8ABQ

Structure of the SNX1-SNX5 complex, Pt derivative


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.257 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Architecture of the ESCPE-1 membrane coat.

Lopez-Robles, C.Scaramuzza, S.Astorga-Simon, E.N.Ishida, M.Williamson, C.D.Banos-Mateos, S.Gil-Carton, D.Romero-Durana, M.Vidaurrazaga, A.Fernandez-Recio, J.Rojas, A.L.Bonifacino, J.S.Castano-Diez, D.Hierro, A.

(2023) Nat Struct Mol Biol 30: 958-969

  • DOI: https://doi.org/10.1038/s41594-023-01014-7
  • Primary Citation of Related Structures:  
    8A1G, 8ABQ, 8AFZ

  • PubMed Abstract: 

    Recycling of membrane proteins enables the reuse of receptors, ion channels and transporters. A key component of the recycling machinery is the endosomal sorting complex for promoting exit 1 (ESCPE-1), which rescues transmembrane proteins from the endolysosomal pathway for transport to the trans-Golgi network and the plasma membrane. This rescue entails the formation of recycling tubules through ESCPE-1 recruitment, cargo capture, coat assembly and membrane sculpting by mechanisms that remain largely unknown. Herein, we show that ESCPE-1 has a single-layer coat organization and suggest how synergistic interactions between ESCPE-1 protomers, phosphoinositides and cargo molecules result in a global arrangement of amphipathic helices to drive tubule formation. Our results thus define a key process of tubule-based endosomal sorting.


  • Organizational Affiliation

    CIC bioGUNE, Derio, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sorting nexin-1A,
C [auth B]
222Homo sapiensMutation(s): 0 
Gene Names: SNX1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q13596 (Homo sapiens)
Explore Q13596 
Go to UniProtKB:  Q13596
PHAROS:  Q13596
GTEx:  ENSG00000028528 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13596
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Sorting nexin-5B [auth C],
D
210Homo sapiensMutation(s): 0 
Gene Names: SNX5
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y5X3 (Homo sapiens)
Explore Q9Y5X3 
Go to UniProtKB:  Q9Y5X3
PHAROS:  Q9Y5X3
GTEx:  ENSG00000089006 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y5X3
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.257 
  • Space Group: P 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.69α = 90
b = 51.47β = 90
c = 192.32γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
autoSHARPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Economy and Competitiveness (MINECO)SpainPID2020-119132GB-I00

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-21
    Type: Initial release
  • Version 1.1: 2023-06-28
    Changes: Database references, Structure summary
  • Version 1.2: 2023-07-26
    Changes: Database references
  • Version 1.3: 2024-06-19
    Changes: Data collection