[English] 日本語
Yorodumi
- PDB-9qnl: BAD pS118 phosphopeptide binding to 14-3-3sigma -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9qnl
TitleBAD pS118 phosphopeptide binding to 14-3-3sigma
Components
  • 14-3-3 protein sigma
  • Bcl2-associated agonist of cell death
KeywordsPEPTIDE BINDING PROTEIN / 14-3-3 protein-protein interactions
Function / homology
Function and homology information


ADP metabolic process / positive regulation of intrinsic apoptotic signaling pathway in response to osmotic stress / positive regulation of type B pancreatic cell development / BAD-BCL-2 complex / glucose catabolic process / pore complex assembly / cysteine-type endopeptidase activator activity / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / type B pancreatic cell proliferation / regulation of mitochondrial membrane permeability ...ADP metabolic process / positive regulation of intrinsic apoptotic signaling pathway in response to osmotic stress / positive regulation of type B pancreatic cell development / BAD-BCL-2 complex / glucose catabolic process / pore complex assembly / cysteine-type endopeptidase activator activity / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / type B pancreatic cell proliferation / regulation of mitochondrial membrane permeability / cellular response to lipid / AKT phosphorylates targets in the cytosol / cysteine-type endopeptidase activator activity involved in apoptotic process / positive regulation of mitochondrial membrane potential / positive regulation of B cell differentiation / positive regulation of T cell differentiation / NRAGE signals death through JNK / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / Constitutive Signaling by AKT1 E17K in Cancer / positive regulation of release of cytochrome c from mitochondria / regulation of cell-cell adhesion / positive regulation of proteolysis / cAMP/PKA signal transduction / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / extrinsic apoptotic signaling pathway via death domain receptors / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / establishment of skin barrier / positive regulation of insulin secretion involved in cellular response to glucose stimulus / 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 / ATP metabolic process / negative regulation of protein kinase activity / negative regulation of stem cell proliferation / RHO GTPases activate PKNs / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / positive regulation of protein localization / extrinsic apoptotic signaling pathway / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of autophagy / positive regulation of cell adhesion / intrinsic apoptotic signaling pathway / 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 epithelial cell proliferation / stem cell proliferation / TP53 Regulates Metabolic Genes / Translocation of SLC2A4 (GLUT4) to the plasma membrane / cellular response to mechanical stimulus / positive regulation of insulin secretion / phospholipid binding / cellular response to nicotine / cytokine-mediated signaling pathway / intrinsic apoptotic signaling pathway in response to DNA damage / intracellular protein localization / glucose homeostasis / regulation of protein localization / positive regulation of cell growth / protein phosphatase binding / cellular response to hypoxia / mitochondrial outer membrane / regulation of cell cycle / positive regulation of apoptotic process / cadherin binding / apoptotic process / lipid binding / protein kinase binding / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / signal transduction / mitochondrion / extracellular space / extracellular exosome / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Bcl2-associated agonist of cell death / Pro-apoptotic Bcl-2 protein, BAD / 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 / Bcl2-associated agonist of cell death
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsPennings, M.A.M.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)101077879European Union
CitationJournal: Digit Discov / Year: 2025
Title: Identifying 14-3-3 interactome binding sites with deep learning.
Authors: van Weesep, L. / Ozcelik, R. / Pennings, M. / Criscuolo, E. / Ottmann, C. / Brunsveld, L. / Grisoni, F.
History
DepositionMar 25, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 14-3-3 protein sigma
B: Bcl2-associated agonist of cell death
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1288
Polymers27,8922
Non-polymers2366
Water4,288238
1
A: 14-3-3 protein sigma
B: Bcl2-associated agonist of cell death
hetero molecules

A: 14-3-3 protein sigma
B: Bcl2-associated agonist of cell death
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,25616
Polymers55,7854
Non-polymers47212
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5690 Å2
ΔGint-97 kcal/mol
Surface area24330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.606, 112.105, 62.952
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-305-

CA

-
Components

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


Mass: 26542.914 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 Bcl2-associated agonist of cell death / BAD / Bcl-2-binding component 6 / Bcl-2-like protein 8 / Bcl2-L-8 / Bcl-xL/Bcl-2-associated death ...BAD / Bcl-2-binding component 6 / Bcl-2-like protein 8 / Bcl2-L-8 / Bcl-xL/Bcl-2-associated death promoter / Bcl2 antagonist of cell death


Mass: 1349.407 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q92934
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#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.: 238 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.92 %
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: ID23-2 / Wavelength: 0.873128 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jun 14, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873128 Å / Relative weight: 1
ReflectionResolution: 1.3→45.76 Å / Num. obs: 63729 / % possible obs: 89.1 % / Redundancy: 13 % / CC1/2: 1 / Net I/σ(I): 19.4
Reflection shellResolution: 1.3→1.33 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3427 / CC1/2: 0.589

-
Processing

Software
NameClassification
PDB-REDOrefinement
autoPROCdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→45.76 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.97 / SU B: 3.896 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.053 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.19484 3239 5.1 %RANDOM
Rwork0.16284 ---
obs0.16453 60467 89.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.216 Å2
Baniso -1Baniso -2Baniso -3
1-4.64 Å20 Å2-0 Å2
2---2.03 Å20 Å2
3----2.62 Å2
Refinement stepCycle: LAST / Resolution: 1.3→45.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1942 0 6 238 2186
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0162046
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161961
X-RAY DIFFRACTIONr_angle_refined_deg0.9321.8232768
X-RAY DIFFRACTIONr_angle_other_deg0.4111.5684538
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7785.281285
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.89210402
X-RAY DIFFRACTIONr_chiral_restr0.0450.2304
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022424
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02448
X-RAY DIFFRACTIONr_mcbond_it14.2582.0881006
X-RAY DIFFRACTIONr_mcbond_other14.2532.0911007
X-RAY DIFFRACTIONr_mcangle_it17.0623.771261
X-RAY DIFFRACTIONr_mcangle_other17.073.7731262
X-RAY DIFFRACTIONr_scbond_it36.9432.6951040
X-RAY DIFFRACTIONr_scbond_other36.9342.6981041
X-RAY DIFFRACTIONr_scangle_other44.5974.6571495
X-RAY DIFFRACTIONr_long_range_B_refined40.44629.092460
X-RAY DIFFRACTIONr_long_range_B_other40.55226.792395
X-RAY DIFFRACTIONr_rigid_bond_restr12.31934007
LS refinement shellResolution: 1.303→1.337 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 279 -
Rwork0.344 4875 -
obs--98.43 %

+
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