[English] 日本語
Yorodumi
- PDB-7a6r: Structure of 14-3-3 gamma in complex with DAPK2 peptide containin... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7a6r
TitleStructure of 14-3-3 gamma in complex with DAPK2 peptide containing the 14-3-3 binding motif
Components
  • 14-3-3 protein gamma
  • DAPK2 C-terminal peptide
KeywordsSIGNALING PROTEIN / 14-3-3 protein / DAPK2 / kinase / complex / phosphorylation
Function / homology
Function and homology information


regulation of neuron differentiation / protein kinase C inhibitor activity / Regulation of localization of FOXO transcription factors / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / regulation of signal transduction / protein targeting / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / cellular response to glucose starvation / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex ...regulation of neuron differentiation / protein kinase C inhibitor activity / Regulation of localization of FOXO transcription factors / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / regulation of signal transduction / protein targeting / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / cellular response to glucose starvation / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / negative regulation of TORC1 signaling / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / insulin-like growth factor receptor binding / protein sequestering activity / AURKA Activation by TPX2 / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / protein kinase C binding / negative regulation of protein kinase activity / regulation of synaptic plasticity / receptor tyrosine kinase binding / cellular response to insulin stimulus / Regulation of PLK1 Activity at G2/M Transition / presynapse / protein domain specific binding / focal adhesion / signal transduction / RNA binding / extracellular exosome / membrane / identical protein binding / cytosol / cytoplasm
Similarity search - Function
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
Similarity search - Domain/homology
14-3-3 protein gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsHorvath, M. / Obsilova, V. / Obsil, T.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Grant Agency of the Czech Republic19-00121S Czech Republic
CitationJournal: Commun Biol / Year: 2021
Title: 14-3-3 proteins inactivate DAPK2 by promoting its dimerization and protecting key regulatory phosphosites.
Authors: Horvath, M. / Petrvalska, O. / Herman, P. / Obsilova, V. / Obsil, T.
History
DepositionAug 26, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 22, 2021Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_scat_Cromer_Mann_a5 / _atom_type.pdbx_scat_Cromer_Mann_b5

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 14-3-3 protein gamma
B: 14-3-3 protein gamma
C: 14-3-3 protein gamma
D: 14-3-3 protein gamma
E: DAPK2 C-terminal peptide
F: DAPK2 C-terminal peptide
G: DAPK2 C-terminal peptide
L: DAPK2 C-terminal peptide


Theoretical massNumber of molelcules
Total (without water)112,5268
Polymers112,5268
Non-polymers00
Water61334
1
A: 14-3-3 protein gamma
C: 14-3-3 protein gamma
E: DAPK2 C-terminal peptide
G: DAPK2 C-terminal peptide


Theoretical massNumber of molelcules
Total (without water)56,2634
Polymers56,2634
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-21 kcal/mol
Surface area22570 Å2
MethodPISA
2
B: 14-3-3 protein gamma
F: DAPK2 C-terminal peptide

D: 14-3-3 protein gamma
L: DAPK2 C-terminal peptide


Theoretical massNumber of molelcules
Total (without water)56,2634
Polymers56,2634
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_556-x+y,-x,z+11
Buried area3760 Å2
ΔGint-20 kcal/mol
Surface area22220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)205.620, 205.620, 74.091
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3

-
Components

#1: Protein
14-3-3 protein gamma / Protein kinase C inhibitor protein 1 / KCIP-1


Mass: 27199.625 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YWHAG / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61981
#2: Protein/peptide
DAPK2 C-terminal peptide


Mass: 931.914 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.08 %
Crystal growTemperature: 290.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: HEPES, MgCl2, PEG400, hexafluoro-2-propanol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54187 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Mar 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 2.7→30.64 Å / Num. obs: 31982 / % possible obs: 99.7 % / Redundancy: 4.39 % / Biso Wilson estimate: 47.96 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.084 / Rrim(I) all: 0.096 / Net I/σ(I): 13.5
Reflection shellResolution: 2.7→2.797 Å / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 3165 / CC1/2: 0.846 / Rrim(I) all: 0.539

-
Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B05

2b05


Resolution: 2.7→30.64 Å / SU ML: 0.4637 / Cross valid method: FREE R-VALUE / σ(F): 0.93 / Phase error: 32.6063
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2754 3015 4.94 %Random selection
Rwork0.2367 57964 --
obs0.2386 31982 95.14 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49 Å2
Refinement stepCycle: LAST / Resolution: 2.7→30.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7375 0 0 34 7409
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00197480
X-RAY DIFFRACTIONf_angle_d0.403910128
X-RAY DIFFRACTIONf_chiral_restr0.03141154
X-RAY DIFFRACTIONf_plane_restr0.00281305
X-RAY DIFFRACTIONf_dihedral_angle_d16.4172762
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.740.42791320.3912379X-RAY DIFFRACTION85.7
2.74-2.790.38251210.36032361X-RAY DIFFRACTION87.39
2.79-2.840.39581210.32132493X-RAY DIFFRACTION87.9
2.84-2.890.38441250.33412461X-RAY DIFFRACTION89.36
2.89-2.940.40491400.32192511X-RAY DIFFRACTION90.66
2.94-30.48161300.33382542X-RAY DIFFRACTION91.95
3-3.070.3971310.31462566X-RAY DIFFRACTION92.94
3.07-3.140.36811360.32892635X-RAY DIFFRACTION95.09
3.14-3.220.37111410.29582735X-RAY DIFFRACTION96.84
3.22-3.30.33151430.26942645X-RAY DIFFRACTION97.69
3.3-3.40.34291450.27912686X-RAY DIFFRACTION97.42
3.4-3.510.30561410.25682696X-RAY DIFFRACTION96.96
3.51-3.640.29951490.2332687X-RAY DIFFRACTION97.86
3.64-3.780.2581360.23822777X-RAY DIFFRACTION97.88
3.78-3.950.25831260.21322663X-RAY DIFFRACTION97.59
3.95-4.160.25411360.20472742X-RAY DIFFRACTION98.02
4.16-4.420.22881380.19622705X-RAY DIFFRACTION98.37
4.42-4.760.22891480.18942765X-RAY DIFFRACTION98.68
4.76-5.240.27861390.19752707X-RAY DIFFRACTION98.75
5.24-5.990.231400.23422742X-RAY DIFFRACTION99.17
5.99-7.520.20481470.20982762X-RAY DIFFRACTION99.08
7.53-30.640.1511500.15922704X-RAY DIFFRACTION97.87

+
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