7BLQ

Vps26 dimer region of the fungal membrane-assembled retromer:Grd19 complex.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.20 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 35A [auth C],
B [auth A]
295Thermochaetoides thermophila DSM 1495Mutation(s): 0 
Gene Names: CTHT_0035730
Membrane Entity: Yes 
UniProt
Find proteins for G0S709 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0S709 
Go to UniProtKB:  G0S709
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UniProt GroupG0S709
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Sorting nexin-3C [auth G],
F [auth L]
116Thermochaetoides thermophila DSM 1495Mutation(s): 0 
Gene Names: CTHT_0011560
Membrane Entity: Yes 
UniProt
Find proteins for G0S0X3 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0S0X3 
Go to UniProtKB:  G0S0X3
Entity Groups  
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UniProt GroupG0S0X3
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Vacuolar protein sorting-associated protein 26-like proteinD [auth J],
E [auth F]
292Thermochaetoides thermophila DSM 1495Mutation(s): 0 
Gene Names: CTHT_0009750
UniProt
Find proteins for G0S0E6 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0S0E6 
Go to UniProtKB:  G0S0E6
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UniProt GroupG0S0E6
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  • Reference Sequence

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
The C-terminal portion of Kex2 cargo, fitted with Phi-X-(L/M) sorting motif of hDMT1-II cargo.G [auth V],
H [auth U]
10Thermochaetoides thermophila DSM 1495Mutation(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 
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UniProt GroupP49281
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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 G],
J [auth L]
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: 9.20 Å
  • Aggregation State: 3D ARRAY 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 

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