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- PDB-4hmy: Structural basis for recruitment and activation of the AP-1 clath... -
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Basic information
Entry | Database: PDB / ID: 4hmy | ||||||
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Title | Structural basis for recruitment and activation of the AP-1 clathrin adaptor complex by Arf1 | ||||||
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![]() | PROTEIN TRANSPORT / protein trafficking / Arf1 GTPase activation / Arf1 GTPase binding / Trans-Golgi membrane | ||||||
Function / homology | ![]() basolateral protein secretion / mitotic cleavage furrow ingression / endosome to melanosome transport / trans-Golgi Network Vesicle Budding / AP-1 adaptor complex / Lysosome Vesicle Biogenesis / platelet dense granule organization / Glycosphingolipid transport / regulation of receptor internalization / melanosome assembly ...basolateral protein secretion / mitotic cleavage furrow ingression / endosome to melanosome transport / trans-Golgi Network Vesicle Budding / AP-1 adaptor complex / Lysosome Vesicle Biogenesis / platelet dense granule organization / Glycosphingolipid transport / regulation of receptor internalization / melanosome assembly / regulation of Arp2/3 complex-mediated actin nucleation / Intra-Golgi traffic / Golgi to vacuole transport / Synthesis of PIPs at the Golgi membrane / Golgi Associated Vesicle Biogenesis / clathrin adaptor activity / MHC class II antigen presentation / Nef Mediated CD4 Down-regulation / dendritic spine organization / determination of left/right symmetry / long-term synaptic depression / clathrin-coated vesicle / COPI-dependent Golgi-to-ER retrograde traffic / Lysosome Vesicle Biogenesis / clathrin binding / Golgi Associated Vesicle Biogenesis / cell leading edge / Synthesis of PIPs at the plasma membrane / intracellular copper ion homeostasis / protein targeting / COPI-mediated anterograde transport / clathrin-coated pit / vesicle-mediated transport / MHC class II antigen presentation / Neutrophil degranulation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / sarcomere / small monomeric GTPase / trans-Golgi network membrane / Nef mediated downregulation of MHC class I complex cell surface expression / kidney development / intracellular protein transport / trans-Golgi network / cytoplasmic vesicle membrane / cellular response to virus / presynapse / heart development / postsynaptic density / early endosome / neuron projection / protein domain specific binding / Golgi membrane / lysosomal membrane / intracellular membrane-bounded organelle / focal adhesion / GTPase activity / synapse / GTP binding / protein kinase binding / perinuclear region of cytoplasm / Golgi apparatus / magnesium ion binding / protein-containing complex / RNA binding / extracellular exosome / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ren, X. / Farias, G.G. / Canagarajah, B.J. / Bonifacino, J.S. / Hurley, J.H. | ||||||
![]() | ![]() Title: Structural Basis for Recruitment and Activation of the AP-1 Clathrin Adaptor Complex by Arf1. Authors: Ren, X. / Farias, G.G. / Canagarajah, B.J. / Bonifacino, J.S. / Hurley, J.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 334.9 KB | Display | ![]() |
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PDB format | ![]() | 254 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2xa7S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-AP-1 complex subunit ... , 4 types, 4 molecules ABMS
#1: Protein | Mass: 68194.094 Da / Num. of mol.: 1 / Fragment: UNP residues 1-595 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 66186.562 Da / Num. of mol.: 1 / Fragment: UNP residues 1-584 / Mutation: I488F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Protein | Mass: 48606.730 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#4: Protein | Mass: 18321.338 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Protein , 1 types, 1 molecules C
#5: Protein | Mass: 19896.678 Da / Num. of mol.: 1 / Fragment: UNP residues 17-181 / Mutation: Q71L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 2 types, 2 molecules ![](data/chem/img/GTP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/MG.gif)
#6: Chemical | ChemComp-GTP / |
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#7: Chemical | ChemComp-MG / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2M lithium sulfate, 0.1M Tris pH 8.5, 0.2M lithium nitrate, 0.7M ammonium sulphate, 1mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 288K |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Apr 12, 2012 |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 7→50 Å / Num. all: 12533 / Num. obs: 12321 / % possible obs: 98.7 % / Observed criterion σ(F): 25 / Observed criterion σ(I): 1.9 / Redundancy: 7.1 % / Rsym value: 0.158 |
Reflection shell | Resolution: 7→7.12 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.695 / Mean I/σ(I) obs: 1.9 / % possible all: 94.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2XA7 Resolution: 7→20 Å / σ(F): 3 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 7→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 7→7.24 Å
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