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- EMDB-30592: Structural insights into membrane remodeling by SNX1 -

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Basic information

Entry
Database: EMDB / ID: EMD-30592
TitleStructural insights into membrane remodeling by SNX1
Map data
Sample
  • Complex: sorting nexin 1
    • Protein or peptide: Sorting nexin-1
KeywordsCoat complex / Membrane deformation / LIPID BINDING PROTEIN / helical assembly / PROTEIN TRANSPORT
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)
Methodhelical reconstruction / cryo EM / Resolution: 9.0 Å
AuthorsZhang Y / Pang X
Funding support China, 5 items
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, 2020-
Header (metadata) releaseMar 17, 2021-
Map releaseMar 17, 2021-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 6.42
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 6.42
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7d6d
  • Surface level: 6.42
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7d6d
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30592.png

Downloads & links

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Map

FileDownload / File: emd_30592.map.gz / Format: CCP4 / Size: 59.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.42 Å/pix.
x 120 pix.
= 170.4 Å		1.42 Å/pix.
x 360 pix.
= 511.2 Å		1.42 Å/pix.
x 360 pix.
= 511.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.42 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 6.42 / Movie #1: 6.42
Minimum - Maximum-8.273277999999999 - 19.960701
Average (Standard dev.)0.39476934 (±3.0503304)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-180-180-60
Dimensions360360120
Spacing360360120
CellA: 511.19998 Å / B: 511.19998 Å / C: 170.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.421.421.42
M x/y/z360360120
origin x/y/z0.0000.0000.000
length x/y/z511.200511.200170.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-180-180-60
NC/NR/NS360360120
D min/max/mean-8.27319.9610.395

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Supplemental data

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Sample components

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Entire : sorting nexin 1

EntireName: sorting nexin 1
Components
  • Complex: sorting nexin 1
    • Protein or peptide: Sorting nexin-1

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Supramolecule #1: sorting nexin 1

SupramoleculeName: sorting nexin 1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: sorting nexin 1 in membrane-bound state
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Sorting nexin-1

MacromoleculeName: Sorting nexin-1 / type: protein_or_peptide / ID: 1 / Number of copies: 16 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 59.740887 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GPLGSPEFMA SGGGGCSASE RLPPPFPGMD PESEGAAGGS EPEAGDSDTE GEDIFTGAAA ATKPQSPKKT TSLFPIKNGS KENGIHEDQ DQEPQDLFAD ATVELSLDST QNNQKTMPGK TLTSHPPQEA TNSPKPQPSY EELEEEQEDQ FDLTVGITDP E KIGDGMNA ...String:
GPLGSPEFMA SGGGGCSASE RLPPPFPGMD PESEGAAGGS EPEAGDSDTE GEDIFTGAAA ATKPQSPKKT TSLFPIKNGS KENGIHEDQ DQEPQDLFAD ATVELSLDST QNNQKTMPGK TLTSHPPQEA TNSPKPQPSY EELEEEQEDQ FDLTVGITDP E KIGDGMNA YVAYKVTTQT SLPMFRSRQF AVKRRFSDFL GLYEKLSEKH SQNGFIVPPP PEKSLIGMTK VKVGKEDSSS AE FLEKRRA ALERYLQRIV NHPTMLQDPD VREFLEKEEL PRAVGTQALS GAGLLKMFNK ATDAVSKMTI KMNESDIWFE EKL QEVECE EQRLRKLHAV VETLVNHRKE LALNTALFAK SLAMLGSSED NTALSRALSQ LAEVEEKIEQ LHQEQANNDF FLLA ELLSD YIRLLAIVRA AFDQRMKTWQ RWQDAQATLQ KKRESEARLL WANKPDKLQQ AKDEITEWES RVTQYERDFE RISTV VRKE VTRFEKEKSK DFKNHVMKYL ETLLHSQQQL AKYWEAFLPE AKAIS

UniProtKB: Sorting nexin-1

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

Concentration0.9 mg/mL
BufferpH: 7.4 / Details: 50 mM HEPES, pH7.4, 100 mM NaCl
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV
Details: blot for 3.5 seconds with a blot force 2 before plunging.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Frames/image: 2-28 / Number grids imaged: 2 / Number real images: 501 / Average exposure time: 2.0 sec. / Average electron dose: 25.0 e/Å2
Details: Images were collected in movie mode at 16 frames per second
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated magnification: 59000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsThe selected images were multiplied by CTF for amplitude correction of reconstruction
Final reconstructionNumber classes used: 1
Applied symmetry - Helical parameters - Δz: 8.76 Å
Applied symmetry - Helical parameters - Δ&Phi: 60.13 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 9.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: IHRSR
Details: IHRSR method were used for helical reconstruction and refinement with a range of out of plane tilt considered
Number images used: 11795
Segment selectionNumber selected: 476
Details: All the segments were selected manually using e2helixboxer.py of EMAN2
Startup modelType of model: OTHER
Details: A cylinder with the same diameter as SNX1 tube was generated by Spider and used as initial model
Final angle assignmentType: NOT APPLICABLE / Software - Name: SPIDER (ver. 24.08)
Software - details: '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.
Details: Final angle assignment were determined by projection matching with finer projection angle steps as the resolution is improved.
FSC plot (resolution estimation)

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Atomic model buiding 1

DetailsThe temperature was kept at 300K, time step was 1 fs, and secondary structure restraints was also included.
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: Correlation coefficient
Output model

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

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