6RIR

Crystal structure of phosphorylated Rab8a in complex with the Rab-binding domain of RILPL2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 

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This is version 1.4 of the entry. See complete history


Literature

Structural Basis for Rab8a Recruitment of RILPL2 via LRRK2 Phosphorylation of Switch 2.

Waschbusch, D.Purlyte, E.Pal, P.McGrath, E.Alessi, D.R.Khan, A.R.

(2020) Structure 28: 406-417.e6

  • DOI: https://doi.org/10.1016/j.str.2020.01.005
  • Primary Citation of Related Structures:  
    6RIR

  • PubMed Abstract: 

    Rab8a is associated with the dynamic regulation of membrane protrusions in polarized cells. Rab8a is one of several Rab GTPases that are substrates of leucine-rich repeat kinase 2 (LRRK2), a serine/threonine kinase that is linked to Parkinson's disease. Rab8a is phosphorylated at T72 (pT72) in its switch 2 helix and recruits the phospho-specific effector RILPL2, which subsequently regulates ciliogenesis. Here, we report the crystal structure of phospho-Rab8a (pRab8a) in complex with the RH2 (RILP homology) domain of RILPL2. The complex is a heterotetramer with RILPL2 forming a central α-helical dimer that bridges two pRab8a molecules. The N termini of the α helices cross over, forming an X-shaped cap (X-cap) that orients Arg residues from RILPL2 toward pT72. X-cap residues critical for pRab8a binding are conserved in JIP3 and JIP4, which also interact with LRRK2-phosphorylated Rab10. We propose a general mode of recognition for phosphorylated Rab GTPases by this family of phospho-specific effectors.


  • Organizational Affiliation

    School of Biochemistry and Immunology, Trinity College, Dublin 2, Ireland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ras-related protein Rab-8A
A, B
184Homo sapiensMutation(s): 1 
Gene Names: RAB8AMELRAB8
UniProt & NIH Common Fund Data Resources
Find proteins for P61006 (Homo sapiens)
Explore P61006 
Go to UniProtKB:  P61006
PHAROS:  P61006
GTEx:  ENSG00000167461 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61006
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
RILP-like protein 2C [auth D],
D [auth C]
43Homo sapiensMutation(s): 0 
Gene Names: RILPL2RLP2
UniProt & NIH Common Fund Data Resources
Find proteins for Q969X0 (Homo sapiens)
Explore Q969X0 
Go to UniProtKB:  Q969X0
PHAROS:  Q969X0
GTEx:  ENSG00000150977 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ969X0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TPO
Query on TPO
A, B
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Binding Affinity Annotations 
IDSourceBinding Affinity
GTP Binding MOAD:  6RIR Kd: 3300 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.333α = 90
b = 71.509β = 90
c = 114.784γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Science Foundation IrelandIreland12/IA/1239
Michael J. Fox FoundationUnited Kingdom6986
Medical Research Council (United Kingdom)United KingdomMC_UU_12016/2

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-29
    Type: Initial release
  • Version 1.1: 2020-02-12
    Changes: Structure summary
  • Version 1.2: 2020-02-19
    Changes: Database references
  • Version 1.3: 2020-04-15
    Changes: Database references
  • Version 1.4: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description