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- PDB-7d6d: Structural insights into membrane remodeling by SNX1 -

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Entry
Database: PDB / ID: 7d6d
TitleStructural insights into membrane remodeling by SNX1
ComponentsSorting nexin-1
KeywordsPROTEIN TRANSPORT / Coat complex / Membrane deformation / LIPID BINDING PROTEIN / helical assembly
Function / homology
Function and homology information


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
Sorting nexin, N-terminal / Sorting nexin-1 / Sorting Nexin 1, PX domain / Sorting nexin, N-terminal domain / Sorting nexin Vps5-like, C-terminal / Vps5 C terminal like / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology ...Sorting nexin, N-terminal / Sorting nexin-1 / Sorting Nexin 1, PX domain / Sorting nexin, N-terminal domain / Sorting nexin Vps5-like, C-terminal / Vps5 C terminal like / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / AH/BAR domain superfamily
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 9 Å
AuthorsZhang, Y. / Pang, X. / Sun, F.
Funding support China, 5items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31670744 China
National Natural Science Foundation of China (NSFC)31961160723 China
National Natural Science Foundation of China (NSFC)31770794 China
National Natural Science Foundation of China (NSFC)31925026 China
National Basic Research Program of China (973 Program)2017YFA0504703 China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2021
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
DepositionSep 30, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: Sorting nexin-1
B: Sorting nexin-1
C: Sorting nexin-1
D: Sorting nexin-1
E: Sorting nexin-1
F: Sorting nexin-1
G: Sorting nexin-1
H: Sorting nexin-1
I: Sorting nexin-1
J: Sorting nexin-1
K: Sorting nexin-1
L: Sorting nexin-1
M: Sorting nexin-1
N: Sorting nexin-1
O: Sorting nexin-1
P: Sorting nexin-1


Theoretical massNumber of molelcules
Total (without water)955,85416
Polymers955,85416
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area31340 Å2
ΔGint-235 kcal/mol
Surface area343410 Å2

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Components

#1: Protein
Sorting nexin-1


Mass: 59740.887 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Snx1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6NZD2

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: sorting nexin 1 / Type: COMPLEX / Details: sorting nexin 1 in membrane-bound state / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4 / Details: 50 mM HEPES, pH7.4, 100 mM NaCl
SpecimenConc.: 0.9 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: 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
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Calibrated magnification: 59000 X / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage 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 scansSampling size: 14 µm / Width: 4096 / Height: 4096 / Movie frames/image: 32 / Used frames/image: 2-28

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Processing

EM software
IDNameVersionCategoryDetails
2SerialEMimage acquisition
4Gctf0.5CTF correction
7UCSF Chimera1.11.2model fittingInitial model generated by i-TASSER was rigid body fitted into the final refined map.
9NAMD2.1model refinementMolecular dynamics flexible fitting was performed using NAMD with the CHARMM36 force field.
10SPIDER24.08initial Euler assignment'pj 3q' was used to make initial model projections and 'ap sh' was used to make projection matching to assign Euler angles for each particle.
11SPIDER24.08final Euler assignment'pj 3q' was used to make initial model projections and 'ap sh' was used to make projection matching to assign Euler angles for each particle.
12MATLAB2013classificationDistance between the two intensity peaks of 1 dimensional projection of each tube is measured as the approximate diameter
13IHRSR3D reconstruction
Image processingDetails: The selected images were multiplied by CTF for amplitude correction of reconstruction
CTF correctionDetails: 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 symmertyAngular rotation/subunit: 60.13 ° / Axial rise/subunit: 8.76 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 476
Details: All the segments were selected manually using e2helixboxer.py of EMAN2
3D reconstructionResolution: 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 buildingProtocol: 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.

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