[English] 日本語
Yorodumi
- PDB-6ge6: X-ray structure of TEAD4(E263A+Y429F mutant) complexed with YAP(w... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ge6
TitleX-ray structure of TEAD4(E263A+Y429F mutant) complexed with YAP(wildtype): The role of residual flexibility and water molecules in the adaptation of a bound intrinsically disordered protein to mutations at a binding interface
Components
  • Transcriptional coactivator YAP1
  • Transcriptional enhancer factor TEF-3
KeywordsTRANSCRIPTION / transcription factor / co-activator / transcription regulation
Function / homology
Function and homology information


trophectodermal cell fate commitment / enterocyte differentiation / regulation of keratinocyte proliferation / bud elongation involved in lung branching / regulation of metanephric nephron tubule epithelial cell differentiation / cardiac muscle tissue regeneration / TEAD-YAP complex / lateral mesoderm development / glandular epithelial cell differentiation / RUNX3 regulates YAP1-mediated transcription ...trophectodermal cell fate commitment / enterocyte differentiation / regulation of keratinocyte proliferation / bud elongation involved in lung branching / regulation of metanephric nephron tubule epithelial cell differentiation / cardiac muscle tissue regeneration / TEAD-YAP complex / lateral mesoderm development / glandular epithelial cell differentiation / RUNX3 regulates YAP1-mediated transcription / polarized epithelial cell differentiation / 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 / 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 / cell fate specification / organ growth / negative regulation of epithelial cell differentiation / muscle organ development / interleukin-6-mediated signaling pathway / positive regulation of Notch signaling pathway / negative regulation of fat cell differentiation / positive regulation of stem cell population maintenance / RUNX2 regulates osteoblast differentiation / Zygotic genome activation (ZGA) / somatic stem cell population maintenance / regulation of neurogenesis / embryonic organ development / vasculogenesis / canonical Wnt signaling pathway / positive regulation of osteoblast differentiation / positive regulation of cardiac muscle cell proliferation / Nuclear signaling by ERBB4 / cellular response to retinoic acid / keratinocyte differentiation / extrinsic apoptotic signaling pathway / embryo implantation / positive regulation of epithelial cell proliferation / epithelial cell proliferation / skeletal system development / response to progesterone / negative regulation of extrinsic apoptotic signaling pathway / transcription coregulator activity / wound healing / cell morphogenesis / cellular response to gamma radiation / positive regulation of protein localization to nucleus / transcription corepressor activity / positive regulation of canonical Wnt signaling pathway / cell-cell junction / cell junction / RUNX1 regulates transcription of genes involved in differentiation of HSCs / positive regulation of cell growth / protein-containing complex assembly / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / transcription regulator complex / transcription coactivator activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / DNA-templated transcription / DNA damage response / chromatin binding / positive regulation of gene expression / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Virus Scaffolding Protein; Chain A / Virus Scaffolding Protein; Chain A - #10 / Transcriptional enhancer factor TEF-3 (TEAD4) / Coagulation Factor XIII; Chain A, domain 1 - #80 / : / Omega loop, TEAD interating region 3 / : / TEA/ATTS domain / Transcriptional enhancer factor, metazoa / TEA/ATTS domain superfamily ...Virus Scaffolding Protein; Chain A / Virus Scaffolding Protein; Chain A - #10 / Transcriptional enhancer factor TEF-3 (TEAD4) / Coagulation Factor XIII; Chain A, domain 1 - #80 / : / Omega loop, TEAD interating region 3 / : / TEA/ATTS domain / Transcriptional enhancer factor, metazoa / TEA/ATTS domain superfamily / TEA/ATTS domain / TEA domain signature. / TEA domain profile. / TEA domain / YAP binding domain / : / YAP binding domain / Coagulation Factor XIII; Chain A, domain 1 / Other non-globular / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / Distorted Sandwich / Special / Mainly Beta
Similarity search - Domain/homology
MYRISTIC ACID / PHOSPHATE ION / Transcriptional coactivator YAP1 / Transcriptional enhancer factor TEF-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsKallen, J.
CitationJournal: Protein Sci. / Year: 2018
Title: Adaptation of the bound intrinsically disordered protein YAP to mutations at the YAP:TEAD interface.
Authors: Mesrouze, Y. / Bokhovchuk, F. / Izaac, A. / Meyerhofer, M. / Zimmermann, C. / Fontana, P. / Schmelzle, T. / Erdmann, D. / Furet, P. / Kallen, J. / Chene, P.
History
DepositionApr 25, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_CC_half / _reflns.pdbx_Rpim_I_all ..._reflns.pdbx_CC_half / _reflns.pdbx_Rpim_I_all / _reflns_shell.pdbx_CC_half / _reflns_shell.pdbx_Rpim_I_all
Revision 1.2Oct 31, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transcriptional enhancer factor TEF-3
L: Transcriptional coactivator YAP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6857
Polymers30,0772
Non-polymers6085
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-39 kcal/mol
Surface area13000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.902, 58.902, 158.628
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-732-

HOH

-
Components

#1: Protein Transcriptional enhancer factor TEF-3 / TEA domain family member 4 / TEAD-4 / Transcription factor 13-like 1 / Transcription factor RTEF-1


Mass: 25426.686 Da / Num. of mol.: 1 / Fragment: C-terminal domain, YAP binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TEAD4, RTEF1, TCF13L1, TEF3 / Plasmid: pET28-derived vector / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q15561
#2: Protein/peptide Transcriptional coactivator YAP1 / Yes-associated protein 1 / Protein yorkie homolog / Yes-associated protein YAP65 homolog


Mass: 4650.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46937
#3: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.29 Å3/Da / Density % sol: 46.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 2M ammonium sulfate, 0.1M Bis-TRIS

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99993 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 25, 2017
RadiationMonochromator: SI 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99993 Å / Relative weight: 1
ReflectionResolution: 1.8→19.49 Å / Num. obs: 26774 / % possible obs: 99.9 % / Redundancy: 12.8 % / Biso Wilson estimate: 28.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.085 / Rrim(I) all: 0.088 / Net I/σ(I): 23 / Num. measured all: 342171
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 13.1 % / Rmerge(I) obs: 0.812 / Mean I/σ(I) obs: 3.8 / CC1/2: 0.919 / Rrim(I) all: 0.845 / % possible all: 99.9

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GE3

6ge3


Resolution: 1.8→19.49 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.931 / SU B: 2.831 / SU ML: 0.089 / SU R Cruickshank DPI: 0.1542 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.154 / ESU R Free: 0.133
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2385 1339 5 %RANDOM
Rwork0.2186 ---
obs0.2196 25434 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 61.33 Å2 / Biso mean: 23 Å2 / Biso min: 12.13 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2--0.06 Å20 Å2
3----0.11 Å2
Refinement stepCycle: final / Resolution: 1.8→19.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2069 0 35 197 2301
Biso mean--35.06 32.45 -
Num. residues----254
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222236
X-RAY DIFFRACTIONr_angle_refined_deg0.9311.9633049
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.935281
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.85524.312109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.27915385
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5751510
X-RAY DIFFRACTIONr_chiral_restr0.0620.2328
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211710
LS refinement shellResolution: 1.8→1.846 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 96 -
Rwork0.273 1827 -
all-1923 -
obs--99.95 %

+
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