7U6F

Mouse retromer (VPS26/VPS35/VPS29) heterotrimers


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Improved mammalian retromer cryo-EM structures reveal a new assembly interface.

Kendall, A.K.Chandra, M.Xie, B.Wan, W.Jackson, L.P.

(2022) J Biol Chem 298: 102523-102523

  • DOI: https://doi.org/10.1016/j.jbc.2022.102523
  • Primary Citation of Related Structures:  
    7U6F

  • PubMed Abstract: 

    Retromer (VPS26/VPS35/VPS29 subunits) assembles with multiple sorting nexin proteins on membranes to mediate endosomal recycling of transmembrane protein cargoes. Retromer has been implicated in other cellular processes, including mitochondrial homeostasis, nutrient sensing, autophagy, and fission events. Mechanisms for mammalian retromer assembly remain undefined, and retromer engages multiple sorting nexin proteins to sort cargoes to different destinations. Published structures demonstrate mammalian retromer forms oligomers in vitro, but several structures were poorly resolved. We report here improved retromer oligomer structures using single-particle cryo-EM by combining data collected from tilted specimens with multiple advancements in data processing, including using a 3D starting model for enhanced automated particle picking in RELION. We used a retromer mutant (3KE retromer) that breaks VPS35-mediated interfaces to determine a structure of a new assembly interface formed by the VPS26A and VPS35 N-termini. The interface reveals how an N-terminal VPS26A arrestin saddle can link retromer chains by engaging a neighboring VPS35 N- terminus, on the opposite side from the well-characterized C-VPS26/N-VPS35 interaction observed within heterotrimers. The new interaction interface exhibits substantial buried surface area (∼7000 Å 2 ) and further suggests that metazoan retromer may serve as an adaptable scaffold.


  • Organizational Affiliation

    Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA; Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Vacuolar protein sorting-associated protein 35A [auth D1]796Mus musculusMutation(s): 0 
Gene Names: Vps35Mem3
UniProt & NIH Common Fund Data Resources
Find proteins for Q9EQH3 (Mus musculus)
Explore Q9EQH3 
Go to UniProtKB:  Q9EQH3
IMPC:  MGI:1890467
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9EQH3
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Vacuolar protein sorting-associated protein 26AB [auth B3]327Mus musculusMutation(s): 0 
Gene Names: Vps26aVps26
UniProt
Find proteins for P40336 (Mus musculus)
Explore P40336 
Go to UniProtKB:  P40336
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40336
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Vacuolar protein sorting-associated protein 29C [auth B4]182Mus musculusMutation(s): 0 
Gene Names: Vps29
UniProt & NIH Common Fund Data Resources
Find proteins for Q9QZ88 (Mus musculus)
Explore Q9QZ88 
Go to UniProtKB:  Q9QZ88
IMPC:  MGI:1928344
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9QZ88
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4 (Subject of Investigation/LOI)
Query on SO4

Download Ideal Coordinates CCD File 
F [auth D1],
G [auth D1],
Q [auth B3]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL (Subject of Investigation/LOI)
Query on GOL

Download Ideal Coordinates CCD File 
D [auth D1]
E [auth D1]
H [auth D1]
R [auth B3]
S [auth B3]
D [auth D1],
E [auth D1],
H [auth D1],
R [auth B3],
S [auth B3],
T [auth B3]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO (Subject of Investigation/LOI)
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth B3]
BA [auth B3]
CA [auth B3]
DA [auth B3]
EA [auth B3]
AA [auth B3],
BA [auth B3],
CA [auth B3],
DA [auth B3],
EA [auth B3],
I [auth D1],
J [auth D1],
K [auth D1],
L [auth D1],
M [auth D1],
N [auth D1],
O [auth D1],
P [auth D1],
U [auth B3],
V [auth B3],
W [auth B3],
X [auth B3],
Y [auth B3],
Z [auth B3]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-12
    Type: Initial release
  • Version 1.1: 2022-11-16
    Changes: Database references