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Yorodumi- PDB-4hmy: Structural basis for recruitment and activation of the AP-1 clath... -
+Open data
-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 | ||||||
Components |
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Keywords | PROTEIN TRANSPORT / protein trafficking / Arf1 GTPase activation / Arf1 GTPase binding / Trans-Golgi membrane | ||||||
Function / homology | Function and homology information basolateral protein secretion / mitotic cleavage furrow ingression / AP-1 adaptor complex / trans-Golgi Network Vesicle Budding / endosome to melanosome transport / positive regulation of natural killer cell degranulation / Lysosome Vesicle Biogenesis / platelet dense granule organization / regulation of receptor internalization / melanosome assembly ...basolateral protein secretion / mitotic cleavage furrow ingression / AP-1 adaptor complex / trans-Golgi Network Vesicle Budding / endosome to melanosome transport / positive regulation of natural killer cell degranulation / Lysosome Vesicle Biogenesis / platelet dense granule organization / regulation of receptor internalization / melanosome assembly / regulation of Arp2/3 complex-mediated actin nucleation / Golgi to lysosome transport / Intra-Golgi traffic / Golgi to vacuole transport / Golgi Associated Vesicle Biogenesis / Synthesis of PIPs at the Golgi membrane / melanosome organization / GTP-dependent protein binding / 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 / COPI-dependent Golgi-to-ER retrograde traffic / clathrin-coated vesicle / Lysosome Vesicle Biogenesis / clathrin binding / Golgi Associated Vesicle Biogenesis / positive regulation of natural killer cell mediated cytotoxicity / cell leading edge / Synthesis of PIPs at the plasma membrane / kinesin binding / intracellular copper ion homeostasis / protein targeting / COPI-mediated anterograde transport / clathrin-coated pit / vesicle-mediated transport / MHC class II antigen presentation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / Neutrophil degranulation / sarcomere / small monomeric GTPase / trans-Golgi network membrane / kidney development / Nef mediated downregulation of MHC class I complex cell surface expression / intracellular protein transport / trans-Golgi network / cytoplasmic vesicle membrane / recycling endosome / small GTPase binding / cellular response to virus / heart development / postsynaptic density / early endosome / neuron projection / lysosomal membrane / protein domain specific binding / Golgi membrane / focal adhesion / intracellular membrane-bounded organelle / GTPase activity / 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 | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 7 Å | ||||||
Authors | Ren, X. / Farias, G.G. / Canagarajah, B.J. / Bonifacino, J.S. / Hurley, J.H. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2013 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hmy.cif.gz | 334.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hmy.ent.gz | 254 KB | Display | PDB format |
PDBx/mmJSON format | 4hmy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hm/4hmy ftp://data.pdbj.org/pub/pdb/validation_reports/hm/4hmy | 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 |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Mus musculus (house mouse) / Gene: Adtg, Ap1g1, Clapg1 / Plasmid: pST44 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) star / References: UniProt: P22892 |
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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.) Homo sapiens (human) / Gene: ADTB1, AP1B1, BAM22, CLAPB2 / Plasmid: pST44 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) star / References: UniProt: Q10567 |
#3: Protein | Mass: 48606.730 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ap1m1, Cltnm / Plasmid: pST44 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) star / References: UniProt: P35585 |
#4: Protein | Mass: 18321.338 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AP1S3 / Plasmid: pST44 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) star / References: UniProt: Q96PC3 |
-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.) Homo sapiens (human) / Gene: ARF1 / Plasmid: pHis2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) star / References: UniProt: P84077 |
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-Non-polymers , 2 types, 2 molecules
#6: Chemical | ChemComp-GTP / |
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#7: Chemical | ChemComp-MG / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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