[English] 日本語
Yorodumi
- PDB-6y8d: 14-3-3 Sigma in complex with phosphorylated caspase{pS164} peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6y8d
Title14-3-3 Sigma in complex with phosphorylated caspase{pS164} peptide
Components
  • 14-3-3 protein sigma
  • VAL-GLU-HIS-SEP-LEU-ASP-ASN-LYS
KeywordsPROTEIN BINDING / 14-3-3 / caspase{pS164} / complex / protein / protein-protein interactions
Function / homology
Function and homology information


caspase-2 / endopeptidase complex / NADE modulates death signalling / neural retina development / luteolysis / execution phase of apoptosis / TP53 Regulates Transcription of Caspase Activators and Caspases / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation ...caspase-2 / endopeptidase complex / NADE modulates death signalling / neural retina development / luteolysis / execution phase of apoptosis / TP53 Regulates Transcription of Caspase Activators and Caspases / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / regulation of cell-cell adhesion / cAMP/PKA signal transduction / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / Activation of BAD and translocation to mitochondria / phosphoserine residue binding / negative regulation of keratinocyte proliferation / establishment of skin barrier / ectopic germ cell programmed cell death / negative regulation of protein localization to plasma membrane / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / negative regulation of protein kinase activity / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / positive regulation of protein localization / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of cell adhesion / protein sequestering activity / protein export from nucleus / negative regulation of innate immune response / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / positive regulation of protein export from nucleus / positive regulation of apoptotic signaling pathway / stem cell proliferation / TP53 Regulates Metabolic Genes / Translocation of SLC2A4 (GLUT4) to the plasma membrane / DNA damage response, signal transduction by p53 class mediator / apoptotic signaling pathway / cellular response to mechanical stimulus / NOD1/2 Signaling Pathway / protein processing / intrinsic apoptotic signaling pathway in response to DNA damage / intracellular protein localization / positive regulation of neuron apoptotic process / regulation of protein localization / positive regulation of cell growth / regulation of cell cycle / positive regulation of apoptotic process / cadherin binding / protein domain specific binding / cysteine-type endopeptidase activity / apoptotic process / DNA damage response / protein kinase binding / negative regulation of apoptotic process / nucleolus / enzyme binding / negative regulation of transcription by RNA polymerase II / signal transduction / extracellular space / extracellular exosome / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Caspase-2 / Caspase recruitment domain / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Peptidase C14 family / 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-2 / Caspase recruitment domain / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Peptidase C14 family / 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 / 14-3-3 protein sigma / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein / Death-like domain superfamily
Similarity search - Domain/homology
14-3-3 protein sigma / Caspase-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsBallone, A. / Lau, R.A. / Zweipfenning, F.P.A. / Ottmann, C.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Marie Sklodowska-Curie Actions, FragNET ITN675179 Netherlands
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2020
Title: A new soaking procedure for X-ray crystallographic structural determination of protein-peptide complexes.
Authors: Ballone, A. / Lau, R.A. / Zweipfenning, F.P.A. / Ottmann, C.
History
DepositionMar 4, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 14-3-3 protein sigma
B: VAL-GLU-HIS-SEP-LEU-ASP-ASN-LYS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3827
Polymers29,2502
Non-polymers1335
Water6,323351
1
A: 14-3-3 protein sigma
B: VAL-GLU-HIS-SEP-LEU-ASP-ASN-LYS
hetero molecules

A: 14-3-3 protein sigma
B: VAL-GLU-HIS-SEP-LEU-ASP-ASN-LYS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,76414
Polymers58,4994
Non-polymers26510
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4350 Å2
ΔGint-72 kcal/mol
Surface area22680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.575, 112.713, 62.661
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-304-

MG

21A-740-

HOH

-
Components

#1: Protein 14-3-3 protein sigma / Epithelial cell marker protein 1 / Stratifin


Mass: 28226.518 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SFN, HME1 / Production host: Escherichia coli (E. coli) / References: UniProt: P31947
#2: Protein/peptide VAL-GLU-HIS-SEP-LEU-ASP-ASN-LYS


Mass: 1022.992 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P42575*PLUS
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 28% PEG400, 5% glycerol, 0.2M CaCl, 0.1M HEPES pH 7.5, 2mM BME

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.973 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.973 Å / Relative weight: 1
ReflectionResolution: 1.51→29.41 Å / Num. obs: 45100 / % possible obs: 97.6 % / Redundancy: 11.4 % / Biso Wilson estimate: 15.38 Å2 / CC1/2: 1 / Net I/σ(I): 64.3
Reflection shellResolution: 1.51→1.54 Å / Num. unique obs: 1757 / CC1/2: 0.986

-
Processing

Software
NameVersionClassification
REFMACv5.5refinement
PHENIX1.16_3549refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3lw1

3lw1


Resolution: 1.51→29.41 Å / SU ML: 0.1182 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.1446
RfactorNum. reflection% reflection
Rfree0.1972 2224 4.93 %
Rwork0.1746 --
obs0.1757 45077 97.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 21.06 Å2
Refinement stepCycle: LAST / Resolution: 1.51→29.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1798 0 42 351 2191
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00561982
X-RAY DIFFRACTIONf_angle_d0.79772711
X-RAY DIFFRACTIONf_chiral_restr0.0413308
X-RAY DIFFRACTIONf_plane_restr0.0049354
X-RAY DIFFRACTIONf_dihedral_angle_d5.11351637
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.51-1.540.20651100.17612154X-RAY DIFFRACTION79.05
1.54-1.580.17661240.17612400X-RAY DIFFRACTION88.59
1.58-1.620.19881480.17042565X-RAY DIFFRACTION94.86
1.62-1.660.22341600.17692638X-RAY DIFFRACTION98.31
1.66-1.710.23141360.17392714X-RAY DIFFRACTION99.93
1.71-1.770.19091360.18782724X-RAY DIFFRACTION100
1.77-1.830.24151290.17752733X-RAY DIFFRACTION100
1.83-1.90.21631180.18582750X-RAY DIFFRACTION100
1.9-1.990.20051380.18612734X-RAY DIFFRACTION100
1.99-2.090.21841370.18072738X-RAY DIFFRACTION100
2.09-2.220.18731490.17092733X-RAY DIFFRACTION100
2.22-2.40.17541520.16982734X-RAY DIFFRACTION99.97
2.4-2.640.20821480.17722754X-RAY DIFFRACTION100
2.64-3.020.20821480.17982768X-RAY DIFFRACTION100
3.02-3.80.17661310.16482808X-RAY DIFFRACTION100
3.8-29.410.1931600.17222906X-RAY DIFFRACTION99.97

+
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