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 9PWA | pdb_00009pwa

Closed AP-2 clathrin adaptor complex in solution

  • Classification: ENDOCYTOSIS
  • Organism(s): Mus musculus
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2025-08-04 Released: 2026-04-08 
  • Deposition Author(s): Baker, R.W., Kikkawa, M., Sloan, D.E., Yanagisawa, H.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Japan Society for the Promotion of Science (JSPS), Japan Agency for Medical Research and Development (AMED), National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR), National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.55 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9PWA

This is version 1.1 of the entry. See complete history. 

Literature

CCDC32 collaborates with the membrane to assemble the AP-2 clathrin adaptor complex.

Sloan, D.E., Matthews, A.E., Yanagisawa, H., Tedamrongwanish, T., Cannon, K., Simmons, J., Chappell, G., Nicely, N.I., Berlow, R., Kikkawa, M., Baker, R.W.

(2026) Sci Adv 12: eaeb2377-eaeb2377

  • DOI: https://doi.org/10.1126/sciadv.aeb2377
  • Primary Citation Related Structures: 
    9PPP, 9PUE, 9PWA, 9PWB, 9PWC

  • PubMed Abstract: 

    Assembly of adaptor protein complex 2 (AP-2), the primary cargo adaptor in clathrin-mediated endocytosis, is regulated by the chaperones alpha- and gamma-adaptin binding protein (AAGAB) and coiled-coil domain-containing protein 32 (CCDC32), whose deletion causes loss of all AP-2 subunits in vivo. Here, we describe the molecular mechanism of CCDC32-mediated AP-2 assembly. CCDC32 interacts with the appendage domain of the AP-2 α subunit with high affinity, using the same binding site as canonical endocytic regulators in addition to a previously unidentified, yet highly conserved pocket on α. CCDC32 contains cargo sorting motifs normally found in transmembrane cargo and binds to AP-2 heterodimers using canonical cargo-binding sites. In addition, two amphipathic helices in CCDC32 bind to the α/σ2 heterodimer. Unexpectedly, in solution, CCDC32 prevents complex assembly and actively disassembles AP-2 tetramers. Inhibition requires the amphipathic helices of CCDC32, which also mediate binding to phosphatidylinositol 4,5-bisphosphate (PIP 2 )-containing membranes. The presence of PIP 2 -containing membrane stabilizes the final stages of assembly. We propose that the membrane acts as a molecular switch to release inhibitory interactions, allowing for full complex assembly to proceed.


  • Organizational Affiliation: 
    • Department of Biochemistry and Biophysics, UNC Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA.

Macromolecule Content 

  • Total Structure Weight: 204.29 kDa 
  • Atom Count: 13,707 
  • Modeled Residue Count: 1,717 
  • Deposited Residue Count: 1,798 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
AP-2 complex subunit alpha-2630Mus musculusMutation(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 Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17427
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
AP-2 complex subunit beta591Mus musculusMutation(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 Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9DBG3
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
AP-2 complex subunit muC [auth M]435Mus musculusMutation(s): 0 
Gene Names: Ap2m1, Clapm1
UniProt
Find proteins for P84091 (Mus musculus)
Explore P84091 
Go to UniProtKB:  P84091
Entity Groups
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UniProt GroupP84091
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
AP-2 complex subunit sigmaD [auth S]142Mus musculusMutation(s): 0 
Gene Names: Ap2s1, Ap17, Claps2
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
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.55 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487
RECONSTRUCTIONcryoSPARC4.6

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM150960
Japan Society for the Promotion of Science (JSPS)Japan21H04762
Japan Society for the Promotion of Science (JSPS)Japan21H05248
Japan Agency for Medical Research and Development (AMED)JapanJP24ama121002
Japan Society for the Promotion of Science (JSPS)JapanSP24007
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)United StatesF31DE034311
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesP30CA016086

Revision History  (Full details and data files)

  • Version 1.0: 2026-04-08
    Type: Initial release
  • Version 1.1: 2026-10-21
    Changes: Data collection, Database references