5J0N

Lambda excision HJ intermediate


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 11.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.2 of the entry. See complete history


Literature

Structure of a Holliday junction complex reveals mechanisms governing a highly regulated DNA transaction.

Laxmikanthan, G.Xu, C.Brilot, A.F.Warren, D.Steele, L.Seah, N.Tong, W.Grigorieff, N.Landy, A.Van Duyne, G.D.

(2016) Elife 5

  • DOI: https://doi.org/10.7554/eLife.14313
  • Primary Citation of Related Structures:  
    5J0N

  • PubMed Abstract: 

    The molecular machinery responsible for DNA expression, recombination, and compaction has been difficult to visualize as functionally complete entities due to their combinatorial and structural complexity. We report here the structure of the intact functional assembly responsible for regulating and executing a site-specific DNA recombination reaction. The assembly is a 240-bp Holliday junction (HJ) bound specifically by 11 protein subunits. This higher-order complex is a key intermediate in the tightly regulated pathway for the excision of bacteriophage λ viral DNA out of the E. coli host chromosome, an extensively studied paradigmatic model system for the regulated rearrangement of DNA. Our results provide a structural basis for pre-existing data describing the excisive and integrative recombination pathways, and they help explain their regulation.


  • Organizational Affiliation

    Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, United States.


Macromolecules

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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Integrase
E, F, G, H
356Lambdavirus lambdaMutation(s): 0 
Gene Names: int
EC: 2.7.7 (PDB Primary Data), 3.1 (PDB Primary Data)
UniProt
Find proteins for P03700 (Escherichia phage lambda)
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Go to UniProtKB:  P03700
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UniProt GroupP03700
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  • Reference Sequence
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Integration host factor subunit alpha
I, K
96Escherichia coliMutation(s): 0 
Gene Names: ihfAhimAECS88_1763
UniProt
Find proteins for P0A6X7 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0A6X7
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UniProt GroupP0A6X7
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Integration host factor subunit beta
J, L
94Escherichia coliMutation(s): 0 
Gene Names: ihfBhimDECS88_0940
UniProt
Find proteins for P0A6Y1 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0A6Y1
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UniProt GroupP0A6Y1
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  • Reference Sequence
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Excisionase
M, N, O
55Lambdavirus lambdaMutation(s): 0 
Gene Names: xis
UniProt
Find proteins for P03699 (Escherichia phage lambda)
Explore P03699 
Go to UniProtKB:  P03699
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UniProt GroupP03699
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Entity ID: 1
MoleculeChains LengthOrganismImage
attP(-117 to +79)197Lambdavirus lambda
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Entity ID: 2
MoleculeChains LengthOrganismImage
attB(-21) to attP(+117)139Lambdavirus lambda
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Entity ID: 3
MoleculeChains LengthOrganismImage
attB(-19 to +21)41Escherichia coli
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Entity ID: 4
MoleculeChains LengthOrganismImage
attP(-79) to attB(+19)99Lambdavirus lambda
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 11.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTCNS1.3
RECONSTRUCTIONFREALIGN9.11

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-02-08
    Type: Initial release
  • Version 1.1: 2018-07-18
    Changes: Data collection, Experimental preparation
  • Version 1.2: 2024-03-06
    Changes: Data collection, Database references