[English] 日本語
Yorodumi
- PDB-8rrk: 14-3-3 sigma complexed with an optimized phosphopeptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8rrk
Title14-3-3 sigma complexed with an optimized phosphopeptide
Components
  • 14-3-3 protein sigma
  • phosphopeptide designed according to the 14-3-3 binding consensus
KeywordsSIGNALING PROTEIN / PROTEIN-PHOSPHOPEPTIDE COMPLEX / 14-3-3 sigma
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 / protein sequestering activity / positive regulation of cell adhesion / negative regulation of innate immune response / protein export from nucleus / release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / stem cell proliferation / positive regulation of protein export from nucleus / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / negative regulation of protein kinase activity / 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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsCousido-Siah, A. / McEwen, A.G. / Monsellier, E. / Trave, G.
Funding support France, 6items
OrganizationGrant numberCountry
French National Research AgencyANR-18-CE92-0017 France
La ligue contre le cancer France
French National Research AgencyANR-10-INSB-05-01 France
French National Research AgencyANR-10-IDEX-0002 France
French National Research AgencyANR 20-SFRI-0012 France
French National Research AgencyANR-17-EURE-0023 France
CitationJournal: J.Am.Chem.Soc. / Year: 2025
Title: Holdup Multiplex Assay for High-Throughput Measurement of Protein-Ligand Affinity Constants Using a Mass Spectrometry Readout.
Authors: Delalande, F. / Ostergaard, S.R. / Gogl, G. / Cousido-Siah, A. / McEwen, A.G. / Men, Y. / Salimova, F. / Rohrbacher, A. / Kostmann, C. / Nomine, Y. / Vincentelli, R. / Eberling, P. / ...Authors: Delalande, F. / Ostergaard, S.R. / Gogl, G. / Cousido-Siah, A. / McEwen, A.G. / Men, Y. / Salimova, F. / Rohrbacher, A. / Kostmann, C. / Nomine, Y. / Vincentelli, R. / Eberling, P. / Carapito, C. / Trave, G. / Monsellier, E.
History
DepositionJan 22, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 16, 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: 14-3-3 protein sigma
C: phosphopeptide designed according to the 14-3-3 binding consensus
D: phosphopeptide designed according to the 14-3-3 binding consensus
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,00110
Polymers58,5014
Non-polymers5006
Water5,008278
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5870 Å2
ΔGint-46 kcal/mol
Surface area23440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.250, 54.880, 82.120
Angle α, β, γ (deg.)90.00, 101.27, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-301-

SO4

-
Components

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

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


Mass: 28137.469 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 BL21(DE3) (bacteria) / References: UniProt: P31947
#2: Protein/peptide phosphopeptide designed according to the 14-3-3 binding consensus


Mass: 1113.225 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: phosphopeptide designed according to the 14-3-3 binding consensus
Source: (synth.) synthetic construct (others)

-
Non-polymers , 4 types, 284 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 2.61 Å3/Da / Density % sol: 52.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 25% PEG 3350, 100mM Bis-Tris pH 6.5, 200mM LiSO4

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 51006 / % possible obs: 97.7 % / Redundancy: 6.76 % / CC1/2: 0.998 / Rmerge(I) obs: 0.082 / Rrim(I) all: 0.09 / Net I/σ(I): 11.01
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.85-1.962.08681290.9732.2641
1.96-2.090.89376060.9510.9671
2.09-2.260.38571700.9790.4191
2.26-2.480.20866390.9880.2241
2.48-2.770.14160100.9920.1531
2.77-3.20.08853540.9950.0961
3.2-3.910.06445480.9960.071
3.91-5.520.05635520.9970.0611
5.52-500.04819980.9980.0521

