[English] 日本語
Yorodumi
- PDB-2wh0: Recognition of an intrachain tandem 14-3-3 binding site within pr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2wh0
TitleRecognition of an intrachain tandem 14-3-3 binding site within protein kinase C epsilon
Components
  • 14-3-3 PROTEIN ZETA/DELTA
  • PROTEIN KINASE C EPSILON TYPE, NPKC-EPSILON
KeywordsSIGNALING PROTEIN / TANDEM BINDING / PHOSPHOPROTEIN / 14-3-3 / CYTOPLASM / ACETYLATION / PKC EPSILON
Function / homology
Function and homology information


ethanol binding / TRAM-dependent toll-like receptor 4 signaling pathway / negative regulation of sodium ion transmembrane transport / positive regulation of mucus secretion / diacylglycerol-dependent, calcium-independent serine/threonine kinase activity / toxin catabolic process / DAG and IP3 signaling / positive regulation of lipid catabolic process / protein kinase C / synaptic target recognition ...ethanol binding / TRAM-dependent toll-like receptor 4 signaling pathway / negative regulation of sodium ion transmembrane transport / positive regulation of mucus secretion / diacylglycerol-dependent, calcium-independent serine/threonine kinase activity / toxin catabolic process / DAG and IP3 signaling / positive regulation of lipid catabolic process / protein kinase C / synaptic target recognition / diacylglycerol-dependent serine/threonine kinase activity / mucus secretion / Golgi reassembly / Effects of PIP2 hydrolysis / NOTCH4 Activation and Transmission of Signal to the Nucleus / regulation of insulin secretion involved in cellular response to glucose stimulus / establishment of Golgi localization / respiratory system process / tube formation / regulation of synapse maturation / intermediate filament cytoskeleton / regulation of release of sequestered calcium ion into cytosol / Rap1 signalling / macrophage activation involved in immune response / negative regulation of protein localization to nucleus / positive regulation of cell-substrate adhesion / positive regulation of fibroblast migration / insulin secretion / KSRP (KHSRP) binds and destabilizes mRNA / response to morphine / GP1b-IX-V activation signalling / positive regulation of wound healing / positive regulation of cytokinesis / synaptic transmission, GABAergic / cell-substrate adhesion / positive regulation of actin filament polymerization / Fc-gamma receptor signaling pathway involved in phagocytosis / locomotory exploration behavior / cellular response to ethanol / signaling receptor activator activity / Interleukin-3, Interleukin-5 and GM-CSF signaling / Regulation of localization of FOXO transcription factors / positive regulation of epithelial cell migration / actin monomer binding / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / Role of phospholipids in phagocytosis / xenobiotic catabolic process / regulation of ERK1 and ERK2 cascade / protein targeting / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / cellular response to glucose starvation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / positive regulation of superoxide anion generation / RHO GTPases activate PKNs / negative regulation of TORC1 signaling / 14-3-3 protein binding / ERK1 and ERK2 cascade / negative regulation of protein ubiquitination / Transcriptional and post-translational regulation of MITF-M expression and activity / SHC1 events in ERBB2 signaling / lung development / protein sequestering activity / negative regulation of innate immune response / lipopolysaccharide-mediated signaling pathway / hippocampal mossy fiber to CA3 synapse / positive regulation of synaptic transmission, GABAergic / cell periphery / TP53 Regulates Metabolic Genes / positive regulation of protein localization to plasma membrane / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Deactivation of the beta-catenin transactivating complex / enzyme activator activity / establishment of localization in cell / Negative regulation of NOTCH4 signaling / positive regulation of insulin secretion / peptidyl-serine phosphorylation / regulation of protein stability / G alpha (z) signalling events / intracellular protein localization / melanosome / cellular response to prostaglandin E stimulus / MAPK cascade / angiogenesis / protein phosphatase binding / blood microparticle / cellular response to hypoxia / vesicle / DNA-binding transcription factor binding / transmembrane transporter binding / protein phosphorylation / positive regulation of canonical NF-kappaB signal transduction / protein kinase activity / positive regulation of MAPK cascade / intracellular signal transduction / cadherin binding / protein domain specific binding / cell division / protein serine kinase activity
Similarity search - Function
Protein kinase C, epsilon / Novel protein kinase C epsilon, catalytic domain / Protein kinase C, delta/epsilon/eta/theta types / Protein kinase, C-terminal / Protein kinase C terminal domain / Diacylglycerol/phorbol-ester binding / 14-3-3 domain / Delta-Endotoxin; domain 1 / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. ...Protein kinase C, epsilon / Novel protein kinase C epsilon, catalytic domain / Protein kinase C, delta/epsilon/eta/theta types / Protein kinase, C-terminal / Protein kinase C terminal domain / Diacylglycerol/phorbol-ester binding / 14-3-3 domain / Delta-Endotoxin; domain 1 / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / Protein kinase C conserved region 2 (CalB) / C2 domain / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / C2 domain / C2 domain profile. / C1-like domain superfamily / 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 / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / C2 domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / 14-3-3 protein zeta/delta / Protein kinase C epsilon type
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsKostelecky, B. / Saurin, A.T. / Purkiss, A. / Parker, P.J. / McDonald, N.Q.
CitationJournal: Embo Rep. / Year: 2009
Title: Recognition of an Intra-Chain Tandem 14-3-3 Binding Site within Pkc Epsilon.
Authors: Kostelecky, B. / Saurin, A.T. / Purkiss, A. / Parker, P.J. / Mcdonald, N.Q.
History
DepositionApr 28, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 14-3-3 PROTEIN ZETA/DELTA
B: 14-3-3 PROTEIN ZETA/DELTA
C: 14-3-3 PROTEIN ZETA/DELTA
D: 14-3-3 PROTEIN ZETA/DELTA
Q: PROTEIN KINASE C EPSILON TYPE, NPKC-EPSILON
R: PROTEIN KINASE C EPSILON TYPE, NPKC-EPSILON
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,7568
Polymers118,5666
Non-polymers1902
Water1,15364
1
A: 14-3-3 PROTEIN ZETA/DELTA
B: 14-3-3 PROTEIN ZETA/DELTA
Q: PROTEIN KINASE C EPSILON TYPE, NPKC-EPSILON
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4334
Polymers59,2833
Non-polymers1501
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3810 Å2
ΔGint-20.45 kcal/mol
Surface area20590 Å2
MethodPISA
2
C: 14-3-3 PROTEIN ZETA/DELTA
D: 14-3-3 PROTEIN ZETA/DELTA
R: PROTEIN KINASE C EPSILON TYPE, NPKC-EPSILON
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3234
Polymers59,2833
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-33.8 kcal/mol
Surface area21250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.130, 78.160, 108.520
Angle α, β, γ (deg.)90.00, 90.10, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.994832, -0.101326, -0.006474), (-0.101381, 0.987854, 0.117757), (-0.005537, 0.117805, -0.993021)67.6781, -0.59923, 65.4697
2given(0.999803, 0.019824, -0.001291), (0.019829, -0.999796, 0.00378), (-0.001216, -0.003805, -0.999992)-39.6941, 10.0708, 54.3752
3given(-0.996404, 0.084209, 0.0094), (-0.084678, -0.985668, -0.145905), (-0.003022, -0.146177, 0.989254)105.66, 20.6159, 13.6988

