+Open data
-Basic information
Entry | Database: PDB / ID: 1jmq | ||||||
---|---|---|---|---|---|---|---|
Title | YAP65 (L30K mutant) WW domain in Complex with GTPPPPYTVG peptide | ||||||
Components |
| ||||||
Keywords | STRUCTURAL PROTEIN / WW domain / polyproline ligand / YAP65 mutant | ||||||
Function / homology | Function and homology information enterocyte differentiation / regulation of keratinocyte proliferation / regulation of metanephric nephron tubule epithelial cell differentiation / cardiac muscle tissue regeneration / glandular epithelial cell differentiation / TEAD-YAP complex / lateral mesoderm development / RUNX3 regulates YAP1-mediated transcription / bud elongation involved in lung branching / polarized epithelial cell differentiation ...enterocyte differentiation / regulation of keratinocyte proliferation / regulation of metanephric nephron tubule epithelial cell differentiation / cardiac muscle tissue regeneration / glandular epithelial cell differentiation / TEAD-YAP complex / lateral mesoderm development / RUNX3 regulates YAP1-mediated transcription / bud elongation involved in lung branching / polarized epithelial cell differentiation / notochord development / negative regulation of cilium assembly / lung epithelial cell differentiation / WW domain binding / YAP1- and WWTR1 (TAZ)-stimulated gene expression / heart process / trophectodermal cell differentiation / paraxial mesoderm development / regulation of stem cell proliferation / hippo signaling / tissue homeostasis / EGR2 and SOX10-mediated initiation of Schwann cell myelination / intestinal epithelial cell development / negative regulation of epithelial cell apoptotic process / Formation of axial mesoderm / negative regulation of stem cell differentiation / embryonic heart tube morphogenesis / female germ cell nucleus / proline-rich region binding / Signaling by Hippo / negative regulation of epithelial cell differentiation / organ growth / interleukin-6-mediated signaling pathway / positive regulation of stem cell population maintenance / positive regulation of Notch signaling pathway / negative regulation of fat cell differentiation / RUNX2 regulates osteoblast differentiation / Zygotic genome activation (ZGA) / somatic stem cell population maintenance / regulation of neurogenesis / canonical Wnt signaling pathway / vasculogenesis / positive regulation of osteoblast differentiation / cellular response to retinoic acid / extrinsic apoptotic signaling pathway / Nuclear signaling by ERBB4 / keratinocyte differentiation / positive regulation of cardiac muscle cell proliferation / epithelial cell proliferation / positive regulation of epithelial cell proliferation / response to progesterone / negative regulation of extrinsic apoptotic signaling pathway / wound healing / cell morphogenesis / cellular response to gamma radiation / positive regulation of protein localization to nucleus / transcription corepressor activity / cell-cell junction / positive regulation of canonical Wnt signaling pathway / cell junction / 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 / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / DNA damage response / chromatin binding / positive regulation of gene expression / 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Pires, J.R. / Taha-Nejad, F. / Toepert, F. / Ast, T. / Hoffmuller, U. / Schneider-Mergener, J. / Kuhne, R. / Macias, M.J. / Oschkinat, H. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: Solution structures of the YAP65 WW domain and the variant L30 K in complex with the peptides GTPPPPYTVG, N-(n-octyl)-GPPPY and PLPPY and the application of peptide libraries reveal a minimal binding epitope. Authors: Pires, J.R. / Taha-Nejad, F. / Toepert, F. / Ast, T. / Hoffmuller, U. / Schneider-Mergener, J. / Kuhne, R. / Macias, M.J. / Oschkinat, H. | ||||||
History |
| ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR | ||||||
Remark 999 | SEQUENCE THE WW DOMAIN BINDING PROTEIN-1 FRAGMENT WAS CHEMICALLY SYNTHESIZED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1jmq.cif.gz | 344.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1jmq.ent.gz | 285 KB | Display | PDB format |
PDBx/mmJSON format | 1jmq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jmq_validation.pdf.gz | 353.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1jmq_full_validation.pdf.gz | 592.7 KB | Display | |
Data in XML | 1jmq_validation.xml.gz | 27 KB | Display | |
Data in CIF | 1jmq_validation.cif.gz | 41.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jm/1jmq ftp://data.pdbj.org/pub/pdb/validation_reports/jm/1jmq | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: Protein/peptide | Mass: 5360.021 Da / Num. of mol.: 1 / Mutation: L30K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: YAP65 / Plasmid: pGAT2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P46937 |
---|---|
#2: Protein/peptide | Mass: 985.090 Da / Num. of mol.: 1 / Fragment: residues 147-156 / Source method: obtained synthetically Details: This peptide was chemically synthesized. The sequence of the peptide is naturally found in Homo sapiens (human). References: GenBank: 4205084, UniProt: Q96G27*PLUS |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
|
-Sample preparation
Details |
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Sample conditions |
| |||||||||||||||
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Radiation wavelength | Relative weight: 1 | |||||||||||||||
NMR spectrometer |
|
-Processing
NMR software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: simulated annealing / Software ordinal: 1 Details: 2000K, 200 runs, force constants for NOE 50 kcalmol-1rad-2, 590 restraints including 20 hydrogen bond restraints | ||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 20 |