6PE2

Drosophila P element transposase strand transfer complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structure of a P element transposase-DNA complex reveals unusual DNA structures and GTP-DNA contacts.

Ghanim, G.E.Kellogg, E.H.Nogales, E.Rio, D.C.

(2019) Nat Struct Mol Biol 26: 1013-1022

  • DOI: https://doi.org/10.1038/s41594-019-0319-6
  • Primary Citation of Related Structures:  
    6P5A, 6PE2

  • PubMed Abstract: 

    P element transposase catalyzes the mobility of P element DNA transposons within the Drosophila genome. P element transposase exhibits several unique properties, including the requirement for a guanosine triphosphate cofactor and the generation of long staggered DNA breaks during transposition. To gain insights into these features, we determined the atomic structure of the Drosophila P element transposase strand transfer complex using cryo-EM. The structure of this post-transposition nucleoprotein complex reveals that the terminal single-stranded transposon DNA adopts unusual A-form and distorted B-form helical geometries that are stabilized by extensive protein-DNA interactions. Additionally, we infer that the bound guanosine triphosphate cofactor interacts with the terminal base of the transposon DNA, apparently to position the P element DNA for catalysis. Our structure provides the first view of the P element transposase superfamily, offers new insights into P element transposition and implies a transposition pathway fundamentally distinct from other cut-and-paste DNA transposases.


  • Organizational Affiliation

    Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transposable element P transposaseA,
F [auth G]
569Drosophila melanogasterMutation(s): 0 
EC: 2.7.7
UniProt
Find proteins for Q7M3K2 (Drosophila melanogaster)
Explore Q7M3K2 
Go to UniProtKB:  Q7M3K2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7M3K2
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Transposable element P transposaseB,
G [auth H]
135Drosophila melanogasterMutation(s): 0 
EC: 2.7.7
UniProt
Find proteins for Q7M3K2 (Drosophila melanogaster)
Explore Q7M3K2 
Go to UniProtKB:  Q7M3K2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7M3K2
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(P*CP*GP*AP*AP*CP*TP*AP*TP*A)-3')C,
H [auth I]
16Drosophila melanogaster
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (27-MER)D,
I [auth J]
38Drosophila melanogaster
Sequence Annotations
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  • Reference Sequence
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (56-MER)E,
J [auth K]
79Drosophila melanogaster
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0
MODEL REFINEMENTRosetta
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesK99GM124463
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM118121

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-30
    Type: Initial release
  • Version 1.1: 2019-11-13
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-27
    Changes: Database references
  • Version 1.3: 2020-01-08
    Changes: Author supporting evidence
  • Version 1.4: 2024-03-20
    Changes: Data collection, Database references