5ZDZ

Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS complex in Ca2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Cracking the DNA Code for V(D)J Recombination

Kim, M.S.Chuenchor, W.Chen, X.Cui, Y.Zhang, X.Zhou, Z.H.Gellert, M.Yang, W.

(2018) Mol Cell 70: 358-370.e4

  • DOI: 10.1016/j.molcel.2018.03.008
  • Primary Citation of Related Structures:  
    6CG0, 6CIM, 6CIL, 6CIK, 6CIJ, 5ZDZ, 5ZE1, 5ZE0, 5ZE2

  • PubMed Abstract: 
  • To initiate V(D)J recombination for generating the adaptive immune response of vertebrates, RAG1/2 recombinase cleaves DNA at a pair of recombination signal sequences, the 12- and 23-RSS. We have determined crystal and cryo-EM structures of RAG1/2 with DNA in the pre-reaction and hairpin-forming complexes up to 2 ...

    To initiate V(D)J recombination for generating the adaptive immune response of vertebrates, RAG1/2 recombinase cleaves DNA at a pair of recombination signal sequences, the 12- and 23-RSS. We have determined crystal and cryo-EM structures of RAG1/2 with DNA in the pre-reaction and hairpin-forming complexes up to 2.75 Å resolution. Both protein and DNA exhibit structural plasticity and undergo dramatic conformational changes. Coding-flank DNAs extensively rotate, shift, and deform for nicking and hairpin formation. Two intertwined RAG1 subunits crisscross four times between the asymmetric pair of severely bent 12/23-RSS DNAs. Location-sensitive bending of 60° and 150° in 12- and 23-RSS spacers, respectively, must occur for RAG1/2 to capture the nonamers and pair the heptamers for symmetric double-strand breakage. DNA pairing is thus sequence-context dependent and structure specific, which partly explains the "beyond 12/23" restriction. Finally, catalysis in crystallo reveals the process of DNA hairpin formation and its stabilization by interleaved base stacking.


    Organizational Affiliation

    Laboratory of Molecular Biology, NIDDK, NIH, Bethesda, MD 20892, USA. Electronic address: weiy@niddk.nih.gov.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
mouse RAG1A, C627Mus musculusMutation(s): 0 
Gene Names: Rag1
EC: 3.1 (PDB Primary Data), 2.3.2.27 (PDB Primary Data)
UniProt
Find proteins for P15919 (Mus musculus)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
mouse RAG2B, D389Mus musculusMutation(s): 1 
Gene Names: Rag2Rag-2
UniProt
Find proteins for P21784 (Mus musculus)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
HMGB1 A-B boxE [auth N]163Mus musculusMutation(s): 0 
Gene Names: Hmgb1Hmg-1Hmg1
UniProt
Find proteins for P63158 (Mus musculus)
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Go to UniProtKB:  P63158
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Entity ID: 4
MoleculeChainsLengthOrganismImage
DNA (5'-D(*TP*AP*TP*CP*TP*GP*GP*CP*CP*TP*GP*TP*CP*TP*TP*A)-3')F45synthetic construct
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  • Entity ID: 5
    MoleculeChainsLengthOrganismImage
    DNA (54-MER)G [auth I]16synthetic construct
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    • Entity ID: 6
      MoleculeChainsLengthOrganismImage
      DNA (30-MER)H [auth J]16synthetic construct
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      Entity ID: 7
      MoleculeChainsLengthOrganismImage
      DNA (39-MER)I [auth G]54synthetic construct
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      Entity ID: 8
      MoleculeChainsLengthOrganismImage
      DNA chain LJ [auth L]30synthetic construct
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      Entity ID: 9
      MoleculeChainsLengthOrganismImage
      DNA chain MK [auth M]39synthetic construct
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      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.80 Å
      • R-Value Free: 0.242 
      • R-Value Work: 0.202 
      • R-Value Observed: 0.204 
      • Space Group: P 1 21 1
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 132.45α = 90
      b = 109β = 114.28
      c = 156.05γ = 90
      Software Package:
      Software NamePurpose
      PHENIXrefinement
      XDSdata reduction
      XDSdata scaling
      PHENIXphasing

      Structure Validation

      View Full Validation Report



      Entry History & Funding Information

      Deposition Data


      Funding OrganizationLocationGrant Number
      NIHUnited States--

      Revision History  (Full details and data files)

      • Version 1.0: 2018-04-25
        Type: Initial release
      • Version 1.1: 2018-05-02
        Changes: Data collection, Database references