8T1O

AP2 bound to MSP2N2 nanodisc with Tgn38 cargo peptide; composite map


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Lipid nanodiscs as a template for high-resolution cryo-EM structures of peripheral membrane proteins.

S Cannon, K.Sarsam, R.D.Tedamrongwanish, T.Zhang, K.Baker, R.W.

(2023) J Struct Biol 215: 107989-107989

  • DOI: https://doi.org/10.1016/j.jsb.2023.107989
  • Primary Citation of Related Structures:  
    8T1O

  • PubMed Abstract: 

    Peripheral membrane proteins are ubiquitous throughout cell biology and are required for a variety of cellular processes such as signal transduction, membrane trafficking, and autophagy. Transient binding to the membrane has a profound impact on protein function, serving to induce conformational changes and alter biochemical and biophysical parameters by increasing the local concentration of factors and restricting diffusion to two dimensions. Despite the centrality of the membrane in serving as a template for cell biology, there are few reported high-resolution structures of peripheral membrane proteins bound to the membrane. We analyzed the utility of lipid nanodiscs to serve as a template for cryo-EM analysis of peripheral membrane proteins. We tested a variety of nanodiscs and we report a 3.3 Å structure of the AP2 clathrin adaptor complex bound to a 17-nm nanodisc, with sufficient resolution to visualize a bound lipid head group. Our data demonstrate that lipid nanodiscs are amenable to high-resolution structure determination of peripheral membrane proteins and provide a framework for extending this analysis to other systems.


  • Organizational Affiliation

    Department of Biochemistry and Biophysics, UNC Chapel Hill School of Medicine, Chapel Hill, NC 27516, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
AP-2 complex subunit alpha-2630Mus musculusMutation(s): 0 
Gene Names: Ap2a2Adtab
UniProt & NIH Common Fund Data Resources
Find proteins for P17427 (Mus musculus)
Explore P17427 
Go to UniProtKB:  P17427
IMPC:  MGI:101920
Entity Groups  
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UniProt GroupP17427
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
AP-2 complex subunit beta591Mus musculusMutation(s): 0 
Gene Names: Ap2b1Clapb1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9DBG3 (Mus musculus)
Explore Q9DBG3 
Go to UniProtKB:  Q9DBG3
IMPC:  MGI:1919020
Entity Groups  
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UniProt GroupQ9DBG3
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
AP-2 complex subunit muC [auth M]435Mus musculusMutation(s): 0 
Gene Names: Ap2m1Clapm1
UniProt
Find proteins for P84091 (Mus musculus)
Explore P84091 
Go to UniProtKB:  P84091
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UniProt GroupP84091
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
AP-2 complex subunit sigmaD [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

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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Trans-Golgi network integral membrane protein TGN38E [auth P]14Rattus norvegicusMutation(s): 0 
Gene Names: Ttgn1
UniProt
Find proteins for P19814 (Rattus norvegicus)
Explore P19814 
Go to UniProtKB:  P19814
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UniProt GroupP19814
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PIO (Subject of Investigation/LOI)
Query on PIO

Download Ideal Coordinates CCD File 
F [auth A][(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate
C25 H49 O19 P3
XLNCEHRXXWQMPK-MJUMVPIBSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3.2

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-12
    Type: Initial release
  • Version 1.1: 2023-07-19
    Changes: Database references
  • Version 1.2: 2024-06-19
    Changes: Data collection