Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 11.56 kDa 
• Atom Count: 891 
• Residue Count: 102 
• Unique protein chains: 2

5EM9

Crystal structure of the SNX27 PDZ domain bound to the phosphorylated C-terminal 5HT4(a)R PDZ binding motif

• DOI: 10.2210/pdb5EM9/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Rattus norvegicus, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-11-06 Released: 2016-09-07 
• Deposition Author(s): Collins, B.M., Clairfeuille, T.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.198 
• R-Value Work: 0.169 
• R-Value Observed: 0.170 

Literature

A molecular code for endosomal recycling of phosphorylated cargos by the SNX27-retromer complex.

Clairfeuille, T., Mas, C., Chan, A.S., Yang, Z., Tello-Lafoz, M., Chandra, M., Widagdo, J., Kerr, M.C., Paul, B., Merida, I., Teasdale, R.D., Pavlos, N.J., Anggono, V., Collins, B.M.

(2016) Nat Struct Mol Biol 23: 921-932

• PubMed: 27595347 
• DOI: 10.1038/nsmb.3290
• Primary Citation of Related Structures:  
  5EM9, 5ELQ, 5EMB, 5EMA


• PubMed Abstract: 
  

Recycling of internalized receptors from endosomal compartments is essential for the receptors' cell-surface homeostasis. Sorting nexin 27 (SNX27) cooperates with the retromer complex in the recycling of proteins containing type I PSD95-Dlg-ZO1 (PDZ)-binding motifs. Here we define specific acidic amino acid sequences upstream of the PDZ-binding motif required for high-affinity engagement of the human SNX27 PDZ domain. However, a subset of SNX27 ligands, such as the β ₂ adrenergic receptor and N-methyl-D-aspartate (NMDA) receptor, lack these sequence determinants. Instead, we identified conserved sites of phosphorylation that substitute for acidic residues and dramatically enhance SNX27 interactions. This newly identified mechanism suggests a likely regulatory switch for PDZ interaction and protein transport by the SNX27-retromer complex. Defining this SNX27 binding code allowed us to classify more than 400 potential SNX27 ligands with broad functional implications in signal transduction, neuronal plasticity and metabolite transport.

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Organizational Affiliation: 

Institute for Molecular Bioscience, University of Queensland, St. Lucia, Queensland, Australia.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sorting nexin-27	A	101	Rattus norvegicus	Mutation(s): 0  Gene Names: Snx27, Mrt1
Find proteins for Q8K4V4 (Rattus norvegicus) Explore Q8K4V4  Go to UniProtKB:  Q8K4V4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SEP-LEU-GLU-SER-CYS-PHE	B	8	Homo sapiens	Mutation(s): 0  Gene Names: HTR4
Find proteins for Q13639 (Homo sapiens) Explore Q13639  Go to UniProtKB:  Q13639
NIH Common Fund Data Resources
PHAROS  Q13639 GTEx  ENSG00000164270

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	B	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.198 
• R-Value Work: 0.169 
• R-Value Observed: 0.170 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.219	α = 90
b = 48.753	β = 90
c = 57.059	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2015-11-06 
• Released Date: 2016-09-07 
Deposition Author(s): Collins, B.M., Clairfeuille, T.

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Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	APP1061574
National Health and Medical Research Council (NHMRC, Australia)	Australia	APP1058734

Revision History 

• Version 1.0: 2016-09-07
  Type: Initial release
  
• Version 1.1: 2016-09-21
  Changes: Database references
• Version 1.2: 2016-10-19
  Changes: Database references
• Version 1.3: 2017-09-27
  Changes: Author supporting evidence, Data collection, Derived calculations
• Version 1.4: 2020-01-08
  Changes: Author supporting evidence