[English] 日本語
Yorodumi
- PDB-6jk1: Crystal Structure of YAP1 and Dendrin complex 2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6jk1
TitleCrystal Structure of YAP1 and Dendrin complex 2
ComponentsDendrin,Transcriptional coactivator YAP1
KeywordsSIGNALING PROTEIN / WW tandem / PY tandem / YAP1 / Dendrin
Function / homology
Function and homology information


Nuclear signaling by ERBB4 / RUNX3 regulates YAP1-mediated transcription / YAP1- and WWTR1 (TAZ)-stimulated gene expression / Signaling by Hippo / enterocyte differentiation / regulation of keratinocyte proliferation / intestinal epithelial cell differentiation / glandular epithelial cell differentiation / regulation of metanephric nephron tubule epithelial cell differentiation / cardiac muscle tissue regeneration ...Nuclear signaling by ERBB4 / RUNX3 regulates YAP1-mediated transcription / YAP1- and WWTR1 (TAZ)-stimulated gene expression / Signaling by Hippo / enterocyte differentiation / regulation of keratinocyte proliferation / intestinal epithelial cell differentiation / glandular epithelial cell differentiation / regulation of metanephric nephron tubule epithelial cell differentiation / cardiac muscle tissue regeneration / TEAD-YAP complex / lateral mesoderm development / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / bud elongation involved in lung branching / RUNX1 regulates transcription of genes involved in differentiation of HSCs / notochord development / negative regulation of cilium assembly / lung epithelial cell differentiation / heart process / positive regulation of organ growth / trophectodermal cell differentiation / paraxial mesoderm development / hippo signaling / regulation of stem cell proliferation / intestinal epithelial cell development / negative regulation of epithelial cell apoptotic process / tissue homeostasis / negative regulation of stem cell differentiation / embryonic heart tube morphogenesis / female germ cell nucleus / proline-rich region binding / dendritic spine membrane / regulation of canonical Wnt signaling pathway / organ growth / interleukin-6-mediated signaling pathway / negative regulation of epithelial cell differentiation / positive regulation of Notch signaling pathway / negative regulation of fat cell differentiation / positive regulation of stem cell population maintenance / signal transduction in response to DNA damage / blastocyst development / somatic stem cell population maintenance / regulation of neurogenesis / bicellular tight junction / canonical Wnt signaling pathway / positive regulation of osteoblast differentiation / vasculogenesis / positive regulation of cardiac muscle cell proliferation / keratinocyte differentiation / extrinsic apoptotic signaling pathway / cellular response to retinoic acid / epithelial cell differentiation / response to progesterone / epithelial cell proliferation / positive regulation of epithelial cell proliferation / negative regulation of extrinsic apoptotic signaling pathway / wound healing / cellular response to gamma radiation / positive regulation of protein localization to nucleus / cell morphogenesis / cell-cell junction / transcription corepressor activity / positive regulation of canonical Wnt signaling pathway / presynapse / regulation of cell population proliferation / regulation of gene expression / positive regulation of cell growth / protein-containing complex assembly / perikaryon / transcription regulator complex / DNA-binding transcription factor binding / postsynaptic membrane / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription coactivator activity / cell population proliferation / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / positive regulation of cell population proliferation / dendrite / chromatin binding / positive regulation of gene expression / endoplasmic reticulum membrane / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion / nucleoplasm / nucleus / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Dendrin / Nephrin and CD2AP-binding protein, Dendrin / : / Omega loop, TEAD interacting region 3 / : / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain
Similarity search - Domain/homology
Transcriptional coactivator YAP1 / Dendrin
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLin, Z. / Yang, Z. / Ji, Z. / Zhang, M.
CitationJournal: Elife / Year: 2019
Title: Decoding WW domain tandem-mediated target recognitions in tissue growth and cell polarity.
Authors: Lin, Z. / Yang, Z. / Xie, R. / Ji, Z. / Guan, K. / Zhang, M.
History
DepositionFeb 27, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: 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: Dendrin,Transcriptional coactivator YAP1
B: Dendrin,Transcriptional coactivator YAP1


Theoretical massNumber of molelcules
Total (without water)25,5362
Polymers25,5362
Non-polymers00
Water3,567198
1
A: Dendrin,Transcriptional coactivator YAP1


Theoretical massNumber of molelcules
Total (without water)12,7681
Polymers12,7681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dendrin,Transcriptional coactivator YAP1


Theoretical massNumber of molelcules
Total (without water)12,7681
Polymers12,7681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.376, 77.376, 116.763
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein Dendrin,Transcriptional coactivator YAP1 / Yes-associated protein 1 / Protein yorkie homolog / Yes-associated protein YAP65 homolog


Mass: 12768.133 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Dendrin (residues 222-241 from Uniprot Q80TS7) linked YAP1 (residues 156-247 from Uniprot P46938)
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ddn, Gm748, Kiaa0749, Yap1, Yap, Yap65 / Production host: Escherichia coli (E. coli) / References: UniProt: Q80TS7, UniProt: P46938
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 3.42 Å3/Da / Density % sol: 64.06 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 28-35% w/v pentaerythritol propoxylat 426 (5/4 PO/OH), 100mM HEPES (pH 7.5)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97855 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97855 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 24702 / % possible obs: 100 % / Redundancy: 12.8 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 32.8
Reflection shellResolution: 2→2.03 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.698 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 1210 / % possible all: 100
Serial crystallography sample deliveryMethod: fixed target

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JK0

6jk0


Resolution: 2→29.191 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 19.21
RfactorNum. reflection% reflection
Rfree0.2111 1941 8.11 %
Rwork0.1853 --
obs0.1874 23948 97.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→29.191 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1433 0 0 198 1631
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071487
X-RAY DIFFRACTIONf_angle_d1.1032043
X-RAY DIFFRACTIONf_dihedral_angle_d14.548537
X-RAY DIFFRACTIONf_chiral_restr0.043203
X-RAY DIFFRACTIONf_plane_restr0.005273
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0002-2.05020.25241290.21711435X-RAY DIFFRACTION91
2.0502-2.10570.22621290.19351467X-RAY DIFFRACTION93
2.1057-2.16760.21791270.18841500X-RAY DIFFRACTION94
2.1676-2.23750.2241370.17911509X-RAY DIFFRACTION95
2.2375-2.31750.21931340.18421540X-RAY DIFFRACTION97
2.3175-2.41020.19561360.18571545X-RAY DIFFRACTION97
2.4102-2.51990.20651400.18661554X-RAY DIFFRACTION97
2.5199-2.65260.20821380.18841580X-RAY DIFFRACTION98
2.6526-2.81870.19931400.19741585X-RAY DIFFRACTION99
2.8187-3.03610.26051400.20561616X-RAY DIFFRACTION99
3.0361-3.34130.25371450.19931622X-RAY DIFFRACTION100
3.3413-3.82380.20791440.17381631X-RAY DIFFRACTION100
3.8238-4.81410.17821480.16031665X-RAY DIFFRACTION100
4.8141-29.19380.19211540.18871758X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 47.8898 Å / Origin y: 63.1532 Å / Origin z: 41.9106 Å
111213212223313233
T0.1619 Å20.0098 Å2-0.0395 Å2-0.1858 Å2-0.0048 Å2--0.1833 Å2
L1.5255 °2-0.7502 °20.3194 °2-0.9231 °20.2065 °2--1.7521 °2
S0.0118 Å °0.1826 Å °0.0339 Å °-0.1718 Å °-0.1726 Å °0.0405 Å °-0.2528 Å °0.0057 Å °0.1386 Å °
Refinement TLS groupSelection details: all

+
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