[English] 日本語
![](img/lk-miru.gif)
- PDB-1h6e: MU2 ADAPTIN SUBUNIT (AP50) OF AP2 ADAPTOR (SECOND DOMAIN), COMPLE... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1h6e | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | MU2 ADAPTIN SUBUNIT (AP50) OF AP2 ADAPTOR (SECOND DOMAIN), COMPLEXED WITH CTLA-4 INTERNALIZATION PEPTIDE TTGVYVKMPPT | |||||||||
![]() |
| |||||||||
![]() | ENDOCYTOSIS/EXOCYTOSIS / ENDOCYTOSIS / ADAPTOR / PEPTIDE COMPLEX / PHOSPHORYLATION / ENDOCYTOSIS-EXOCYTOSIS complex | |||||||||
Function / homology | ![]() Nef mediated downregulation of CD28 cell surface expression / Gap junction degradation / Formation of annular gap junctions / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / VLDLR internalisation and degradation / Retrograde neurotrophin signalling / protein complex involved in cell adhesion / Nef Mediated CD8 Down-regulation / WNT5A-dependent internalization of FZD4 ...Nef mediated downregulation of CD28 cell surface expression / Gap junction degradation / Formation of annular gap junctions / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / VLDLR internalisation and degradation / Retrograde neurotrophin signalling / protein complex involved in cell adhesion / Nef Mediated CD8 Down-regulation / WNT5A-dependent internalization of FZD4 / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / Trafficking of GluR2-containing AMPA receptors / extrinsic component of presynaptic endocytic zone membrane / WNT5A-dependent internalization of FZD4 / MHC class II antigen presentation / negative regulation of regulatory T cell differentiation / AP-2 adaptor complex / regulation of vesicle size / postsynaptic neurotransmitter receptor internalization / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / Recycling pathway of L1 / Retrograde neurotrophin signalling / Formation of annular gap junctions / Cargo recognition for clathrin-mediated endocytosis / positive regulation of synaptic vesicle endocytosis / clathrin-coated endocytic vesicle / Gap junction degradation / LDL clearance / Clathrin-mediated endocytosis / clathrin adaptor activity / vesicle budding from membrane / clathrin-dependent endocytosis / signal sequence binding / Nef Mediated CD4 Down-regulation / endolysosome membrane / negative regulation of protein localization to plasma membrane / low-density lipoprotein particle receptor binding / CTLA4 inhibitory signaling / negative regulation of B cell proliferation / Recycling pathway of L1 / Trafficking of GluR2-containing AMPA receptors / positive regulation of receptor internalization / synaptic vesicle endocytosis / EPH-ephrin mediated repulsion of cells / negative regulation of T cell proliferation / clathrin-coated pit / vesicle-mediated transport / MHC class II antigen presentation / VLDLR internalisation and degradation / B cell receptor signaling pathway / intracellular protein transport / clathrin-coated endocytic vesicle membrane / terminal bouton / receptor internalization / cytoplasmic side of plasma membrane / endocytosis / endocytic vesicle membrane / disordered domain specific binding / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / T cell receptor signaling pathway / cytoplasmic vesicle / postsynapse / protein-containing complex assembly / adaptive immune response / transmembrane transporter binding / Potential therapeutics for SARS / immune response / positive regulation of apoptotic process / lysosomal membrane / external side of plasma membrane / glutamatergic synapse / lipid binding / DNA damage response / perinuclear region of cytoplasm / Golgi apparatus / extracellular exosome / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Rowsell, S. / Pauptit, R.A. | |||||||||
![]() | ![]() Title: Study of the Interaction of the Medium Chain Mu2 Subunit of the Clathrin-Associated Adapter Protein Complex 2 with Cytotoxic T-Lymphocyte Antigen 4 and Cd28 Authors: Follows, E.R. / Mcpheat, J.C. / Minshull, C. / Moore, N.C. / Pauptit, R.A. / Rowsell, S. / Stacey, C.L. / Stanway, J.J. / Taylor, I.W. / Abbott, W.M. #1: ![]() Title: A Structural Explanation for the Recognition of Tyrosine-Based Endocytotic Signals Authors: Owen, D.J. / Evans, P.R. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 60.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 43.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 433.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 446.8 KB | Display | |
Data in XML | ![]() | 12.3 KB | Display | |
Data in CIF | ![]() | 15.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1bxxS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 33014.516 Da / Num. of mol.: 1 / Fragment: INTERNALIZATION SIGNAL BINDING DOMAIN Source method: isolated from a genetically manipulated source Details: THE FIRST 16 RESIDUES OF THE POLYMER MAKE UP A 6HIS-CMYC-TAG (HHHHHHEQKLISEEDL) Source: (gene. exp.) ![]() ![]() ![]() |
---|---|
#2: Protein/peptide | Mass: 1194.419 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: 11-MER INTERNALISATION SIGNAL MOTIF FROM CTLA-4 (HOMO SAPIENS), TTGVYVKMPPT Source: (synth.) ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 5.03 Å3/Da / Density % sol: 75 % / Description: ISOMORPHOUS TO 1BXX | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Method: vapor diffusion, hanging drop / pH: 7 Details: HANGING DROPS CONTAINING A 1:1 MIXTURE OF COMPLEX SOLUTION 6MG/ML PROTEIN AND 1MM 11MER PEPTIDE SOLUTION IN 20MM HEPES PH7.5, 1MM DTT AND RESERVOIR BUFFER 1.4-2.4M SODIUM CHLORIDE, 0.1M MES ...Details: HANGING DROPS CONTAINING A 1:1 MIXTURE OF COMPLEX SOLUTION 6MG/ML PROTEIN AND 1MM 11MER PEPTIDE SOLUTION IN 20MM HEPES PH7.5, 1MM DTT AND RESERVOIR BUFFER 1.4-2.4M SODIUM CHLORIDE, 0.1M MES PH6.2-7.0, 0.4M NA/K PHOSPHATE, 15% GLYCEROL, pH 7.00 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 15 ℃ / pH: 7.5 / Method: vapor diffusion | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 26, 1999 / Details: MIRROR |
Radiation | Monochromator: YES / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 3.6→48.2 Å / Num. obs: 6681 / % possible obs: 83.2 % / Redundancy: 2.2 % / Biso Wilson estimate: 0 Å2 / Rmerge(I) obs: 0.133 / Net I/σ(I): 4 |
Reflection shell | Resolution: 3.6→3.8 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 1.7 / % possible all: 85.9 |
Reflection | *PLUS Num. measured all: 14633 |
Reflection shell | *PLUS % possible obs: 85.9 % / Num. unique obs: 992 / Num. measured obs: 2081 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1BXX Resolution: 3.6→7.99 Å / Rfactor Rfree error: 0.013 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.14399 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.6 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.6→7.99 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.6→3.8 Å / Rfactor Rfree error: 0.067 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file | Serial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|