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- EMDB-20555: The cryo-EM structure of the SNX-BAR Mvp1 tetramer -

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Basic information

Entry
Database: EMDB / ID: EMD-20555
TitleThe cryo-EM structure of the SNX-BAR Mvp1 tetramer
Map dataMvp1 tetramer, masked and sharpend
Sample
  • Complex: Mvp1 tetramer
    • Protein or peptide: Sorting nexin MVP1
KeywordsMvp1 / sorting nexin / SNX / PX / BAR / SNX-BAR / LIPID BINDING PROTEIN
Function / homology
Function and homology information


plasma membrane tubulation / protein targeting to vacuole / phosphatidylinositol-3-phosphate binding / retrograde transport, endosome to Golgi / endosome / endosome membrane / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Sorting nexin-8/Mvp1 / SNX8/Mvp1, PX domain / Sorting nexin 8/Mvp1, BAR domain / Sorting nexin 8/Mvp1 BAR domain / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae W303 (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsSun D / Ford MGJ
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM120102 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24GM116790 United States
CitationJournal: Nat Commun / Year: 2020
Title: The cryo-EM structure of the SNX-BAR Mvp1 tetramer.
Authors: Dapeng Sun / Natalia V Varlakhanova / Bryan A Tornabene / Rajesh Ramachandran / Peijun Zhang / Marijn G J Ford /
Abstract: Sorting nexins (SNX) are a family of PX domain-containing proteins with pivotal roles in trafficking and signaling. SNX-BARs, which also have a curvature-generating Bin/Amphiphysin/Rvs (BAR) domain, ...Sorting nexins (SNX) are a family of PX domain-containing proteins with pivotal roles in trafficking and signaling. SNX-BARs, which also have a curvature-generating Bin/Amphiphysin/Rvs (BAR) domain, have membrane-remodeling functions, particularly at the endosome. The minimal PX-BAR module is a dimer mediated by BAR-BAR interactions. Many SNX-BAR proteins, however, additionally have low-complexity N-terminal regions of unknown function. Here, we present the cryo-EM structure of the full-length SNX-BAR Mvp1, which is an autoinhibited tetramer. The tetramer is a dimer of dimers, wherein the membrane-interacting BAR surfaces are sequestered and the PX lipid-binding sites are occluded. The N-terminal low-complexity region of Mvp1 is essential for tetramerization. Mvp1 lacking its N-terminus is dimeric and exhibits enhanced membrane association. Membrane binding and remodeling by Mvp1 therefore requires unmasking of the PX and BAR domain lipid-interacting surfaces. This work reveals a tetrameric configuration of a SNX-BAR protein that provides critical insight into SNX-BAR function and regulation.
History
DepositionAug 2, 2019-
Header (metadata) releaseJan 29, 2020-
Map releaseApr 1, 2020-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 4
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6q0x
  • Surface level: 4
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20555.png

Downloads & links

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Map

FileDownload / File: emd_20555.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMvp1 tetramer, masked and sharpend
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.06 Å/pix.
x 256 pix.
= 270.336 Å		1.06 Å/pix.
x 256 pix.
= 270.336 Å		1.06 Å/pix.
x 256 pix.
= 270.336 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.056 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.0 / Movie #1: 4
Minimum - Maximum-15.929338 - 23.551335999999999
Average (Standard dev.)-0.000000000002128 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 270.336 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0561.0561.056
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z270.336270.336270.336
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ256256256
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-15.92923.551-0.000

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Supplemental data

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Sample components

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Entire : Mvp1 tetramer

EntireName: Mvp1 tetramer
Components
  • Complex: Mvp1 tetramer
    • Protein or peptide: Sorting nexin MVP1

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Supramolecule #1: Mvp1 tetramer

SupramoleculeName: Mvp1 tetramer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: recombinant purified Mvp1
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: W303 / Location in cell: Cytosol / endosome
Molecular weightTheoretical: 242.362 KDa

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Macromolecule #1: Sorting nexin MVP1

MacromoleculeName: Sorting nexin MVP1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae W303 (yeast)
Molecular weightTheoretical: 61.902852 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSHHHHHH SSGLVPRGSH MDNYEGSDPW NTSSNAWTKD DDHVVSTTNS EPSLNGISGE FNTLNFSTPL DTNEEDTGFL PTNDVLEES IWDDSRNPLG ATGMSQTPNI AANETVIDKN DARDQNIEES EADLLDWTNN VRKTYRPLDA DIIIIEEIPE R EGLLFKHA ...String:
MGSSHHHHHH SSGLVPRGSH MDNYEGSDPW NTSSNAWTKD DDHVVSTTNS EPSLNGISGE FNTLNFSTPL DTNEEDTGFL PTNDVLEES IWDDSRNPLG ATGMSQTPNI AANETVIDKN DARDQNIEES EADLLDWTNN VRKTYRPLDA DIIIIEEIPE R EGLLFKHA NYLVKHLIAL PSTSPSEERT VVRRYSDFLW LREILLKRYP FRMIPELPPK RIGSQNADQL FLKKRRIGLS RF INLVMKH PKLSNDDLVL TFLTVRTDLT SWRKQATYDT SNEFADKKIS QEFMKMWKKE FAEQWNQAAS CIDTSMELWY RIT LLLERH EKRIMQMVHE RNFFETLVDN FSEVTPKLYP VQQNDTILDI NNNLSIIKKH LETTSSICKQ ETEEISGTLS PKFK IFTDI LLSLRSLFER YKIMAANNVV ELQRHVELNK EKLESMKGKP DVSGAEYDRI KKIIQKDRRS IIEQSNRAWL IRQCI LEEF TIFQETQFLI TRAFQDWAKL NSNHAGLKLN EWEKLVTSIM DMPISRE

UniProtKB: Sorting nexin MVP1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.32 mg/mL
BufferpH: 7.5
GridDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 58.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 49000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

3dyt

chain_id: A, source_name: PDB, initial_model_type: experimental model

3dyt

chain_id: B, source_name: PDB, initial_model_type: experimental model

6h7w

chain_id: A, source_name: PDB, initial_model_type: experimental model

6h7w

chain_id: B, source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 88.91 / Target criteria: Overall correlation coefficients
Output model

PDB-6q0x:
The cryo-EM structure of the SNX-BAR Mvp1 tetramer

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