[English] 日本語
Yorodumi
- PDB-6g8p: 14-3-3sigma in complex with a P129beta3P and L132beta3L mutated Y... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6g8p
Title14-3-3sigma in complex with a P129beta3P and L132beta3L 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 / regulation of metanephric nephron tubule epithelial cell differentiation / cardiac muscle tissue regeneration / TEAD-YAP complex / lateral mesoderm development / glandular epithelial cell differentiation / bud elongation involved in lung branching / RUNX3 regulates YAP1-mediated transcription / polarized epithelial cell differentiation ...enterocyte differentiation / regulation of keratinocyte proliferation / regulation of metanephric nephron tubule epithelial cell differentiation / cardiac muscle tissue regeneration / TEAD-YAP complex / lateral mesoderm development / glandular epithelial cell differentiation / bud elongation involved in lung branching / RUNX3 regulates YAP1-mediated transcription / polarized epithelial cell differentiation / notochord development / negative regulation of cilium assembly / lung epithelial cell differentiation / YAP1- and WWTR1 (TAZ)-stimulated gene expression / heart process / trophectodermal cell differentiation / paraxial mesoderm development / hippo signaling / EGR2 and SOX10-mediated initiation of Schwann cell myelination / regulation of stem cell proliferation / tissue homeostasis / intestinal epithelial cell development / negative regulation of epithelial cell apoptotic process / Formation of axial mesoderm / negative regulation of stem cell differentiation / female germ cell nucleus / embryonic heart tube morphogenesis / proline-rich region binding / Signaling by Hippo / Differentiation of keratinocytes in interfollicular epidermis in mammalian skin / organ growth / negative regulation of epithelial cell differentiation / interleukin-6-mediated signaling pathway / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of Notch signaling pathway / negative regulation of fat cell differentiation / positive regulation of epidermal cell differentiation / positive regulation of stem cell population maintenance / keratinocyte development / keratinization / regulation of cell-cell adhesion / RUNX2 regulates osteoblast differentiation / Zygotic genome activation (ZGA) / somatic stem cell population maintenance / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / regulation of neurogenesis / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / establishment of skin barrier / vasculogenesis / negative regulation of protein localization to plasma membrane / canonical Wnt signaling pathway / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / positive regulation of osteoblast differentiation / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / Nuclear signaling by ERBB4 / positive regulation of protein localization / RHO GTPases activate PKNs / positive regulation of cardiac muscle cell proliferation / cellular response to retinoic acid / keratinocyte differentiation / extrinsic apoptotic signaling pathway / 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 / positive regulation of epithelial cell proliferation / stem cell proliferation / epithelial cell proliferation / response to progesterone / Translocation of SLC2A4 (GLUT4) to the plasma membrane / negative regulation of extrinsic apoptotic signaling pathway / TP53 Regulates Metabolic Genes / transcription coregulator activity / negative regulation of protein kinase activity / wound healing / cell morphogenesis / cellular response to gamma radiation / positive regulation of protein localization to nucleus / intrinsic apoptotic signaling pathway in response to DNA damage / transcription corepressor activity / cell-cell junction / protein localization / positive regulation of canonical Wnt signaling pathway / cell junction / regulation of protein localization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / positive regulation of cell growth / protein-containing complex assembly / DNA-binding transcription factor binding / transcription coactivator activity
Similarity search - Function
: / Omega loop, TEAD interating 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 interating 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: 1.9 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 9, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 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: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / 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 / _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_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_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_ptnr2_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)27,8485
Polymers27,7322
Non-polymers1163
Water6,287349
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)55,69510
Polymers55,4644
Non-polymers2316
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)82.037, 111.499, 62.460
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-731-

