[English] 日本語
Yorodumi
- PDB-6g6x: 14-3-3sigma in complex with a P129beta3P mutated YAP pS127 phosph... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6g6x
Title14-3-3sigma in complex with a P129beta3P mutated YAP pS127 phosphopeptide
Components
  • 14-3-3 protein sigma
  • Transcriptional coactivator YAP1
KeywordsONCOPROTEIN / beta amino acid hippo pathway YAP/TAZ
Function / homology
Function and homology information


enterocyte differentiation / regulation of keratinocyte proliferation / glandular epithelial cell differentiation / regulation of metanephric nephron tubule epithelial cell differentiation / cardiac muscle tissue regeneration / TEAD-YAP complex / lateral mesoderm development / bud elongation involved in lung branching / polarized epithelial cell differentiation / RUNX3 regulates YAP1-mediated transcription ...enterocyte differentiation / regulation of keratinocyte proliferation / glandular epithelial cell differentiation / regulation of metanephric nephron tubule epithelial cell differentiation / cardiac muscle tissue regeneration / TEAD-YAP complex / lateral mesoderm development / bud elongation involved in lung branching / polarized epithelial cell differentiation / RUNX3 regulates YAP1-mediated transcription / notochord development / negative regulation of cilium assembly / lung epithelial cell differentiation / heart process / YAP1- and WWTR1 (TAZ)-stimulated gene expression / trophectodermal cell differentiation / paraxial mesoderm development / hippo signaling / regulation of stem cell proliferation / intestinal epithelial cell development / negative regulation of epithelial cell apoptotic process / EGR2 and SOX10-mediated initiation of Schwann cell myelination / tissue homeostasis / Formation of axial mesoderm / negative regulation of stem cell differentiation / embryonic heart tube morphogenesis / female germ cell nucleus / Signaling by Hippo / proline-rich region binding / Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin / organ growth / interleukin-6-mediated signaling pathway / negative regulation of epithelial cell differentiation / regulation of epidermal cell division / negative regulation of fat cell differentiation / protein kinase C inhibitor activity / positive regulation of Notch signaling pathway / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / RUNX2 regulates osteoblast differentiation / Zygotic genome activation (ZGA) / regulation of cell-cell adhesion / positive regulation of stem cell population maintenance / cAMP/PKA signal transduction / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / somatic stem cell population maintenance / Activation of BAD and translocation to mitochondria / phosphoserine residue binding / bicellular tight junction / canonical Wnt signaling pathway / negative regulation of keratinocyte proliferation / regulation of neurogenesis / establishment of skin barrier / negative regulation of protein localization to plasma membrane / positive regulation of osteoblast differentiation / vasculogenesis / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Nuclear signaling by ERBB4 / negative regulation of protein kinase activity / negative regulation of stem cell proliferation / positive regulation of cardiac muscle cell proliferation / keratinocyte differentiation / RHO GTPases activate PKNs / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / positive regulation of protein localization / extrinsic apoptotic signaling pathway / cellular response to retinoic acid / positive regulation of cell adhesion / protein sequestering activity / negative regulation of innate immune response / response to progesterone / protein export from nucleus / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / positive regulation of protein export from nucleus / epithelial cell proliferation / stem cell proliferation / positive regulation of epithelial cell proliferation / negative regulation of extrinsic apoptotic signaling pathway / transcription coregulator activity / TP53 Regulates Metabolic Genes / Translocation of SLC2A4 (GLUT4) to the plasma membrane / wound healing / cellular response to gamma radiation / positive regulation of protein localization to nucleus / cell morphogenesis / intrinsic apoptotic signaling pathway in response to DNA damage / cell-cell junction / cell junction / transcription corepressor activity / intracellular protein localization / positive regulation of canonical Wnt signaling pathway / regulation of protein localization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / positive regulation of cell growth / protein-containing complex assembly
Similarity search - Function
: / Omega loop, TEAD interacting region 3 / : / 14-3-3 domain / Delta-Endotoxin; domain 1 / 14-3-3 protein sigma / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. ...: / Omega loop, TEAD interacting region 3 / : / 14-3-3 domain / Delta-Endotoxin; domain 1 / 14-3-3 protein sigma / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
14-3-3 protein sigma / Transcriptional coactivator YAP1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.13 Å
AuthorsAndrei, S.A. / Thijssen, V. / Brunsveld, L. / Ottmann, C. / Milroy, L.G.
Funding support Netherlands, 2items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific ResearchECHO-STIP 717.014.001 Netherlands
Netherlands Organisation for Scientific ResearchGravity program 024.001.035 Netherlands
CitationJournal: Chem.Commun.(Camb.) / Year: 2019
Title: A study on the effect of synthetic alpha-to-beta3-amino acid mutations on the binding of phosphopeptides to 14-3-3 proteins.
Authors: Andrei, S.A. / Thijssen, V. / Brunsveld, L. / Ottmann, C. / Milroy, L.G.
History
DepositionApr 3, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Dec 18, 2019Group: 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 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conn / struct_conn_type
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Revision 2.1Jan 17, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 14-3-3 protein sigma
P: Transcriptional coactivator YAP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9068
Polymers27,7182
Non-polymers1886
Water7,188399
1
A: 14-3-3 protein sigma
P: Transcriptional coactivator YAP1
hetero molecules

