6CG0

Cryo-EM structure of mouse RAG1/2 HFC complex (3.17 A)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.17 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 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:  
    5ZDZ, 5ZE0, 5ZE1, 5ZE2, 6CG0, 6CIJ, 6CIK, 6CIL, 6CIM

  • 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
V(D)J recombination-activating protein 1A, B [auth C]775Mus 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
V(D)J recombination-activating protein 2D [auth B], C [auth D]520Mus musculusMutation(s): 0 
Gene Names: Rag2Rag-2
UniProt
Find proteins for P21784 (Mus musculus)
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
High mobility group protein B1K [auth N]126Homo sapiensMutation(s): 0 
Gene Names: HMGB1HMG1
UniProt & NIH Common Fund Data Resources
Find proteins for P09429 (Homo sapiens)
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Go to UniProtKB:  P09429
PHAROS:  P09429
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Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA (46-MER)E [auth F]46Escherichia coli K-12
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  • Entity ID: 4
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*GP*AP*TP*CP*TP*GP*GP*CP*CP*TP*GP*TP*CP*TP*TP*A)-3')F [auth I]16Homo sapiens
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    • Entity ID: 5
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(P*CP*TP*GP*GP*AP*TP*CP*TP*GP*GP*CP*CP*TP*GP*TP*CP*TP*TP*A)-3')G [auth J]19Escherichia coli K-12
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      Entity ID: 6
      MoleculeChainsLengthOrganismImage
      DNA (60-MER)H [auth G]60Escherichia coli K-12
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      Entity ID: 7
      MoleculeChainsLengthOrganismImage
      DNA (30-MER)I [auth L]30Escherichia coli K-12
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      Entity ID: 8
      MoleculeChainsLengthOrganismImage
      DNA (41-MER)J [auth M]41Escherichia coli K-12
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      • Reference Sequence
      Small Molecules
      Ligands 2 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      ZN
      Query on ZN

      Download Ideal Coordinates CCD File 
      L [auth A], N [auth C]ZINC ION
      Zn
      PTFCDOFLOPIGGS-UHFFFAOYSA-N
       Ligand Interaction
      CA
      Query on CA

      Download Ideal Coordinates CCD File 
      M [auth A], O [auth C]CALCIUM ION
      Ca
      BHPQYMZQTOCNFJ-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: ELECTRON MICROSCOPY
      • Resolution: 3.17 Å
      • Aggregation State: PARTICLE 
      • Reconstruction Method: SINGLE PARTICLE 

      Structure Validation

      View Full Validation Report




      Entry History & Funding Information

      Deposition Data


      Funding OrganizationLocationGrant Number
      National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United States1ZIADK036167-11

      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
      • Version 1.2: 2019-02-20
        Changes: Author supporting evidence, Data collection
      • Version 1.3: 2019-12-18
        Changes: Author supporting evidence, Other