+Open data
-Basic information
Entry | Database: PDB / ID: 8abq | ||||||
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Title | Structure of the SNX1-SNX5 complex, Pt derivative | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / SNX / Membrane trafficking / PROTEIN TRANSPORT | ||||||
Function / homology | Function and homology information retromer, tubulation complex / lamellipodium morphogenesis / pinocytosis / cytoplasmic side of early endosome membrane / leptin receptor binding / tubular endosome / macropinocytic cup / early endosome to Golgi transport / retromer complex / transferrin receptor binding ...retromer, tubulation complex / lamellipodium morphogenesis / pinocytosis / cytoplasmic side of early endosome membrane / leptin receptor binding / tubular endosome / macropinocytic cup / early endosome to Golgi transport / retromer complex / transferrin receptor binding / retrograde transport, endosome to Golgi / phagocytic cup / epidermal growth factor receptor binding / Golgi Associated Vesicle Biogenesis / dynactin binding / regulation of macroautophagy / positive regulation of insulin receptor signaling pathway / ruffle / phosphatidylinositol binding / intracellular protein transport / insulin receptor binding / cytoplasmic side of plasma membrane / receptor internalization / lamellipodium / early endosome membrane / vesicle / lysosome / endosome membrane / endosome / cadherin binding / protein heterodimerization activity / intracellular membrane-bounded organelle / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / Golgi apparatus / protein homodimerization activity / protein-containing complex / membrane / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.81 Å | ||||||
Authors | Lopez-Robles, C. / Scaramuzza, S. / Astorga-Simon, E.N. / Banos-Mateos, S. / Vidaurrazaga, A. / Rojas, A.L. / Castano, D. / Hierro, A. | ||||||
Funding support | Spain, 1items
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Citation | Journal: Nat Struct Mol Biol / Year: 2023 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8abq.cif.gz | 171.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8abq.ent.gz | 138.2 KB | Display | PDB format |
PDBx/mmJSON format | 8abq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ab/8abq ftp://data.pdbj.org/pub/pdb/validation_reports/ab/8abq | HTTPS FTP |
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-Related structure data
Related structure data | 8a1gC 8afzC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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.) Homo sapiens (human) / Gene: SNX1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13596 #2: Protein | Mass: 24644.385 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SNX5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y5X3 #3: Chemical | ChemComp-PT / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.55 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: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.07158 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.81→51.47 Å / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 33.72 / Stereochemistry target values: TWIN_LSQ_F
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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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