[English] 日本語
Yorodumi
- PDB-7pwt: Crystal structure of 14-3-3 sigma in complex with a C-terminal Es... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7pwt
TitleCrystal structure of 14-3-3 sigma in complex with a C-terminal Estrogen Receptor alpha phosphopeptide, stabilised by pyrrolidone derivative 228
Components
  • 14-3-3 protein sigma
  • C-terminus of Estrogen receptor alpha
KeywordsCHAPERONE / Nuclear receptor / phosphorylation / trafficking / PPI stabiliser
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 / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding / Activation of BAD and translocation to mitochondria ...regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / regulation of cell-cell adhesion / 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 / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / positive regulation of protein localization / RHO GTPases activate PKNs / protein kinase A signaling / protein sequestering activity / protein export from nucleus / negative regulation of innate immune response / positive regulation of cell adhesion / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / positive regulation of protein export from nucleus / stem cell proliferation / 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
Chem-PJN / 14-3-3 protein sigma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.312 Å
AuthorsAndrei, S.A. / Bosica, F. / O'Mahony, G. / Ottmann, C.
Funding support Netherlands, 2items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission675179 Netherlands
Netherlands Organisation for Scientific Research (NWO)717.014.001 Netherlands
CitationJournal: J.Med.Chem. / Year: 2022
Title: Designing Selective Drug-like Molecular Glues for the Glucocorticoid Receptor/14-3-3 Protein-Protein Interaction.
Authors: Pallesen, J.S. / Munier, C.C. / Bosica, F. / Andrei, S.A. / Edman, K. / Gunnarsson, A. / La Sala, G. / Putra, O.D. / Srdanovic, S. / Wilson, A.J. / Wissler, L. / Ottmann, C. / Perry, M.W.D. / O'Mahony, G.
History
DepositionOct 7, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2023Group: 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
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 14-3-3 protein sigma
B: C-terminus of Estrogen receptor alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8544
Polymers27,4142
Non-polymers4412
Water3,909217
1
A: 14-3-3 protein sigma
B: C-terminus of Estrogen receptor alpha
hetero molecules

A: 14-3-3 protein sigma
B: C-terminus of Estrogen receptor alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7098
Polymers54,8284
Non-polymers8814
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+11
Buried area4050 Å2
ΔGint-40 kcal/mol
Surface area22060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.838, 151.081, 77.721
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222

-
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 C-terminus of Estrogen receptor alpha


Mass: 870.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PJN / (2~{R})-1-(2-hydroxyphenyl)-2-(4-nitrophenyl)-4-oxidanyl-3-(phenylcarbonyl)-2~{H}-pyrrol-5-one


Mass: 416.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H16N2O6 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.51 Å3/Da / Density % sol: 65 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 1 : 1 (v/v) 0.1 M Tris, pH 7.0, 0.2 magnesium chloride hexahydrate and 10 % v/v PEG 8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.5419 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Feb 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 2.31→29.53 Å / Num. obs: 16214 / % possible obs: 96.1 % / Redundancy: 5.6 % / CC1/2: 0.982 / Rmerge(I) obs: 0.16 / Rpim(I) all: 0.07 / Rrim(I) all: 0.176 / Net I/σ(I): 5.5
Reflection shellResolution: 2.31→2.35 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.792 / Num. unique obs: 551 / CC1/2: 0.881 / Rpim(I) all: 0.429 / Rrim(I) all: 0.907

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.9 Å29.53 Å
Translation4.9 Å29.53 Å

-
Processing

Software
NameVersionClassification
PHENIX3500refinement
Aimlessdata scaling
PHASER2.8.3phasing
PDB_EXTRACT3.25data extraction
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JC3

4jc3


Resolution: 2.312→29.526 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2535 771 4.83 %
Rwork0.228 15206 -
obs0.2293 15977 94.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 185.96 Å2 / Biso mean: 52.6796 Å2 / Biso min: 12.93 Å2
Refinement stepCycle: final / Resolution: 2.312→29.526 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1826 0 48 218 2092
Biso mean--83.55 45.69 -
Num. residues----232
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3123-2.45710.39191240.4029207179
2.4571-2.64670.29011130.3114262799
2.6467-2.91280.27221380.2734262399
2.9128-3.33380.27521340.2409260599
3.3338-4.19830.24791280.1945257095
4.1983-29.520.20171340.185271097
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)
12.1856-1.0767-0.42833.62930.88083.4823-0.04990.3694-0.0903-0.0893-0.23480.4330.488-1.04810.22470.4239-0.2381-0.02890.6583-0.07560.306718.869412.269814.5058
21.99637.43195.04912.0274-1.684.11460.8973-1.1802-0.10131.4582-0.27210.02720.06760.1439-0.27950.4566-0.22390.01650.5518-0.09170.376920.048813.117325.7761
34.2653-0.2169-0.37964.3227-3.25229.2903-0.13180.2153-0.117-0.15560.16230.01520.11750.0043-0.0270.2475-0.0850.02120.1904-0.06470.282640.085529.239124.2912
45.1497-0.4373-3.51790.90650.38343.7232-0.30540.5072-0.2551-0.05410.0150.04210.1085-0.59560.32260.2664-0.0401-0.04470.2522-0.04080.262621.522225.822832.406
55.06660.2583-2.46445.49641.03638.3334-0.32271.0185-0.0382-0.46820.0447-0.1457-0.3105-0.67030.34120.3818-0.113-0.09220.46820.00220.276923.024925.417617.2466
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 137 through 231 )A137 - 231
2X-RAY DIFFRACTION2chain 'B' and (resid 591 through 595 )B591 - 595
3X-RAY DIFFRACTION3chain 'A' and (resid -4 through 37 )A-4 - 37
4X-RAY DIFFRACTION4chain 'A' and (resid 38 through 105 )A38 - 105
5X-RAY DIFFRACTION5chain 'A' and (resid 106 through 136 )A106 - 136

+
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