HOH

21A-734-

HOH

31A-736-

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: 1189.217 Da / Num. of mol.: 1 / Fragment: UNP residues 124-133 / Source method: obtained synthetically / Details: EOE and B3L are beta3-amino acid mutations / Source: (synth.) Homo sapiens (human) / References: UniProt: P46937
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / 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.: 349 / 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: 2.57 Å3/Da / Density % sol: 52.12 %
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: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.9→66.08 Å / Num. obs: 22902 / % possible obs: 99.7 % / Redundancy: 11.2 % / Biso Wilson estimate: 15.47 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.026 / Rrim(I) all: 0.089 / Net I/σ(I): 21.1 / Num. measured all: 257393 / Scaling rejects: 1018
Reflection shell

CC1/2: 0.983 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.9-1.948.20.1821143113990.0660.19410.395.7
9.11-66.08100.07924912490.0270.08426.199.9

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.36 Å55.75 Å
Translation5.36 Å55.75 Å

-
Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
Aimless0.6.2data scaling
PHASER2.8.1phasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3mhr

3mhr


Resolution: 1.9→41.592 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 15.16
RfactorNum. reflection% reflection
Rfree0.1586 1181 5.17 %
Rwork0.1334 --
obs0.1348 22861 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 125.11 Å2 / Biso mean: 22.0283 Å2 / Biso min: 6.66 Å2
Refinement stepCycle: final / Resolution: 1.9→41.592 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1888 0 19 349 2256
Biso mean--17.59 32.28 -
Num. residues----240
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.98650.17921430.14142599274297
1.9865-2.09120.17141690.126326452814100
2.0912-2.22220.17591490.1226992848100
2.2222-2.39380.1441320.115327022834100
2.3938-2.63470.15061410.121526992840100
2.6347-3.01580.17991480.14127362884100
3.0158-3.79920.13891450.126227342879100
3.7992-41.60160.15661540.154328663020100
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)
10.4856-0.1810.40341.3786-0.52951.0288-0.05690.00010.03760.00130.06090.05690.0055-0.03910.00130.0783-0.00390.00120.07640.00930.096728.8215-10.77760.5812
21.8316-0.62560.90430.2137-0.32870.94230.06770.50010.4334-0.66870.24010.6798-0.3186-0.579-0.03850.60010.0916-0.110.43210.12710.413925.504111.6251-27.8111
30.41170.02380.05492.1022-0.47020.769-0.04290.0267-0.0366-0.18630.0381-0.09740.03960.03940.00370.0763-0.0260.00080.1030.00330.08731.3424-14.8718-10.3289
42.38381.4979-1.1333.2788-2.10093.4216-0.09960.1226-0.1814-0.32210.0032-0.1690.18680.12530.03940.10870.00020.00770.1115-0.03670.099726.1721-27.0878-16.0835
51.18840.4706-0.21130.4716-0.17221.2650.0019-0.01890.0339-0.03870.04520.08530.0442-0.1159-0.0270.1112-0.0321-0.00660.1468-0.00490.137812.459-25.9129-12.2695
61.5810.1837-0.35163.8375-3.55055.5881-0.063-0.05150.11440.3180.03650.0878-0.4522-0.4255-0.04970.13080.0178-0.00120.1894-0.00870.17786.8649-20.6132-6.468
75.14331.51850.33524.0218-1.35076.855-0.10270.00270.1504-0.14140.01670.3723-0.4275-0.53030.05490.1294-0.00470.0110.1906-0.02720.208615.3041-14.3131-9.882
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -4 through 70 )A-4 - 70
2X-RAY DIFFRACTION2chain 'A' and (resid 71 through 79 )A71 - 79
3X-RAY DIFFRACTION3chain 'A' and (resid 80 through 139 )A80 - 139
4X-RAY DIFFRACTION4chain 'A' and (resid 140 through 161 )A140 - 161
5X-RAY DIFFRACTION5chain 'A' and (resid 162 through 209 )A162 - 209
6X-RAY DIFFRACTION6chain 'A' and (resid 210 through 231 )A210 - 231
7X-RAY DIFFRACTION7chain 'P' and (resid 125 through 128 )P125 - 128

+
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