σ(F): 1.99 / Phase error: 20.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2016 2000 5.02 %RANDOM
Rwork0.1692 ---
obs0.1708 39831 99.12 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.743 Å2 / ksol: 0.327 e/Å3
Displacement parametersBiso max: 119.46 Å2 / Biso mean: 41.2819 Å2 / Biso min: 19.53 Å2
Baniso -1Baniso -2Baniso -3
1-7.6768 Å2-0 Å2-0 Å2
2--7.6768 Å20 Å2
3----15.3536 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19.866 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3768 0 0 276 4044
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083862
X-RAY DIFFRACTIONf_angle_d1.0525208
X-RAY DIFFRACTIONf_chiral_restr0.075571
X-RAY DIFFRACTIONf_plane_restr0.004662
X-RAY DIFFRACTIONf_dihedral_angle_d12.791385
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.27850.30381710.27753440361192
2.2785-2.36960.24032040.182137443948100
2.3696-2.47730.20522010.159537623963100
2.4773-2.60760.20071770.163137683945100
2.6076-2.77060.20892120.176437583970100
2.7706-2.98390.2491970.184537843981100
2.9839-3.28290.22691990.172737953994100
3.2829-3.75520.1652100.153738194029100
3.7552-4.72060.15322010.130338944095100
4.7206-19.86720.19982280.171240674295100
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)
11.2845-0.02210.33570.5407-0.10311.4784-0.0730.0035-0.0382-0.05980.1040.1132-0.285-0.5284-0.00010.20370.1486-0.01360.37860.00930.240810.308159.8111-15.0187
21.07160.04330.58180.5449-0.42361.2736-0.0026-0.0917-0.18280.00120.1568-0.03360.1586-0.45-0.02560.20250.07170.00130.36720.04360.273713.424746.7214-7.3924
31.1296-0.0799-0.22520.5835-0.06561.6649-0.1153-0.0011-0.0323-0.10220.0834-0.10420.29820.2304-00.28790.1336-0.00350.266-0.00050.237540.144241.6971-6.8798
40.6284-0.0925-0.09310.65330.34970.5685-0.01-0.05690.153-0.0950.11180.0492-0.1710.0509-00.2650.087-0.03380.2529-0.01590.246535.286956.0951-4.1
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and (resseq 31:166)A31 - 166
2X-RAY DIFFRACTION2chain A and (resseq 187:292)A187 - 292
3X-RAY DIFFRACTION3chain B and (resseq 31:166)B31 - 166
4X-RAY DIFFRACTION4chain B and (resseq 187:292)B187 - 292

+
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