5IL7 | pdb_00005il7

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 (Depositor), 0.253 (DCC) 
  • R-Value Work: 
    0.214 (Depositor) 
  • R-Value Observed: 
    0.216 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5IL7

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 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;

Macromolecule Content 

  • Total Structure Weight: 97.41 kDa 
  • Atom Count: 6,871 
  • Modeled Residue Count: 880 
  • Deposited Residue Count: 894 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Rab family protein
A, B
447Chlorobaculum tepidum TLSMutation(s): 0 
Gene Names: CT1526
EC: 2.7.11.1
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 (Depositor), 0.253 (DCC) 
  • R-Value Work:  0.214 (Depositor) 
  • R-Value Observed: 0.216 (Depositor) 
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

View Full Validation Report



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