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Yorodumi- PDB-1hes: MU2 ADAPTIN SUBUNIT (AP50) OF AP2 ADAPTOR (SECOND DOMAIN), COMPLE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hes | ||||||
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Title | MU2 ADAPTIN SUBUNIT (AP50) OF AP2 ADAPTOR (SECOND DOMAIN), COMPLEXED WITH P-selectin INTERNALIZATION PEPTIDE SHLGTYGVFTNAA | ||||||
Components |
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Keywords | ENDOCYTOSIS/EXOCYTOSIS / ENDOCYTOSIS / ADAPTOR / PEPTIDE COMPLEX / PEPTIDE BINDING PROTE / ENDOCYTOSIS-EXOCYTOSIS complex | ||||||
Function / homology | Function and homology information regulation of integrin activation / Gap junction degradation / Formation of annular gap junctions / fucose binding / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / VLDLR internalisation and degradation / Retrograde neurotrophin signalling / platelet dense granule membrane / glycosphingolipid binding ...regulation of integrin activation / Gap junction degradation / Formation of annular gap junctions / fucose binding / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / VLDLR internalisation and degradation / Retrograde neurotrophin signalling / platelet dense granule membrane / glycosphingolipid binding / WNT5A-dependent internalization of FZD4 / extrinsic component of presynaptic endocytic zone membrane / MHC class II antigen presentation / positive regulation of leukocyte tethering or rolling / sialic acid binding / AP-2 adaptor complex / oligosaccharide binding / regulation of vesicle size / postsynaptic neurotransmitter receptor internalization / Recycling pathway of L1 / platelet alpha granule membrane / Cargo recognition for clathrin-mediated endocytosis / positive regulation of synaptic vesicle endocytosis / Clathrin-mediated endocytosis / clathrin adaptor activity / vesicle budding from membrane / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / leukocyte tethering or rolling / clathrin-dependent endocytosis / signal sequence binding / positive regulation of platelet activation / negative regulation of protein localization to plasma membrane / positive regulation of leukocyte migration / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / leukocyte cell-cell adhesion / low-density lipoprotein particle receptor binding / Trafficking of GluR2-containing AMPA receptors / positive regulation of receptor internalization / synaptic vesicle endocytosis / clathrin-coated pit / vesicle-mediated transport / response to cytokine / Cell surface interactions at the vascular wall / lipopolysaccharide binding / cell-cell adhesion / intracellular protein transport / terminal bouton / receptor internalization / integrin binding / endocytosis / calcium-dependent protein binding / disordered domain specific binding / synaptic vesicle / Platelet degranulation / heparin binding / cytoplasmic vesicle / protein-containing complex assembly / defense response to Gram-negative bacterium / transmembrane transporter binding / postsynapse / response to lipopolysaccharide / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell adhesion / inflammatory response / external side of plasma membrane / lipid binding / glutamatergic synapse / synapse / calcium ion binding / extracellular space / plasma membrane Similarity search - Function | ||||||
Biological species | RATTUS NORVEGICUS (Norway rat) HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Owen, D.J. / Evans, P.R. / Green, S.A. | ||||||
Citation | Journal: Traffic / Year: 2001 Title: A Third Specificity-Determining Site in Mu 2 Adaptin for Sequences Upstream of Yxx Phi Sorting Motifs Authors: Owen, D.J. / Setiadi, H. / Evans, P.R. / Mcever, R.P. / Green, S.A. #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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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hes.cif.gz | 67.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hes.ent.gz | 49.4 KB | Display | PDB format |
PDBx/mmJSON format | 1hes.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1hes_validation.pdf.gz | 438.4 KB | Display | wwPDB validaton report |
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Full document | 1hes_full_validation.pdf.gz | 445.9 KB | Display | |
Data in XML | 1hes_validation.xml.gz | 13 KB | Display | |
Data in CIF | 1hes_validation.cif.gz | 17.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/he/1hes ftp://data.pdbj.org/pub/pdb/validation_reports/he/1hes | HTTPS FTP |
-Related structure data
Related structure data | 1bw8S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 32758.363 Da / Num. of mol.: 1 / Fragment: INTERNALIZATION SIGNAL BINDING DOMAIN Source method: isolated from a genetically manipulated source Details: THE FIRST SEVEN RESIDUES OF THE POLYMER MAKE UP A HIS-TAG Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Gene: AP50 / Plasmid: PMW172H6 / Gene (production host): AP50 / Production host: ESCHERICHIA COLI BL21 (bacteria) / References: UniProt: P20172, UniProt: P84092*PLUS |
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#2: Protein/peptide | Mass: 1882.015 Da / Num. of mol.: 1 / Fragment: INTERNALIZATION SIGNAL / Source method: obtained synthetically Details: PEPTIDE INTERNALISATION SIGNAL MOTIF FROM P-SELECTIN SHLGTYGVFTNAAFDPSP Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P16109 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.7 Å3/Da / Density % sol: 79 % / Description: ISOMORPHOUS TO 1BW8 | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.1 Details: HANGING DROP, 2.2M NACL, 0.4M NA/K PHOSPHATE, 10MM DTT 0.1M MES PH 7.1, 15% GLYCEROL, 16 DEGREES, MOLAR RATIO OF PEPTIDE TO PROTEIN 3:1 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 16 ℃ / Method: vapor diffusion, hanging drop / Details: Owen, D.J., (1998) Science, 282, 1327. / PH range low: 7.1 / PH range high: 6.5 | ||||||||||||||||||||||||||||||||||||||||||
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: 0.877 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 18, 2000 / Details: MIRROR |
Radiation | Monochromator: YES / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.877 Å / Relative weight: 1 |
Reflection | Resolution: 3→22 Å / Num. obs: 13729 / % possible obs: 100 % / Observed criterion σ(I): 4 / Redundancy: 9.2 % / Biso Wilson estimate: 90 Å2 / Rmerge(I) obs: 0.146 / Rsym value: 0.146 / Net I/σ(I): 17.4 |
Reflection shell | Resolution: 3→3.16 Å / Redundancy: 14.7 % / Rmerge(I) obs: 0.0106 / Mean I/σ(I) obs: 2 / Rsym value: 0.0106 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BW8 Resolution: 3→100 Å / SU B: 18.91 / SU ML: 0.359 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.442 / ESU R Free: 0.329 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Displacement parameters | Biso mean: 51 Å2
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Refinement step | Cycle: LAST / Resolution: 3→100 Å
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Software | *PLUS Name: REFMAC / Version: 5 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Rfactor Rwork: 0.21 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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