5IL7

Leucine rich repeat domain of the Chlorobium tepidum Roco protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Structural model of the dimeric Parkinson's protein LRRK2 reveals a compact architecture involving distant interdomain contacts.

Guaitoli, G.Raimondi, F.Gilsbach, B.K.Gomez-Llorente, Y.Deyaert, E.Renzi, F.Li, X.Schaffner, A.Jagtap, P.K.Boldt, K.von Zweydorf, F.Gotthardt, K.Lorimer, D.D.Yue, Z.Burgin, A.Janjic, N.Sattler, M.Versees, W.Ueffing, M.Ubarretxena-Belandia, I.Kortholt, A.Gloeckner, C.J.

(2016) Proc Natl Acad Sci U S A 113: E4357-E4366

  • DOI: https://doi.org/10.1073/pnas.1523708113
  • Primary Citation of Related Structures:  
    5IL7

  • PubMed Abstract: 

    Leucine-rich repeat kinase 2 (LRRK2) is a large, multidomain protein containing two catalytic domains: a Ras of complex proteins (Roc) G-domain and a kinase domain. Mutations associated with familial and sporadic Parkinson's disease (PD) have been identified in both catalytic domains, as well as in several of its multiple putative regulatory domains. Several of these mutations have been linked to increased kinase activity. Despite the role of LRRK2 in the pathogenesis of PD, little is known about its overall architecture and how PD-linked mutations alter its function and enzymatic activities. Here, we have modeled the 3D structure of dimeric, full-length LRRK2 by combining domain-based homology models with multiple experimental constraints provided by chemical cross-linking combined with mass spectrometry, negative-stain EM, and small-angle X-ray scattering. Our model reveals dimeric LRRK2 has a compact overall architecture with a tight, multidomain organization. Close contacts between the N-terminal ankyrin and C-terminal WD40 domains, and their proximity-together with the LRR domain-to the kinase domain suggest an intramolecular mechanism for LRRK2 kinase activity regulation. Overall, our studies provide, to our knowledge, the first structural framework for understanding the role of the different domains of full-length LRRK2 in the pathogenesis of PD.


  • Organizational Affiliation

    German Center for Neurodegenerative Diseases, 72076 Tübingen, Germany; Center for Ophthalmology, Institute for Ophthalmic Research, Eberhard Karls University, 72076 Tübingen, Germany;


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Rab family protein
A, B
447Chlorobaculum tepidum TLSMutation(s): 0 
Gene Names: CT1526
UniProt
Find proteins for Q8KC98 (Chlorobaculum tepidum (strain ATCC 49652 / DSM 12025 / NBRC 103806 / TLS))
Explore Q8KC98 
Go to UniProtKB:  Q8KC98
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8KC98
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.223α = 90
b = 98.941β = 90
c = 155.397γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-16
    Type: Initial release
  • Version 1.1: 2016-06-29
    Changes: Database references
  • Version 1.2: 2016-07-13
    Changes: Database references
  • Version 1.3: 2016-08-10
    Changes: Database references
  • Version 1.4: 2017-01-25
    Changes: Database references
  • Version 1.5: 2024-05-01
    Changes: Data collection, Database references, Refinement description