-
Components

#1: Protein
14-3-3 PROTEIN ZETA/DELTA / 14-3-3 ZETA / KCIP-1 / PROTEIN KINASE C INHIBITOR PROTEIN 1


Mass: 27777.092 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PACYC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P63104
#2: Protein/peptide PROTEIN KINASE C EPSILON TYPE, NPKC-EPSILON / PKCEV3


Mass: 3728.884 Da / Num. of mol.: 2 / Fragment: PKC EPSILON V3-DERIVED PEPTIDE, RESIDUES 342-372 / Source method: obtained synthetically / Details: SYNTHETIC FRAGMENT OF PKC EPSILON V3 REGION / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q02156, protein kinase C
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O
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: 52.3 % / Description: NONE
Crystal growpH: 7.4
Details: 16 MG/ML PROTEIN 9% (W/V) POLYETHYLENE GLYCOL 3350, 25 MM CALCIUM ACETATE, 25 MM SODIUM FLUORIDE, pH 7.4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 13, 2008 / Details: OSMIC MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.441
ReflectionResolution: 2.25→24.5 Å / Num. obs: 56277 / % possible obs: 99.4 % / Observed criterion σ(I): 3.9 / Redundancy: 4.9 % / Biso Wilson estimate: 39.6 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 19.4
Reflection shellResolution: 2.25→2.45 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3.9 / % possible all: 82.4

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QJB

1qjb


Resolution: 2.25→24.46 Å / σ(F): 1.99 / Phase error: 37.54 / Stereochemistry target values: TWIN_LSQ_F / Details: TWINNED REFINEMENT
RfactorNum. reflection% reflection
Rfree0.235 2000 3.5 %
Rwork0.181 --
obs0.183 56277 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.57 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 34.93 Å2
Baniso -1Baniso -2Baniso -3
1--3.3597 Å20 Å2-1.0192 Å2
2--13.3635 Å2-0 Å2
3----10.0038 Å2
Refinement stepCycle: LAST / Resolution: 2.25→24.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6805 0 8 64 6877
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056901
X-RAY DIFFRACTIONf_angle_d0.8839347
X-RAY DIFFRACTIONf_dihedral_angle_d16.8942391
X-RAY DIFFRACTIONf_chiral_restr0.0571084
X-RAY DIFFRACTIONf_plane_restr0.0031202
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.28880.3007960.24422549X-RAY DIFFRACTION98
2.2888-2.33040.2768980.2352672X-RAY DIFFRACTION98
2.3304-2.37520.2857990.24182716X-RAY DIFFRACTION98
2.3752-2.42360.2118980.22682694X-RAY DIFFRACTION98
2.4236-2.47620.2895990.21972712X-RAY DIFFRACTION98
2.4762-2.53380.2973990.2282742X-RAY DIFFRACTION98
2.5338-2.59710.2897990.22122692X-RAY DIFFRACTION98
2.5971-2.66720.2968990.21332696X-RAY DIFFRACTION98
2.6672-2.74560.2657980.20252723X-RAY DIFFRACTION98
2.7456-2.83410.25931000.19542721X-RAY DIFFRACTION98
2.8341-2.93520.29041020.19572732X-RAY DIFFRACTION98
2.9352-3.05250.2899980.19532705X-RAY DIFFRACTION98
3.0525-3.19120.24991050.1862719X-RAY DIFFRACTION98
3.1912-3.3590.23091010.19042726X-RAY DIFFRACTION98
3.359-3.56890.25831020.17842728X-RAY DIFFRACTION98
3.5689-3.84350.20431060.16062720X-RAY DIFFRACTION98
3.8435-4.22850.1849980.13912769X-RAY DIFFRACTION98
4.2285-4.83620.2032970.13512744X-RAY DIFFRACTION98
4.8362-6.07770.22891030.18152746X-RAY DIFFRACTION98
6.0777-24.46540.1691990.1642775X-RAY DIFFRACTION98

+
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