6QH5

AP2 clathrin adaptor mu2T156-phosphorylated core in closed conformation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.56 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.226 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
AP-2 complex subunit alpha621Rattus norvegicusMutation(s): 0 
Gene Names: Ap2a2
UniProt
Find proteins for P18484 (Rattus norvegicus)
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Go to UniProtKB:  P18484
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UniProt GroupP18484
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  • Reference Sequence
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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 
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UniProt GroupP63010
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
AP-2 complex subunit muC [auth N]446Rattus norvegicusMutation(s): 0 
Gene Names: Ap2m1
UniProt
Find proteins for P84092 (Rattus norvegicus)
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Go to UniProtKB:  P84092
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UniProt GroupP84092
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
AP-2 complex subunit muD [auth M]446Rattus norvegicusMutation(s): 0 
Gene Names: Ap2m1
UniProt
Find proteins for P84092 (Rattus norvegicus)
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UniProt GroupP84092
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
AP-2 complex subunit sigmaE [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
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UniProt GroupP62743
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IHP
Query on IHP

Download Ideal Coordinates CCD File 
F [auth A]INOSITOL HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TPO
Query on TPO
D [auth M]L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.56 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.226 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.037α = 90
b = 121.037β = 90
c = 257.671γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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: 2020-10-07
    Changes: Structure summary
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description