[English] 日本語
Yorodumi
- PDB-8qs3: Ternary structure of 14-3-3s, C-RAF phosphopeptide (pS259) and co... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8qs3
TitleTernary structure of 14-3-3s, C-RAF phosphopeptide (pS259) and compound 23 (1083848)
Components
  • 14-3-3 protein sigma
  • C-RAF peptide pS259
KeywordsPEPTIDE BINDING PROTEIN / Stabilizer / protein-protein interaction
Function / homology
Function and homology information


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 / phosphoserine residue binding ...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 / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / establishment of skin barrier / 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 stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / positive regulation of protein localization / positive regulation of cell adhesion / protein sequestering activity / negative regulation of innate immune response / release of cytochrome c from mitochondria / protein export from nucleus / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of protein export from nucleus / negative regulation of protein kinase activity / stem cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / intrinsic apoptotic signaling pathway in response to DNA damage / protein localization / regulation of protein localization / positive regulation of cell growth / regulation of cell cycle / cadherin binding / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / extracellular space / extracellular exosome / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
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
Similarity search - Domain/homology
: / 14-3-3 protein sigma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsKonstantinidou, M. / Vickery, H. / Pennings, M.A.M. / Virta, J. / Visser, E.J. / Oetelaar, M.C.M. / Overmans, M. / Neitz, J. / Ottmann, C. / Brunsveld, L. / Arkin, M.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM147696 United States
CitationJournal: To Be Published
Title: Small molecule stabilization of the 14-3-3sigma/CRAF complex inhibits the MAPK pathway
Authors: Konstantinidou, M. / Vickery, H. / Pennings, M.A.M. / Virta, J. / Visser, E.J. / Oetelaar, M.C.M. / Overmans, M. / Neitz, J. / Ottmann, C. / Brunsveld, L. / Arkin, M.R.
History
DepositionOct 10, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 14-3-3 protein sigma
K: C-RAF peptide pS259
M: 14-3-3 protein sigma
Y: C-RAF peptide pS259
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,68620
Polymers55,3884
Non-polymers1,29816
Water8,035446
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6200 Å2
ΔGint-110 kcal/mol
Surface area22350 Å2
Unit cell
Length a, b, c (Å)60.685, 89.262, 116.969
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

-
Components

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

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


Mass: 26485.865 Da / Num. of mol.: 2
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 C-RAF peptide pS259


Mass: 1208.175 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

-
Non-polymers , 4 types, 462 molecules

#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-WQI / 2-chloranyl-~{N}-[[1-(4-iodophenyl)sulfonylpiperidin-4-yl]methyl]ethanamide


Mass: 456.727 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H18ClIN2O3S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 446 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.86 Å3/Da / Density % sol: 57.02 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.095 M HEPES pH=7.1-7.7 0.19 M CaCl2 5% glycerol 24-29% PEG400

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.885603 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 30, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.885603 Å / Relative weight: 1
ReflectionResolution: 1.6→116.97 Å / Num. obs: 83028 / % possible obs: 98.2 % / Redundancy: 13.1 % / CC1/2: 0.999 / Net I/σ(I): 16.6
Reflection shellResolution: 1.6→1.63 Å / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4109 / CC1/2: 0.727

-
Processing

Software
NameClassification
PDB-REDOrefinement
autoPROCdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→70.96 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.964 / SU B: 3.017 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.19922 4186 5 %RANDOM
Rwork0.18397 ---
obs0.18475 78774 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.435 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0.84 Å2-0 Å2
3----0.82 Å2
Refinement stepCycle: LAST / Resolution: 1.6→70.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3812 0 56 446 4314
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0163909
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163695
X-RAY DIFFRACTIONr_angle_refined_deg1.0841.8235266
X-RAY DIFFRACTIONr_angle_other_deg0.4511.5688541
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2025.277505
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.45552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.29210727
X-RAY DIFFRACTIONr_chiral_restr0.0520.2583
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024543
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02849
X-RAY DIFFRACTIONr_mcbond_it1.9141.9051923
X-RAY DIFFRACTIONr_mcbond_other1.9141.9051923
X-RAY DIFFRACTIONr_mcangle_it2.8273.4112395
X-RAY DIFFRACTIONr_mcangle_other2.8273.4112396
X-RAY DIFFRACTIONr_scbond_it3.3082.2961986
X-RAY DIFFRACTIONr_scbond_other3.3092.2951984
X-RAY DIFFRACTIONr_scangle_other5.0994.0392872
X-RAY DIFFRACTIONr_long_range_B_refined7.48921.074755
X-RAY DIFFRACTIONr_long_range_B_other7.39519.934622
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 306 -
Rwork0.275 5864 -
obs--100 %
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)
10.5064-0.32560.05141.8162-0.60460.64830.0389-0.0019-0.1282-0.1186-0.02020.12190.0046-0.0296-0.01870.01130.0074-0.00820.0930.00850.098-26.119-21.4188.438
25.90170.8378-1.191112.4801-2.748310.06560.1239-0.3317-0.25290.4492-0.128-0.4709-0.27180.38710.00410.08780.0422-0.07490.1097-0.00710.1007-19.794-15.40812.486
32.50170.0019-0.89510.6953-0.07941.32550.0361-0.40880.11350.12910.0314-0.0509-0.02710.2158-0.06750.02510.00260.00020.1311-0.00580.11250.075-39.33329.016
45.2367-1.30011.47996.8139-1.112212.470.1824-0.35120.6670.0433-0.04190.2046-0.6067-0.1195-0.14050.05420.00710.0380.1307-0.09790.3088-0.884-30.95231.757
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION2K255 - 264
2X-RAY DIFFRACTION4Y255 - 264

+
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