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

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Basic information

Entry
Database: PDB / ID: 6q0x
TitleThe cryo-EM structure of the SNX-BAR Mvp1 tetramer
ComponentsSorting nexin MVP1
KeywordsLIPID BINDING PROTEIN / Mvp1 / sorting nexin / SNX / PX / BAR / SNX-BAR
Function / homology
Function and homology information


plasma membrane tubulation / protein targeting to vacuole / phosphatidylinositol-3-phosphate binding / retrograde transport, endosome to Golgi / endosome / membrane / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Sorting nexin 8/Mvp1 BAR domain / Sorting nexin-8/Mvp1 / SNX8/Mvp1, PX 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 W303 (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsSun, D. / Ford, M.G.J. / Zhang, P.
Funding support United States, 2items
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, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
A: Sorting nexin MVP1
B: Sorting nexin MVP1
C: Sorting nexin MVP1
D: Sorting nexin MVP1


Theoretical massNumber of molelcules
Total (without water)247,6114
Polymers247,6114
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering, gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Sorting nexin MVP1


Mass: 61902.852 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae W303 (yeast) / Gene: MVP1, YMR004W, YM8270.06 / Plasmid: pET-15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): CODON PLUS / References: UniProt: P40959

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Mvp1 tetramer / Type: COMPLEX / Details: recombinant purified Mvp1 / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.242362 MDa / Experimental value: YES
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: W303 / Cellular location: Cytosol / endosome
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21DE3 CODON PLUS / Plasmid: pET-15b
Buffer solutionpH: 7.5
SpecimenConc.: 0.32 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationCryogen name: ETHANE

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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 FIELDBright-field microscopy
Image recordingElectron dose: 58 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.16rc1_3531refinement
PHENIX1.16rc1_3531refinement
EM software
IDNameVersionCategory
2RELIONparticle selection
8Coot0.9model fitting
9UCSF Chimeramodel fitting
15PHENIX1.16model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: D2 (2x2 fold dihedral)
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 49000 / Symmetry type: POINT
Atomic model buildingB value: 88.91 / Protocol: AB INITIO MODEL / Space: REAL / Target criteria: Overall correlation coefficients
Atomic model building

3D fitting-ID: 1 / Source name: PDB / Type: experimental model

IDPDB-IDPdb chain-IDAccession codeInitial refinement model-ID
13DYT

3dyt

A3DYT1
23DYT

3dyt

B3DYT1
36H7W

6h7w

A6H7W2
46H7W

6h7w

B6H7W2
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 88.91 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.007612724
ELECTRON MICROSCOPYf_angle_d1.01817152
ELECTRON MICROSCOPYf_chiral_restr0.0481916
ELECTRON MICROSCOPYf_plane_restr0.00912168
ELECTRON MICROSCOPYf_dihedral_angle_d5.86827852

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