6OWO

CRYO-EM STRUCTURE OF PHOSPHORYLATED AP-2 CORE BOUND TO NECAP

• PDB DOI:  https://doi.org/10.2210/pdb6OWO/pdb
• EM Map EMD-20215: EMDB EMDataResource

• Classification: ENDOCYTOSIS
• Organism(s): Mus musculus, Rattus norvegicus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-05-10 Released: 2019-09-11 
• Deposition Author(s): Partlow, E.A., Baker, R.W., Beacham, G.M., Chappie, J.S., Leschziner, A.E., Hollopeter, G.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

A structural mechanism for phosphorylation-dependent inactivation of the AP2 complex.

Partlow, E.A., Baker, R.W., Beacham, G.M., Chappie, J.S., Leschziner, A.E., Hollopeter, G.

(2019) Elife 8

• PubMed: 31464684 
• DOI: https://doi.org/10.7554/eLife.50003
• Primary Citation of Related Structures:  
  6OWO, 6OXL


• PubMed Abstract: 
  

Endocytosis of transmembrane proteins is orchestrated by the AP2 clathrin adaptor complex. AP2 dwells in a closed, inactive state in the cytosol, but adopts an open, active conformation on the plasma membrane. Membrane-activated complexes are also phosphorylated, but the significance of this mark is debated. We recently proposed that NECAP negatively regulates AP2 by binding open and phosphorylated complexes (Beacham et al., 2018). Here, we report high-resolution cryo-EM structures of NECAP bound to phosphorylated AP2. The site of AP2 phosphorylation is directly coordinated by residues of the NECAP PHear domain that are predicted from genetic screens in C. elegans . Using membrane mimetics to generate conformationally open AP2, we find that a second domain of NECAP binds these complexes and cryo-EM reveals both domains of NECAP engaging closed, inactive AP2. Assays in vitro and in vivo confirm these domains cooperate to inactivate AP2. We propose that phosphorylation marks adaptors for inactivation.

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Organizational Affiliation: 

Department of Molecular Medicine, Cornell University, New York, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A2B1C1D1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 232.08 kDa 
• Atom Count: 14,276 
• Modelled Residue Count: 1,786 
• Deposited Residue Count: 2,055 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AP-2 complex subunit alpha-2	A	621	Mus musculus	Mutation(s): 0  Gene Names: Ap2a2, Adtab
UniProt & NIH Common Fund Data Resources
Find proteins for P17427 (Mus musculus) Explore P17427  Go to UniProtKB:  P17427
IMPC:  MGI:101920

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
AP-2 complex subunit beta	B	591	Mus musculus	Mutation(s): 0  Gene Names: Ap2b1, Clapb1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9DBG3 (Mus musculus) Explore Q9DBG3  Go to UniProtKB:  Q9DBG3
IMPC:  MGI:1919020

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
AP-2 complex subunit mu	C [auth M]	435	Mus musculus	Mutation(s): 0  Gene Names: Ap2m1, Clapm1
UniProt
Find proteins for P84091 (Mus musculus) Explore P84091  Go to UniProtKB:  P84091

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
AP-2 complex subunit sigma	D [auth S]	142	Rattus norvegicus	Mutation(s): 0  Gene Names: Ap2s1, Ap17, Claps2
UniProt
Find proteins for P62744 (Rattus norvegicus) Explore P62744  Go to UniProtKB:  P62744

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Adaptin ear-binding coat-associated protein 2	E [auth N]	266	Mus musculus	Mutation(s): 0  Gene Names: Necap2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9D1J1 (Mus musculus) Explore Q9D1J1  Go to UniProtKB:  Q9D1J1
IMPC:  MGI:1913397

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPO	C [auth M]	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION
RECONSTRUCTION	RELION
MODEL REFINEMENT	Rosetta

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-09-11 
Deposition Author(s): Partlow, E.A., Baker, R.W., Beacham, G.M., Chappie, J.S., Leschziner, A.E., Hollopeter, G.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01 GM127548-01A1

Revision History  

• Version 1.0: 2019-09-11
  Type: Initial release
  
• Version 1.1: 2020-01-08
  Changes: Author supporting evidence