8A1G | pdb_00008a1g

Deposited: 2022-06-01 Released: 2023-06-14
Deposition Author(s): Lopez-Robles, C., Scaramuzza, S., Astorga-Simon, E.N., Banos-Mateos, S., Vidaurrazaga, A., Rojas, A.L., Castano, D., Hierro, A.
Funding Organization(s): Spanish Ministry of Economy and Competitiveness

Experimental Data Snapshot

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

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

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

Macromolecule Content

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sorting nexin-1	A, B	222	Homo sapiens	Mutation(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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q13596
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Sorting nexin-5	C, D	210	Homo sapiens	Mutation(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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9Y5X3
Sequence Annotations Expand
Reference Sequence

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
POL (Subject of Investigation/LOI) Query on POL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth B] SDF format, chain I [auth D] SDF format, chain J [auth D] SDF format, chain K [auth D] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth D] MOL2 format, chain J [auth D] MOL2 format, chain K [auth D] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth D] mmCIF format, chain J [auth D] mmCIF format, chain K [auth D] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth A] H [auth B] I [auth D] E [auth A], F [auth A], G [auth A], H [auth B], I [auth D], J [auth D], K [auth D]	N-PROPANOL C₃ H₈ O BDERNNFJNOPAEC-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth D] Focus chain J [auth D] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth D] Focus chain J [auth D] Focus chain K [auth D]