2C9O

3D Structure of the human RuvB-like helicase RuvBL1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of the human AAA+ protein RuvBL1.

Matias, P.M.Gorynia, S.Donner, P.Carrondo, M.A.

(2006) J. Biol. Chem. 281: 38918-38929

  • DOI: 10.1074/jbc.M605625200

  • PubMed Abstract: 
  • RuvBL1 is an evolutionarily highly conserved eukaryotic protein belonging to the AAA(+)-family of ATPases (ATPase associated with diverse cellular activities). It plays important roles in essential signaling pathways such as the c-Myc and Wnt pathway ...

    RuvBL1 is an evolutionarily highly conserved eukaryotic protein belonging to the AAA(+)-family of ATPases (ATPase associated with diverse cellular activities). It plays important roles in essential signaling pathways such as the c-Myc and Wnt pathways in chromatin remodeling, transcriptional and developmental regulation, and DNA repair and apoptosis. Herein we present the three-dimensional structure of the selenomethionine variant of human RuvBL1 refined using diffraction data to 2.2A of resolution. The crystal structure of the hexamer is formed of ADP-bound RuvBL1 monomers. The monomers contain three domains, of which the first and the third are involved in ATP binding and hydrolysis. Although it has been shown that ATPase activity of RuvBL1 is needed for several in vivo functions, we could only detect a marginal activity with the purified protein. Structural homology and DNA binding studies demonstrate that the second domain, which is unique among AAA(+) proteins and not present in the bacterial homolog RuvB, is a novel DNA/RNA-binding domain. We were able to demonstrate that RuvBL1 interacted with single-stranded DNA/RNA and double-stranded DNA. The structure of the RuvBL1.ADP complex, combined with our biochemical results, suggest that although RuvBL1 has all the structural characteristics of a molecular motor, even of an ATP-driven helicase, one or more as yet undetermined cofactors are needed for its enzymatic activity.


    Related Citations: 
    • Expression, Purification, Crystallization and Preliminary X-Ray Analysis of the Human Ruvb-Like Protein Ruvbl1.
      Gorynia, S.,Matias, P.M.,Goncalves, S.,Coelho, R.,Lopes, G.,Thomaz, M.,Huber, M.,Haendler, B.,Donner, P.,Carrondo, M.A.
      (2006) Acta Crystallogr.,Sect.F 62: 61


    Organizational Affiliation

    Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Apartado 127, 2781-901 Oeiras, Portugal.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RUVB-LIKE 1
A, B, C
456Homo sapiensMutation(s): 0 
Gene Names: RUVBL1 (INO80H, NMP238, TIP49, TIP49A)
EC: 3.6.4.12
Find proteins for Q9Y265 (Homo sapiens)
Go to Gene View: RUVBL1
Go to UniProtKB:  Q9Y265
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download SDF File 
Download CCD File 
A, B, C
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.206 
  • Space Group: P 6
Unit Cell:
Length (Å)Angle (°)
a = 207.080α = 90.00
b = 207.080β = 90.00
c = 60.710γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
SHARPphasing
SHARPmodel building
SHELXEphasing
SCALAdata scaling
SHELXCDphasing
SHELXDphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-10-23
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-03-28
    Type: Database references, Source and taxonomy