A: 14-3-3 protein sigma
P: Transcriptional coactivator YAP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,81216
Polymers55,4364
Non-polymers37612
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area6130 Å2
ΔGint-138 kcal/mol
Surface area23930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.118, 111.849, 62.630
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-413-

HOH

21A-700-

HOH

31A-771-

HOH

-
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 Transcriptional coactivator YAP1 / Yes-associated protein 1 / Protein yorkie homolog / Yes-associated protein YAP65 homolog


Mass: 1175.190 Da / Num. of mol.: 1 / Mutation: Proline 129 to beta3-proline / Source method: obtained synthetically / Details: EOE = beta3-proline / Source: (synth.) Homo sapiens (human) / References: UniProt: P46937
#3: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 399 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.76 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.095 M HEPES, pH 7.1, 29% PEG 400, 0.19 M CaCl2, 5% glycerol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.13→45.49 Å / Num. obs: 107708 / % possible obs: 100 % / Redundancy: 11.2 % / Biso Wilson estimate: 10.45 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.025 / Rrim(I) all: 0.086 / Net I/σ(I): 14.1 / Num. measured all: 1208392 / Scaling rejects: 9132
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.13-1.158.11.35952830.7670.5051.45599.9
6.19-45.4912.90.0727440.9930.0210.07599.8

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.3 Å45.49 Å
Translation5.3 Å45.49 Å

-
Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
Aimless0.6.3data scaling
PHASER2.8.1phasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3mhr

3mhr


Resolution: 1.13→45.49 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 16.29
RfactorNum. reflection% reflection
Rfree0.1678 2705 2.51 %
Rwork0.1496 --
obs0.15 107651 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 75.71 Å2 / Biso mean: 17.7075 Å2 / Biso min: 4.11 Å2
Refinement stepCycle: final / Resolution: 1.13→45.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1925 0 6 399 2330
Biso mean--19.67 28.93 -
Num. residues----245
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.13-1.15060.35391320.407154725604
1.1506-1.17270.33771190.294955135632
1.1727-1.19660.23651230.24154895612
1.1966-1.22260.24041530.212954395592
1.2226-1.25110.20611380.186654715609
1.2511-1.28240.20471510.175254985649
1.2824-1.3170.17051360.160654855621
1.317-1.35580.18721470.152554765623
1.3558-1.39960.15241360.128754865622
1.3996-1.44960.13691390.122655065645
1.4496-1.50760.15041440.112155305674
1.5076-1.57630.14191520.112454825634
1.5763-1.65940.13671400.113854955635
1.6594-1.76330.13021370.122755305667
1.7633-1.89950.16281440.131155405684
1.8995-2.09060.14461510.128455565707
2.0906-2.39310.14531560.127655755731
2.3931-3.0150.16281570.152456045761
3.015-45.53060.18151500.162257995949

+
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