[English] 日本語
Yorodumi- PDB-7yo9: Crystal structure of fusion protein of human TP53INP2 LIR and hum... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7yo9 | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of fusion protein of human TP53INP2 LIR and human GABARAP | |||||||||||||||
Components | Tumor protein p53-inducible nuclear protein 2,Gamma-aminobutyric acid receptor-associated protein | |||||||||||||||
Keywords | PROTEIN TRANSPORT / Autophagy | |||||||||||||||
Function / homology | Function and homology information negative regulation of protein localization / positive regulation of protein K48-linked ubiquitination / regulation of Rac protein signal transduction / GABA receptor binding / tissue homeostasis / cellular response to nitrogen starvation / phosphatidylethanolamine binding / TBC/RABGAPs / microtubule associated complex / Macroautophagy ...negative regulation of protein localization / positive regulation of protein K48-linked ubiquitination / regulation of Rac protein signal transduction / GABA receptor binding / tissue homeostasis / cellular response to nitrogen starvation / phosphatidylethanolamine binding / TBC/RABGAPs / microtubule associated complex / Macroautophagy / beta-tubulin binding / axoneme / autophagosome membrane / autophagosome maturation / autophagosome assembly / extrinsic apoptotic signaling pathway via death domain receptors / smooth endoplasmic reticulum / autophagosome / protein targeting / sperm midpiece / ubiquitin binding / protein localization / PML body / microtubule cytoskeleton organization / osteoblast differentiation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / protein transport / actin cytoskeleton / cytoplasmic vesicle / ubiquitin-dependent protein catabolic process / microtubule binding / chemical synaptic transmission / microtubule / lysosome / Golgi membrane / ubiquitin protein ligase binding / synapse / positive regulation of DNA-templated transcription / nucleus / plasma membrane / cytosol Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | |||||||||||||||
Authors | Yamasaki, A. / Noda, N.N. | |||||||||||||||
Funding support | Japan, 4items
| |||||||||||||||
Citation | Journal: Autophagy / Year: 2023 Title: Development of new tools to study membrane-anchored mammalian Atg8 proteins. Authors: Park, S.W. / Jeon, P. / Yamasaki, A. / Lee, H.E. / Choi, H. / Mun, J.Y. / Jun, Y.W. / Park, J.H. / Lee, S.H. / Lee, S.K. / Lee, Y.K. / Song, H.K. / Lazarou, M. / Cho, D.H. / Komatsu, M. / ...Authors: Park, S.W. / Jeon, P. / Yamasaki, A. / Lee, H.E. / Choi, H. / Mun, J.Y. / Jun, Y.W. / Park, J.H. / Lee, S.H. / Lee, S.K. / Lee, Y.K. / Song, H.K. / Lazarou, M. / Cho, D.H. / Komatsu, M. / Noda, N.N. / Jang, D.J. / Lee, J.A. | |||||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7yo9.cif.gz | 86.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7yo9.ent.gz | 52.5 KB | Display | PDB format |
PDBx/mmJSON format | 7yo9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7yo9_validation.pdf.gz | 975.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7yo9_full_validation.pdf.gz | 976.6 KB | Display | |
Data in XML | 7yo9_validation.xml.gz | 8.1 KB | Display | |
Data in CIF | 7yo9_validation.cif.gz | 10.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yo/7yo9 ftp://data.pdbj.org/pub/pdb/validation_reports/yo/7yo9 | HTTPS FTP |
-Related structure data
Related structure data | 7yo8C 1gnuS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 15452.565 Da / Num. of mol.: 1 Fragment: Tumor protein p53-inducible nuclear protein 2(1-15), Gamma-aminobutyric acid receptor-associated protein(16-131) Mutation: F18S,V19T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TP53INP2, C20orf110, DOR, PINH, GABARAP, FLC3B, HT004 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8IXH6, UniProt: O95166 |
---|---|
#2: Chemical | ChemComp-IPA / |
#3: Chemical | ChemComp-PO4 / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.15 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: 10% 2-propanol, 0.1 M sodium phosphate/citric acid pH 4.2, 0.2 M lithium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 24, 2019 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.75→46.392 Å / Num. obs: 31600 / % possible obs: 99.5 % / Redundancy: 3.554 % / Biso Wilson estimate: 43.736 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.091 / Rrim(I) all: 0.106 / Χ2: 0.994 / Net I/σ(I): 7.66 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1GNU Resolution: 1.75→46.39 Å / SU ML: 0.2862 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 29.911 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.46 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→46.39 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
|