Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 34.35 kDa 
• Atom Count: 2209 
• Modelled Residue Count: 257 
• Deposited Residue Count: 308 
• Unique protein chains: 2

3L81

Crystal structure of adaptor protein complex 4 (AP-4) mu4 subunit C-terminal domain, in complex with a sorting peptide from the amyloid precursor protein (APP)

• DOI: 10.2210/pdb3L81/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-12-29 Released: 2010-06-02 
• Deposition Author(s): Mardones, G.A., Rojas, A.L., Burgos, P.V., Dasilva, L.L.P., Prabhu, Y., Bonifacino, J.S., Hurley, J.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.252 
• R-Value Work: 0.207 
• R-Value Observed: 0.209 

Literature

Sorting of the Alzheimer's disease amyloid precursor protein mediated by the AP-4 complex.

Burgos, P.V., Mardones, G.A., Rojas, A.L., daSilva, L.L., Prabhu, Y., Hurley, J.H., Bonifacino, J.S.

(2010) Dev Cell 18: 425-436

• PubMed: 20230749 
• DOI: 10.1016/j.devcel.2010.01.015
• Primary Citation of Related Structures:  
  3L81


• PubMed Abstract: 
  

Adaptor protein 4 (AP-4) is the most recently discovered and least well-characterized member of the family of heterotetrameric adaptor protein (AP) complexes that mediate sorting of transmembrane cargo in post-Golgi compartments. Herein, we report the interaction of an YKFFE sequence from the cytosolic tail of the Alzheimer's disease amyloid precursor protein (APP) with the mu4 subunit of AP-4. Biochemical and X-ray crystallographic analyses reveal that the properties of the APP sequence and the location of the binding site on mu4 are distinct from those of other signal-adaptor interactions. Disruption of the APP-AP-4 interaction decreases localization of APP to endosomes and enhances gamma-secretase-catalyzed cleavage of APP to the pathogenic amyloid-beta peptide. These findings demonstrate that APP and AP-4 engage in a distinct type of signal-adaptor interaction that mediates transport of APP from the trans-Golgi network (TGN) to endosomes, thereby reducing amyloidogenic processing of the protein.

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Organizational Affiliation: 

Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AP-4 complex subunit mu-1	A	301	Homo sapiens	Mutation(s): 2  Gene Names: AP4M1, MUARP2
Find proteins for O00189 (Homo sapiens) Explore O00189  Go to UniProtKB:  O00189
NIH Common Fund Data Resources
PHAROS:  O00189 GTEx:  ENSG00000221838

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Amyloid beta A4 protein	B	7	N/A	Mutation(s): 0
Find proteins for P05067 (Homo sapiens) Explore P05067  Go to UniProtKB:  P05067
NIH Common Fund Data Resources
PHAROS:  P05067

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.252 
• R-Value Work: 0.207 
• R-Value Observed: 0.209 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.672	α = 90
b = 56.91	β = 106.53
c = 60.664	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-12-29 
• Released Date: 2010-06-02 
Deposition Author(s): Mardones, G.A., Rojas, A.L., Burgos, P.V., Dasilva, L.L.P., Prabhu, Y., Bonifacino, J.S., Hurley, J.H.

Revision History  

• Version 1.0: 2010-06-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description