6QH6

AP2 clathrin adaptor core with two cargo peptides in open+ conformation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.00 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.259 
  • R-Value Observed: 0.260 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Temporal Ordering in Endocytic Clathrin-Coated Vesicle Formation via AP2 Phosphorylation.

Wrobel, A.G.Kadlecova, Z.Kamenicky, J.Yang, J.C.Herrmann, T.Kelly, B.T.McCoy, A.J.Evans, P.R.Martin, S.Muller, S.Sroubek, F.Neuhaus, D.Honing, S.Owen, D.J.

(2019) Dev Cell 50: 494-508.e11

  • DOI: https://doi.org/10.1016/j.devcel.2019.07.017
  • Primary Citation of Related Structures:  
    6QH5, 6QH6, 6QH7, 6RH5, 6RH6

  • PubMed Abstract: 

    Clathrin-mediated endocytosis (CME) is key to maintaining the transmembrane protein composition of cells' limiting membranes. During mammalian CME, a reversible phosphorylation event occurs on Thr156 of the μ2 subunit of the main endocytic clathrin adaptor, AP2. We show that this phosphorylation event starts during clathrin-coated pit (CCP) initiation and increases throughout CCP lifetime. μ2Thr156 phosphorylation favors a new, cargo-bound conformation of AP2 and simultaneously creates a binding platform for the endocytic NECAP proteins but without significantly altering AP2's cargo affinity in vitro. We describe the structural bases of both. NECAP arrival at CCPs parallels that of clathrin and increases with μ2Thr156 phosphorylation. In turn, NECAP recruits drivers of late stages of CCP formation, including SNX9, via a site distinct from where NECAP binds AP2. Disruption of the different modules of this phosphorylation-based temporal regulatory system results in CCP maturation being delayed and/or stalled, hence impairing global rates of CME.


  • Organizational Affiliation

    CIMR, WT/MRC Building, Hills Road, Cambridge CB2 0QQ, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
AP-2 complex subunit alpha621Rattus norvegicusMutation(s): 0 
Gene Names: Ap2a2
UniProt
Find proteins for P18484 (Rattus norvegicus)
Explore P18484 
Go to UniProtKB:  P18484
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18484
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
AP-2 complex subunit beta592Homo sapiensMutation(s): 0 
Gene Names: AP2B1ADTB2CLAPB1
UniProt & NIH Common Fund Data Resources
Find proteins for P63010 (Homo sapiens)
Explore P63010 
Go to UniProtKB:  P63010
PHAROS:  P63010
GTEx:  ENSG00000006125 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63010
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
AP-2 complex subunit muC [auth M]446Bos taurusMutation(s): 0 
Gene Names: AP2M1
UniProt
Find proteins for Q3ZC13 (Bos taurus)
Explore Q3ZC13 
Go to UniProtKB:  Q3ZC13
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3ZC13
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
AP-2 complex subunit muD [auth N]446Rattus norvegicusMutation(s): 0 
Gene Names: Ap2m1
UniProt
Find proteins for P84092 (Rattus norvegicus)
Explore P84092 
Go to UniProtKB:  P84092
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP84092
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
TGN38 CARGO PEPTIDEE [auth P]6Homo sapiensMutation(s): 0 
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
CD4 CARGO PEPTIDEF [auth Q]10Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P01730 (Homo sapiens)
Explore P01730 
Go to UniProtKB:  P01730
PHAROS:  P01730
GTEx:  ENSG00000010610 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01730
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
AP-2 complex subunit sigmaG [auth S]142Mus musculusMutation(s): 0 
Gene Names: Ap2s1Ap17Claps2
UniProt & NIH Common Fund Data Resources
Find proteins for P62743 (Mus musculus)
Explore P62743 
Go to UniProtKB:  P62743
IMPC:  MGI:2141861
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62743
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
TPO
Query on TPO
C [auth M]L-PEPTIDE LINKINGC4 H10 N O6 PTHR
SEP
Query on SEP
F [auth Q]L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.00 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.259 
  • R-Value Observed: 0.260 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 180.5α = 90
b = 180.5β = 90
c = 210.06γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom090909/Z/09/Z
Wellcome TrustUnited Kingdom097040/Z/11/Z

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-04
    Type: Initial release
  • Version 1.1: 2022-12-07
    Changes: Advisory, Database references, Derived calculations, Source and taxonomy