5U9I

Crystal structure of the FKBP domain of human aryl hydrocarbon receptor-interacting protein-like 1 (AIPL1) complexed with S-farnesyl-L-cysteine methyl ester


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.236 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

Unique structural features of the AIPL1-FKBP domain that support prenyl lipid binding and underlie protein malfunction in blindness.

Yadav, R.P.Gakhar, L.Yu, L.Artemyev, N.O.

(2017) Proc Natl Acad Sci U S A 114: E6536-E6545

  • DOI: https://doi.org/10.1073/pnas.1704782114
  • Primary Citation of Related Structures:  
    5U9A, 5U9I, 5U9J, 5U9K, 5V35

  • PubMed Abstract: 

    FKBP-domain proteins (FKBPs) are pivotal modulators of cellular signaling, protein folding, and gene transcription. Aryl hydrocarbon receptor-interacting protein-like 1 (AIPL1) is a distinctive member of the FKBP superfamily in terms of its biochemical properties, and it plays an important biological role as a chaperone of phosphodiesterase 6 (PDE6), an effector enzyme of the visual transduction cascade. Malfunction of mutant AIPL1 proteins triggers a severe form of Leber congenital amaurosis and leads to blindness. The mechanism underlying the chaperone activity of AIPL1 is largely unknown, but involves the binding of isoprenyl groups on PDE6 to the FKBP domain of AIPL1. We solved the crystal structures of the AIPL1-FKBP domain and its pathogenic mutant V71F, both in the apo form and in complex with isoprenyl moieties. These structures reveal a module for lipid binding that is unparalleled within the FKBP superfamily. The prenyl binding is enabled by a unique "loop-out" conformation of the β4-α1 loop and a conformational "flip-out" switch of the key W72 residue. A second major conformation of apo AIPL1-FKBP was identified by NMR studies. This conformation, wherein W72 flips into the ligand-binding pocket and renders the protein incapable of prenyl binding, is supported by molecular dynamics simulations and appears to underlie the pathogenicity of the V71F mutant. Our findings offer critical insights into the mechanisms that underlie AIPL1 function in health and disease, and highlight the structural and functional diversity of the FKBPs.


  • Organizational Affiliation

    Department of Molecular Physiology and Biophysics, University of Iowa Carver College of Medicine, Iowa City, IA 52242.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aryl hydrocarbon receptor-interacting protein-like 1 (AIPL1)169Homo sapiensMutation(s): 0 
Gene Names: AIPL1AIPL2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NZN9 (Homo sapiens)
Explore Q9NZN9 
Go to UniProtKB:  Q9NZN9
PHAROS:  Q9NZN9
GTEx:  ENSG00000129221 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NZN9
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAR
Query on FAR

Download Ideal Coordinates CCD File 
B [auth A]FARNESYL
C15 H26
JXBSHSBNOVLGHF-BUJBXKITSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.236 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.97α = 90
b = 66.18β = 90
c = 106.96γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Blu-Icedata collection
XDSdata scaling
PHASERphasing
Cootmodel building
SCALAdata scaling
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Eye Institute (NIH/NEI)United StatesEY-10843

Revision History  (Full details and data files)

  • Version 1.0: 2017-07-26
    Type: Initial release
  • Version 1.1: 2017-08-09
    Changes: Database references
  • Version 1.2: 2017-08-23
    Changes: Database references
  • Version 1.3: 2017-11-22
    Changes: Refinement description
  • Version 1.4: 2019-12-11
    Changes: Author supporting evidence
  • Version 1.5: 2023-10-04
    Changes: Data collection, Database references, Refinement description