-
Processing

Software
NameVersionClassification
PHENIX(1.20rc2_4400: ???)refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→47.49 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2178 2233 5 %
Rwork0.1802 --
obs0.182 44657 97.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.93→47.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3805 0 30 278 4113
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083975
X-RAY DIFFRACTIONf_angle_d0.6865364
X-RAY DIFFRACTIONf_dihedral_angle_d13.3171543
X-RAY DIFFRACTIONf_chiral_restr0.042594
X-RAY DIFFRACTIONf_plane_restr0.007696
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.970.34271390.3462631X-RAY DIFFRACTION96
1.97-2.020.31631380.28592601X-RAY DIFFRACTION97
2.02-2.070.34041360.29452578X-RAY DIFFRACTION95
2.07-2.120.27181370.22192615X-RAY DIFFRACTION97
2.12-2.190.2651390.21622635X-RAY DIFFRACTION97
2.19-2.260.27851350.22872581X-RAY DIFFRACTION96
2.26-2.340.19481400.17772650X-RAY DIFFRACTION98
2.34-2.430.22371380.17822635X-RAY DIFFRACTION98
2.43-2.540.22081390.17732654X-RAY DIFFRACTION98
2.54-2.680.22631400.19052649X-RAY DIFFRACTION98
2.68-2.840.26281410.19482684X-RAY DIFFRACTION99
2.84-3.060.23071410.20292673X-RAY DIFFRACTION99
3.06-3.370.2331400.18782669X-RAY DIFFRACTION98
3.37-3.860.21451420.16072694X-RAY DIFFRACTION99
3.86-4.860.17521430.14572708X-RAY DIFFRACTION99
4.86-47.490.18871450.16692767X-RAY DIFFRACTION98
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)
10.7362-0.41260.42611.308-0.09421.37250.0970.19840.3170.08620.1214-0.1099-0.25330.10140.00010.40150.02150.0390.32830.04080.41229.06059.92178.6398
22.0763-1.31020.20660.98350.37011.8489-0.076-0.2668-0.66540.71140.2395-0.1885-0.0732-0.15730.00010.41170.07550.04360.42390.0810.500825.4994-7.292417.8776
33.8692-0.85970.26551.3824-0.20472.1629-0.1967-0.4933-0.21790.22610.1754-0.10850.00790.20840.00510.42280.11740.03070.38960.03160.423638.3411-9.269220.4153
40.03180.00310.01130.017-0.01210.0101-0.22380.2153-0.1010.099-0.4186-0.0640.2425-0.3313-0.00161.18340.12920.26791.45230.41091.116733.8815-23.284338.3776
51.0506-0.7765-0.14971.2655-0.72530.9239-0.19290.2476-0.9279-0.3345-0.05070.16220.5282-0.032200.5589-0.01870.06450.5715-0.05230.72972.9867-13.649411.7302
61.6085-1.0485-0.02470.7597-0.08441.61290.06510.20160.21550.34110.19090.1882-0.0807-0.1724-0.00010.37770.04880.06510.39140.05110.40326.40684.579416.6375
7-0.00380.00860.0070.03570.0390.03980.2143-0.63990.78710.7345-0.26980.2052-0.5720.2408-0.00330.7242-0.0870.15680.9530.07721.208722.37324.9311.9933
81.9905-1.24290.66451.74850.29921.82170.09610.6692-0.2181-0.15210.02020.09710.0331-0.41970.00270.41490.053-0.00190.460.0420.3328-0.66345.07910.2929
90.7611-0.27070.44561.18340.83471.25130.05830.7450.3633-0.31270.18580.437-0.1526-0.69790.00080.45570.1273-0.02160.61410.10370.4573-12.179310.264813.9507
100.9405-0.42720.53380.2323-0.02131.30150.0090.02780.1386-0.05130.15190.2283-0.0677-0.19530.00010.41190.06820.02720.47130.06430.3488-8.95478.924324.0559
110.89750.00690.36060.24020.33310.83420.18770.0012-0.0590.32410.03960.9357-0.2717-0.59510.00060.49970.06940.07220.7436-0.0370.5106-12.65869.075933.5031
121.5444-0.61390.25210.343-0.26221.83880.1913-0.1882-0.3290.6296-0.147-0.11050.15620.3417-0.00030.53580.0871-0.02190.67960.02490.4728-3.90426.775733.4811
130.4857-0.13890.16090.09810.06520.61540.2062-0.914-0.38350.4368-0.07241.00980.2294-0.0121-0.0010.55790.11170.03350.73680.00810.721431.2855-8.951926.949
140.5387-0.25370.06230.1975-0.06190.6355-0.16270.0003-0.2850.66530.3483-0.3691-0.07220.3578-0.00030.4570.03640.04350.63720.12490.51161.81437.990225.2698
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -3 through 37 )
2X-RAY DIFFRACTION2chain 'A' and (resid 38 through 70 )
3X-RAY DIFFRACTION3chain 'A' and (resid 71 through 230 )
4X-RAY DIFFRACTION4chain 'A' and (resid 231 through 235 )
5X-RAY DIFFRACTION5chain 'B' and (resid -3 through 37 )
6X-RAY DIFFRACTION6chain 'B' and (resid 38 through 68 )
7X-RAY DIFFRACTION7chain 'B' and (resid 69 through 79 )
8X-RAY DIFFRACTION8chain 'B' and (resid 80 through 137 )
9X-RAY DIFFRACTION9chain 'B' and (resid 138 through 161 )
10X-RAY DIFFRACTION10chain 'B' and (resid 162 through 186 )
11X-RAY DIFFRACTION11chain 'B' and (resid 187 through 209 )
12X-RAY DIFFRACTION12chain 'B' and (resid 210 through 233 )
13X-RAY DIFFRACTION13chain 'C'
14X-RAY DIFFRACTION14chain 'D'

+
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