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Open data
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Basic information
Entry | Database: PDB / ID: 7d6d | ||||||||||||||||||
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Title | Structural insights into membrane remodeling by SNX1 | ||||||||||||||||||
![]() | Sorting nexin-1 | ||||||||||||||||||
![]() | PROTEIN TRANSPORT / Coat complex / Membrane deformation / LIPID BINDING PROTEIN / helical assembly | ||||||||||||||||||
Function / homology | ![]() retromer, tubulation complex / lamellipodium morphogenesis / leptin receptor binding / early endosome to Golgi transport / transferrin receptor binding / epidermal growth factor receptor binding / phosphatidylinositol binding / intracellular protein transport / insulin receptor binding / receptor internalization ...retromer, tubulation complex / lamellipodium morphogenesis / leptin receptor binding / early endosome to Golgi transport / transferrin receptor binding / epidermal growth factor receptor binding / phosphatidylinositol binding / intracellular protein transport / insulin receptor binding / receptor internalization / lamellipodium / early endosome membrane / lysosome / protein heterodimerization activity / Golgi apparatus / protein homodimerization activity / cytosol Similarity search - Function | ||||||||||||||||||
Biological species | ![]() ![]() | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 9 Å | ||||||||||||||||||
![]() | Zhang, Y. / Pang, X. / Sun, F. | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural insights into membrane remodeling by SNX1. Authors: Yan Zhang / Xiaoyun Pang / Jian Li / Jiashu Xu / Victor W Hsu / Fei Sun / ![]() ![]() Abstract: The sorting nexin (SNX) family of proteins deform the membrane to generate transport carriers in endosomal pathways. Here, we elucidate how a prototypic member, SNX1, acts in this process. Performing ...The sorting nexin (SNX) family of proteins deform the membrane to generate transport carriers in endosomal pathways. Here, we elucidate how a prototypic member, SNX1, acts in this process. Performing cryoelectron microscopy, we find that SNX1 assembles into a protein lattice that consists of helical rows of SNX1 dimers wrapped around tubular membranes in a crosslinked fashion. We also visualize the details of this structure, which provides a molecular understanding of how various parts of SNX1 contribute to its ability to deform the membrane. Moreover, we have compared the SNX1 structure with a previously elucidated structure of an endosomal coat complex formed by retromer coupled to a SNX, which reveals how the molecular organization of the SNX in this coat complex is affected by retromer. The comparison also suggests insight into intermediary stages of assembly that results in the formation of the retromer-SNX coat complex on the membrane. | ||||||||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1 MB | Display | ![]() |
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PDB format | ![]() | 896.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 30592MC ![]() 7d6eC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 59740.887 Da / Num. of mol.: 16 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction |
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Sample preparation
Component | Name: sorting nexin 1 / Type: COMPLEX / Details: sorting nexin 1 in membrane-bound state / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.4 / Details: 50 mM HEPES, pH7.4, 100 mM NaCl |
Specimen | Conc.: 0.9 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % Details: blot for 3.5 seconds with a blot force 2 before plunging |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Calibrated magnification: 59000 X / Cs: 2.7 mm / C2 aperture diameter: 50 µm |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 2 sec. / Electron dose: 25 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 501 Details: Images were collected in movie mode at 16 frames per second |
Image scans | Sampling size: 14 µm / Width: 4096 / Height: 4096 / Movie frames/image: 32 / Used frames/image: 2-28 |
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Processing
EM software |
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Image processing | Details: The selected images were multiplied by CTF for amplitude correction of reconstruction | |||||||||||||||||||||||||||||||||||||||||||||
CTF correction | Details: CTF was multiplied to each micrographs before tubes selection, and finally CTF amplitude correction was performed following 3D reconstruction Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: 60.13 ° / Axial rise/subunit: 8.76 Å / Axial symmetry: C1 | |||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 476 Details: All the segments were selected manually using e2helixboxer.py of EMAN2 | |||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 11795 / Algorithm: BACK PROJECTION Details: IHRSR method were used for helical reconstruction and refinement with a range of out of plane tilt considered Num. of class averages: 1 / Symmetry type: HELICAL | |||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Correlation coefficient Details: The temperature was kept at 300K, time step was 1 fs, and secondary structure restraints was also included. |