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Open data
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Basic information
Entry | Database: PDB / ID: 8abq | ||||||
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Title | Structure of the SNX1-SNX5 complex, Pt derivative | ||||||
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![]() | TRANSPORT PROTEIN / SNX / Membrane trafficking / PROTEIN TRANSPORT | ||||||
Function / homology | ![]() retromer, tubulation complex / lamellipodium morphogenesis / epidermal growth factor catabolic process / pinocytosis / cytoplasmic side of early endosome membrane / leptin receptor binding / tubular endosome / macropinocytic cup / early endosome to Golgi transport / retromer complex ...retromer, tubulation complex / lamellipodium morphogenesis / epidermal growth factor catabolic process / pinocytosis / cytoplasmic side of early endosome membrane / leptin receptor binding / tubular endosome / macropinocytic cup / early endosome to Golgi transport / retromer complex / phosphatidylinositol-5-phosphate binding / transferrin receptor binding / retrograde transport, endosome to Golgi / phosphatidylinositol-4-phosphate binding / phosphatidylinositol-3,5-bisphosphate binding / epidermal growth factor receptor binding / Golgi Associated Vesicle Biogenesis / brush border / dynactin binding / phagocytic cup / D1 dopamine receptor binding / regulation of macroautophagy / positive regulation of insulin receptor signaling pathway / ruffle / negative regulation of blood pressure / phosphatidylinositol binding / intracellular protein transport / insulin receptor binding / receptor internalization / cytoplasmic side of plasma membrane / lamellipodium / early endosome membrane / vesicle / lysosome / endosome membrane / endosome / cadherin binding / protein heterodimerization activity / intracellular membrane-bounded organelle / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / Golgi apparatus / protein homodimerization activity / protein-containing complex / identical protein binding / membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lopez-Robles, C. / Scaramuzza, S. / Astorga-Simon, E.N. / Banos-Mateos, S. / Vidaurrazaga, A. / Rojas, A.L. / Castano, D. / Hierro, A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Architecture of the ESCPE-1 membrane coat. Authors: Carlos Lopez-Robles / Stefano Scaramuzza / Elsa N Astorga-Simon / Morié Ishida / Chad D Williamson / Soledad Baños-Mateos / David Gil-Carton / Miguel Romero-Durana / Ander Vidaurrazaga / ...Authors: Carlos Lopez-Robles / Stefano Scaramuzza / Elsa N Astorga-Simon / Morié Ishida / Chad D Williamson / Soledad Baños-Mateos / David Gil-Carton / Miguel Romero-Durana / Ander Vidaurrazaga / Juan Fernandez-Recio / Adriana L Rojas / Juan S Bonifacino / Daniel Castaño-Díez / Aitor Hierro / ![]() ![]() ![]() Abstract: Recycling of membrane proteins enables the reuse of receptors, ion channels and transporters. A key component of the recycling machinery is the endosomal sorting complex for promoting exit 1 (ESCPE-1) ...Recycling of membrane proteins enables the reuse of receptors, ion channels and transporters. A key component of the recycling machinery is the endosomal sorting complex for promoting exit 1 (ESCPE-1), which rescues transmembrane proteins from the endolysosomal pathway for transport to the trans-Golgi network and the plasma membrane. This rescue entails the formation of recycling tubules through ESCPE-1 recruitment, cargo capture, coat assembly and membrane sculpting by mechanisms that remain largely unknown. Herein, we show that ESCPE-1 has a single-layer coat organization and suggest how synergistic interactions between ESCPE-1 protomers, phosphoinositides and cargo molecules result in a global arrangement of amphipathic helices to drive tubule formation. Our results thus define a key process of tubule-based endosomal sorting. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 175.6 KB | Display | ![]() |
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PDB format | ![]() | 138.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
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Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 29.2 KB | Display | |
Data in CIF | ![]() | 38.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8a1gC ![]() 8afzC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 26397.990 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 24644.385 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | ChemComp-PT / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.85 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 11% PVA, 10% 1-propanol, 100mM HEPES pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 17, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.07158 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection twin | Operator: h,-k,-l / Fraction: 0.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.8→192.319 Å / Num. all: 24815 / Num. obs: 24815 / % possible obs: 96.2 % / Redundancy: 6.3 % / Rpim(I) all: 0.038 / Rrim(I) all: 0.095 / Rsym value: 0.07 / Net I/av σ(I): 4.8 / Net I/σ(I): 10.3 / Num. measured all: 155315 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 231.88 Å2 / Biso mean: 72.0214 Å2 / Biso min: 16.14 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.81→51.47 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7
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