+Open data
-Basic information
Entry | Database: PDB / ID: 1.0E+42 | ||||||
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Title | Beta2-adaptin appendage domain, from clathrin adaptor AP2 | ||||||
Components | AP-2 COMPLEX SUBUNIT BETA | ||||||
Keywords | ENDOCYTOSIS / ADAPTOR | ||||||
Function / homology | Function and homology information Nef Mediated CD8 Down-regulation / clathrin adaptor complex / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / Trafficking of GluR2-containing AMPA receptors / WNT5A-dependent internalization of FZD4 / AP-2 adaptor complex / postsynaptic neurotransmitter receptor internalization / Retrograde neurotrophin signalling / clathrin-coated endocytic vesicle / LDL clearance ...Nef Mediated CD8 Down-regulation / clathrin adaptor complex / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / Trafficking of GluR2-containing AMPA receptors / WNT5A-dependent internalization of FZD4 / AP-2 adaptor complex / postsynaptic neurotransmitter receptor internalization / Retrograde neurotrophin signalling / clathrin-coated endocytic vesicle / LDL clearance / clathrin-dependent endocytosis / coronary vasculature development / signal sequence binding / Nef Mediated CD4 Down-regulation / endolysosome membrane / aorta development / ventricular septum development / clathrin binding / Recycling pathway of L1 / synaptic vesicle endocytosis / EPH-ephrin mediated repulsion of cells / vesicle-mediated transport / MHC class II antigen presentation / VLDLR internalisation and degradation / clathrin-coated endocytic vesicle membrane / kidney development / intracellular protein transport / cytoplasmic side of plasma membrane / Cargo recognition for clathrin-mediated endocytosis / endocytic vesicle membrane / Clathrin-mediated endocytosis / presynapse / Potential therapeutics for SARS / postsynapse / glutamatergic synapse / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.7 Å | ||||||
Authors | Owen, D.J. / Evans, P.R. / McMahon, H.T. | ||||||
Citation | Journal: Embo J. / Year: 2000 Title: The Structure and Function of the Beta2-Adaptin Appendage Domain Authors: Owen, D.J. / Vallis, Y. / Pearse, B.M.F. / Mcmahon, H.T. / 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 | 1e42.cif.gz | 128 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1e42.ent.gz | 98.8 KB | Display | PDB format |
PDBx/mmJSON format | 1e42.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1e42_validation.pdf.gz | 470.3 KB | Display | wwPDB validaton report |
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Full document | 1e42_full_validation.pdf.gz | 480.3 KB | Display | |
Data in XML | 1e42_validation.xml.gz | 30 KB | Display | |
Data in CIF | 1e42_validation.cif.gz | 46.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e4/1e42 ftp://data.pdbj.org/pub/pdb/validation_reports/e4/1e42 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.379985, 0.020033, -0.924776), Vector: Details | THE BETA-ADAPTIN PROTEIN IS PART OF THE ASSEMBLY PROTEINCOMPLEX 2, (AP-2), THAT IS A HETEROTETRAMER COMPOSED OF TWO LARGE CHAINS (ALPHA AND BETA), A MEDIUM CHAIN (AP50)AND A SMALL CHAIN (AP17). | |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 29088.453 Da / Num. of mol.: 2 / Fragment: APPENDAGE DOMAIN, RESIDUES 701-937 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: P63010 |
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-Non-polymers , 6 types, 835 molecules
#2: Chemical | #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-CL / #5: Chemical | #6: Chemical | ChemComp-NI / | #7: Water | ChemComp-HOH / | |
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-Details
Sequence details | CLONING HEADER MGSSHHHHHH |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 55 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.8 Details: WELL SOLUTION: 1.6 - 2.0M MGCL2, 0.1M BICINE PH 8.7 - 9.0, 15% GLYCEROL, 1MM DTT. PROTEIN: 40MG/ML, 5MM HEPES, 50MM NACL, 4MM DTT, 1:1 MIXTURE | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / PH range low: 9 / PH range high: 8.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 0.88 |
Detector | Type: ADSC QUANTUM / Detector: CCD / Date: Sep 15, 1998 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.88 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→19.96 Å / Num. obs: 71562 / % possible obs: 98.4 % / Observed criterion σ(I): 4 / Redundancy: 6.85 % / Biso Wilson estimate: 33 Å2 / Rmerge(I) obs: 0.157 / Rsym value: 0.157 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 1.48 / Rsym value: 0.75 / % possible all: 89.6 |
Reflection shell | *PLUS % possible obs: 98.3 % |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 1.7→67.42 Å / SU B: 3.538 / SU ML: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.179 / ESU R Free: 0.164 Details: RESIDUES A980 AND B980 WERE MODELLED AS GLYCEROL, BUT IDENTIFICATION IS NOT CERTAIN. RESIDUE B970 WAS MODELLED AS A 50% NI ION, SINCE IT IS BOUND TO A HISTIDINE, BUT IT MAY BE ANOTHER MG ION
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Displacement parameters | Biso mean: 32 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→67.42 Å
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Software | *PLUS Name: REFMAC / Version: VERSION 5 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.196 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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