6CIJ

Cryo-EM structure of mouse RAG1/2 HFC complex containing partial HMGB1 linker(3.9 A)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 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

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 D ...

    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 1 AC776Mus musculusMutation(s): 0 
Gene Names: Rag1
EC: 3.1 (PDB Primary Data), 2.3.2.27 (PDB Primary Data)
Find proteins for P15919 (Mus musculus)
Explore P15919 
Go to UniProtKB:  P15919
Protein Feature View
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  • Reference Sequence
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
High mobility group protein B1 N163Homo sapiensMutation(s): 0 
Gene Names: HMGB1HMG1
Find proteins for P09429 (Homo sapiens)
Explore P09429 
Go to UniProtKB:  P09429
NIH Common Fund Data Resources
PHAROS:  P09429
Protein Feature View
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  • Reference Sequence
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
V(D)J recombination-activating protein 2 BD520Mus musculusMutation(s): 0 
Gene Names: Rag2Rag-2
Find proteins for P21784 (Mus musculus)
Explore P21784 
Go to UniProtKB:  P21784
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (46-MER)F46Homo sapiens
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 3
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*GP*AP*TP*CP*TP*GP*GP*CP*CP*TP*GP*TP*CP*TP*TP*A)-3')I16Homo sapiens
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 4
      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')J20Homo sapiens
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      (by identity cutoff)  |  Structure
      Entity ID: 5
      MoleculeChainsLengthOrganismImage
      DNA (60-MER)G61Homo sapiens
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      Entity ID: 7
      MoleculeChainsLengthOrganismImage
      DNA (30-MER)L30Homo sapiens
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      Entity ID: 9
      MoleculeChainsLengthOrganismImage
      DNA (41-MER)M41Homo sapiens
      Small Molecules
      Ligands 2 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      ZN
      Query on ZN

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

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

      Experimental Data

      • Method: ELECTRON MICROSCOPY
      • Resolution: 3.90 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 

      • Version 1.0: 2018-04-25
        Type: Initial release
      • Version 1.1: 2018-05-02
        Changes: Data collection, Database references
      • Version 1.2: 2018-05-09
        Changes: Data collection, Data processing
      • Version 1.3: 2019-02-20
        Changes: Author supporting evidence, Data collection
      • Version 1.4: 2019-12-18
        Changes: Author supporting evidence, Other