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Yorodumi- PDB-1h6e: MU2 ADAPTIN SUBUNIT (AP50) OF AP2 ADAPTOR (SECOND DOMAIN), COMPLE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1h6e | |||||||||
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Title | MU2 ADAPTIN SUBUNIT (AP50) OF AP2 ADAPTOR (SECOND DOMAIN), COMPLEXED WITH CTLA-4 INTERNALIZATION PEPTIDE TTGVYVKMPPT | |||||||||
Components |
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Keywords | ENDOCYTOSIS/EXOCYTOSIS / ENDOCYTOSIS / ADAPTOR / PEPTIDE COMPLEX / PHOSPHORYLATION / ENDOCYTOSIS-EXOCYTOSIS complex | |||||||||
Function / homology | Function and homology information Nef mediated downregulation of CD28 cell surface expression / Gap junction degradation / Formation of annular gap junctions / protein complex involved in cell adhesion / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / VLDLR internalisation and degradation / Retrograde neurotrophin signalling / 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 / protein complex involved in cell adhesion / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / VLDLR internalisation and degradation / Retrograde neurotrophin signalling / 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 / Cargo recognition for clathrin-mediated endocytosis / positive regulation of synaptic vesicle endocytosis / clathrin-coated endocytic vesicle / LDL clearance / Clathrin-mediated endocytosis / clathrin adaptor activity / Formation of annular gap junctions / Gap junction degradation / 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 / clathrin-coated endocytic vesicle membrane / B cell receptor signaling pathway / intracellular protein transport / terminal bouton / receptor internalization / cytoplasmic side of plasma membrane / endocytosis / Cargo recognition for clathrin-mediated endocytosis / disordered domain specific binding / endocytic vesicle membrane / Clathrin-mediated endocytosis / T cell receptor signaling pathway / cytoplasmic vesicle / Potential therapeutics for SARS / protein-containing complex assembly / adaptive immune response / transmembrane transporter binding / postsynapse / immune response / positive regulation of apoptotic process / external side of plasma membrane / lysosomal membrane / DNA damage response / lipid binding / glutamatergic synapse / perinuclear region of cytoplasm / Golgi apparatus / extracellular exosome / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | HOMO SAPIENS (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.6 Å | |||||||||
Authors | Rowsell, S. / Pauptit, R.A. | |||||||||
Citation | Journal: Biochem.J. / Year: 2001 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: Journal: Science / Year: 1998 Title: A Structural Explanation for the Recognition of Tyrosine-Based Endocytotic Signals Authors: Owen, D.J. / Evans, P.R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1h6e.cif.gz | 60.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1h6e.ent.gz | 43.3 KB | Display | PDB format |
PDBx/mmJSON format | 1h6e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h6/1h6e ftp://data.pdbj.org/pub/pdb/validation_reports/h6/1h6e | HTTPS FTP |
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-Related structure data
Related structure data | 1bxxS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-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.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P20172, UniProt: Q96CW1*PLUS |
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#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.) HOMO SAPIENS (human) / References: UniProt: P16410 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.03 Å3/Da / Density % sol: 75 % / Description: ISOMORPHOUS TO 1BXX | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
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 |
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Refinement | Method to determine structure: FOURIER SYNTHESIS 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
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.14399 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.6→7.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.6→3.8 Å / Rfactor Rfree error: 0.067 / Total num. of bins used: 6
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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
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