7BLO

VPS26 dimer region of metazoan membrane-assembled retromer:SNX3 complex modelled with human proteins


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.50 Å
  • Aggregation State: 3D ARRAY 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Architecture and mechanism of metazoan retromer:SNX3 tubular coat assembly.

Leneva, N.Kovtun, O.Morado, D.R.Briggs, J.A.G.Owen, D.J.

(2021) Sci Adv 7

  • DOI: https://doi.org/10.1126/sciadv.abf8598
  • Primary Citation of Related Structures:  
    7BLN, 7BLO, 7BLP, 7BLQ, 7BLR

  • PubMed Abstract: 

    Retromer is a master regulator of cargo retrieval from endosomes, which is critical for many cellular processes including signaling, immunity, neuroprotection, and virus infection. The retromer core (VPS26/VPS29/VPS35) is present on cargo-transporting, tubular carriers along with a range of sorting nexins. Here, we elucidate the structural basis of membrane tubulation and coupled cargo recognition by metazoan and fungal retromer coats assembled with the non-Bin1/Amphiphysin/Rvs (BAR) sorting nexin SNX3 using cryo-electron tomography. The retromer core retains its arched, scaffolding structure but changes its mode of membrane recruitment when assembled with different SNX adaptors, allowing cargo recognition at subunit interfaces. Thus, membrane bending and cargo incorporation can be modulated to allow retromer to traffic cargoes along different cellular transport routes.


  • Organizational Affiliation

    Cambridge Institute for Medical Research, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK. nl365@cam.ac.uk okovtun@mrc-lmb.cam.ac.uk jbriggs@mrc-lmb.cam.ac.uk djo30@cam.ac.uk.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Vacuolar protein sorting-associated protein 26AA [auth J],
D [auth F]
294Homo sapiensMutation(s): 0 
Gene Names: VPS26AVPS26
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for O75436 (Homo sapiens)
Explore O75436 
Go to UniProtKB:  O75436
PHAROS:  O75436
GTEx:  ENSG00000122958 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75436
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Sorting nexin-3B [auth L],
E [auth G]
155Mus musculusMutation(s): 0 
Gene Names: Snx3
UniProt & NIH Common Fund Data Resources
Find proteins for O60493 (Homo sapiens)
Explore O60493 
Go to UniProtKB:  O60493
PHAROS:  O60493
GTEx:  ENSG00000112335 
Entity Groups  
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UniProt GroupO60493
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
C-term (residues 493-54) of Wls (fitted sequence corresponds to hDMT1-II)C [auth N],
F [auth H]
10Mus musculusMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P49281 (Homo sapiens)
Explore P49281 
Go to UniProtKB:  P49281
PHAROS:  P49281
GTEx:  ENSG00000110911 
Entity Groups  
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UniProt GroupP49281
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Vacuolar protein sorting-associated protein 35G [auth A],
H [auth C]
352Homo sapiensMutation(s): 0 
Gene Names: VPS35MEM3TCCCTA00141
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q96QK1 (Homo sapiens)
Explore Q96QK1 
Go to UniProtKB:  Q96QK1
PHAROS:  Q96QK1
GTEx:  ENSG00000069329 
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UniProt GroupQ96QK1
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PIB (Subject of Investigation/LOI)
Query on PIB

Download Ideal Coordinates CCD File 
I [auth L],
J [auth G]
2-(BUTANOYLOXY)-1-{[(HYDROXY{[2,3,4,6-TETRAHYDROXY-5-(PHOSPHONOOXY)CYCLOHEXYL]OXY}PHOSPHORYL)OXY]METHYL}ETHYL BUTANOATE
C17 H32 O16 P2
NKJZZWLREOAJGO-HODIZBBFSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.50 Å
  • Aggregation State: 3D ARRAY 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom207455/Z/17/Z
Wellcome TrustUnited Kingdom206171/Z/17/Z
Wellcome TrustUnited Kingdom202905/Z/16/Z
Medical Research Council (MRC, United Kingdom)United KingdomMC_UP_1201/16
European Research Council (ERC)United KingdomERC-CoG-648432 MEMBRANEFUSION

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-03
    Type: Initial release
  • Version 1.1: 2021-04-07
    Changes: Database references