2XSZ

The dodecameric human RuvBL1:RuvBL2 complex with truncated domains II


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural and Functional Insights Into a Dodecameric Molecular Machine - the Ruvbl1/Ruvbl2 Complex.

Gorynia, S.Bandeiras, T.M.Pinho, F.G.Mcvey, C.E.Vonrhein, C.Round, A.Svergun, D.I.Donner, P.Matias, P.M.Carrondo, M.A.

(2011) J.Struct.Biol. 176: 279

  • DOI: 10.1016/j.jsb.2011.09.001

  • PubMed Abstract: 
  • RuvBL1 (RuvB-like 1) and its homolog RuvBL2 are evolutionarily highly conserved AAA(+) ATPases essential for many cellular activities. They play an important role in chromatin remodeling, transcriptional regulation and DNA damage repair. RuvBL1 and R ...

    RuvBL1 (RuvB-like 1) and its homolog RuvBL2 are evolutionarily highly conserved AAA(+) ATPases essential for many cellular activities. They play an important role in chromatin remodeling, transcriptional regulation and DNA damage repair. RuvBL1 and RuvBL2 are overexpressed in different types of cancer and interact with major oncogenic factors, such as β-catenin and c-Myc regulating their function. We solved the first three-dimensional crystal structure of the human RuvBL complex with a truncated domain II and show that this complex is competent for helicase activity. The structure reveals a dodecamer consisting of two heterohexameric rings with alternating RuvBL1 and RuvBL2 monomers bound to ADP/ATP, that interact with each other via the retained part of domain II. The dodecameric quaternary structure of the R1ΔDII/R2ΔDII complex observed in the crystal structure was confirmed by small-angle X-ray scattering analysis. Interestingly, truncation of domain II led to a substantial increase in ATP consumption of RuvBL1, RuvBL2 and their complex. In addition, we present evidence that DNA unwinding of the human RuvBL proteins can be auto-inhibited by domain II, which is not present in the homologous bacterial helicase RuvB. Our data give new insights into the molecular arrangement of RuvBL1 and RuvBL2 and strongly suggest that in vivo activities of these highly interesting therapeutic drug targets are regulated by cofactors inducing conformational changes via domain II in order to modulate the enzyme complex into its active state.


    Related Citations: 
    • Cloning, Expression, Purification, Crystallization and Preliminary X-Ray Analysis of the Human Ruvbl1- Ruvbl2 Complex.
      Gorynia, S.,Matias, P.M.,Bandeiras, T.M.,Donner, P.,Carrondo, M.A.
      (2008) Acta Crystallogr.,Sect.F 64: 840


    Organizational Affiliation

    Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RUVB-LIKE 1
A, B, C
367Homo sapiensGene 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
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
RUVB-LIKE 2
D, E, F
378Homo sapiensGene Names: RUVBL2 (INO80J, TIP48, TIP49B)
EC: 3.6.4.12
Find proteins for Q9Y230 (Homo sapiens)
Go to Gene View: RUVBL2
Go to UniProtKB:  Q9Y230
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
A, B, C, D, E, F
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E, F
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.178 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 111.824α = 90.00
b = 187.925β = 90.00
c = 244.889γ = 90.00
Software Package:
Software NamePurpose
autoSHARPphasing
PHASERphasing
BUSTERrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-10-05
    Type: Initial release
  • Version 1.1: 2011-11-16
    Type: Database references
  • Version 1.2: 2014-08-13
    Type: Refinement description