6KVO

Crystal structure of chloroplast resolvase in complex with Holliday junction


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.203 

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Literature

Structural insights into sequence-dependent Holliday junction resolution by the chloroplast resolvase MOC1.

Yan, J.Hong, S.Guan, Z.He, W.Zhang, D.Yin, P.

(2020) Nat Commun 11: 1417-1417

  • DOI: https://doi.org/10.1038/s41467-020-15242-8
  • Primary Citation of Related Structures:  
    6KVN, 6KVO, 6LCM, 6LCT

  • PubMed Abstract: 

    Holliday junctions (HJs) are key DNA intermediates in genetic recombination and are eliminated by nuclease, termed resolvase, to ensure genome stability. HJ resolvases have been identified across all kingdoms of life, members of which exhibit sequence-dependent HJ resolution. However, the molecular basis of sequence selectivity remains largely unknown. Here, we present the chloroplast resolvase MOC1, which cleaves HJ in a cytosine-dependent manner. We determine the crystal structure of MOC1 with and without HJs. MOC1 exhibits an RNase H fold, belonging to the retroviral integrase family. MOC1 functions as a dimer, and the HJ is embedded into the basic cleft of the dimeric enzyme. We characterize a base recognition loop (BR loop) that protrudes into and opens the junction. Residues from the BR loop intercalate into the bases, disrupt the C-G base pairing at the crossover and recognize the cytosine, providing the molecular basis for sequence-dependent HJ resolution by a resolvase.


  • Organizational Affiliation

    National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, 430070, Wuhan, China.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NtMOC1
A, B
171Nicotiana tabacumMutation(s): 3 
Gene Names: LOC107823122
UniProt
Find proteins for A0A1S4CVP6 (Nicotiana tabacum)
Explore A0A1S4CVP6 
Go to UniProtKB:  A0A1S4CVP6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1S4CVP6
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*AP*CP*AP*AP*CP*AP*GP*AP*TP*GP*AP*TP*GP*GP*AP*GP*CP*T)-3')18synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(*GP*CP*CP*TP*TP*GP*CP*TP*TP*GP*GP*AP*CP*AP*TP*CP*TP*T)-3')18synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (5'-D(P*AP*GP*CP*TP*CP*CP*AP*TP*CP*AP*AP*GP*CP*AP*AP*GP*GP*C)-3')18synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (5'-D(P*AP*AP*GP*AP*TP*GP*TP*CP*CP*AP*TP*CP*TP*GP*TP*TP*GP*T)-3')18synthetic construct
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.203 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.316α = 90
b = 92.155β = 90
c = 65.894γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHENIXrefinement
Blu-Icedata collection
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-08
    Type: Initial release
  • Version 1.1: 2024-03-27
    Changes: Data collection, Database references, Derived calculations