4D1Q

Hermes transposase bound to its terminal inverted repeat


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural Basis of Hat Transposon End Recognition by Hermes, an Octameric DNA Transposase from Musca Domestica.

Hickman, A.B.Ewis, H.E.Li, X.Knapp, J.A.Laver, T.Doss, A.Tolun, G.Steven, A.C.Grishaev, A.Bax, A.Atkinson, P.W.Craig, N.L.Dyda, F.

(2014) Cell 158: 353

  • DOI: 10.1016/j.cell.2014.05.037

  • PubMed Abstract: 
  • Hermes is a member of the hAT transposon superfamily that has active representatives, including McClintock's archetypal Ac mobile genetic element, in many eukaryotic species. The crystal structure of the Hermes transposase-DNA complex reveals that He ...

    Hermes is a member of the hAT transposon superfamily that has active representatives, including McClintock's archetypal Ac mobile genetic element, in many eukaryotic species. The crystal structure of the Hermes transposase-DNA complex reveals that Hermes forms an octameric ring organized as a tetramer of dimers. Although isolated dimers are active in vitro for all the chemical steps of transposition, only octamers are active in vivo. The octamer can provide not only multiple specific DNA-binding domains to recognize repeated subterminal sequences within the transposon ends, which are important for activity, but also multiple nonspecific DNA binding surfaces for target capture. The unusual assembly explains the basis of bipartite DNA recognition at hAT transposon ends, provides a rationale for transposon end asymmetry, and suggests how the avidity provided by multiple sites of interaction could allow a transposase to locate its transposon ends amidst a sea of chromosomal DNA.


    Organizational Affiliation

    Graduate Program in Cell, Molecular, and Developmental Biology, University of California Riverside, Riverside, CA 92521, USA.,Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.,Graduate Program in Genetics, Genomics, and Bioinformatics, University of California Riverside, Riverside, CA 92521, USA.,Laboratory of Structural Biology Research, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA.,Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA. Electronic address: fred.dyda@nih.gov.,Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.,Graduate Program in Biochemistry and Molecular Biology, University of California Riverside, Riverside, CA 92521, USA; Graduate Program in Genetics, Genomics, and Bioinformatics, University of California Riverside, Riverside, CA 92521, USA; Graduate Program in Cell, Molecular, and Developmental Biology, University of California Riverside, Riverside, CA 92521, USA; Department of Entomology and Institute for Integrative Genome Biology, University of California Riverside, Riverside, CA 92521, USA.,Graduate Program in Biochemistry and Molecular Biology, University of California Riverside, Riverside, CA 92521, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TRANSPOSASE
A, B, G, H
536Musca domesticaMutation(s): 2 
Find proteins for Q25442 (Musca domestica)
Go to UniProtKB:  Q25442
Entity ID: 2
MoleculeChainsLengthOrganism
TERMINAL INVERTED REPEATC,E,I,K15Musca domestica
Entity ID: 3
MoleculeChainsLengthOrganism
TERMINAL INVERTED REPEATD,F,J,L16Musca domestica
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, B, G, H
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.212 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 265.150α = 90.00
b = 265.150β = 90.00
c = 157.640γ = 120.00
Software Package:
Software NamePurpose
SHARPphasing
CNSrefinement
XDSdata scaling
XDSdata reduction
DMphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-30
    Type: Initial release
  • Version 1.1: 2017-06-28
    Type: Data collection