6CIM

Pre-Reaction Complex, RAG1(E962Q)/2-nicked/intact 12/23RSS complex in Mn2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 

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:  
    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
V(D)J recombination-activating protein 1A, C625Mus musculusMutation(s): 1 
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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Go to UniProtKB:  P15919
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
V(D)J recombination-activating protein 2B, D359Mus musculusMutation(s): 0 
Gene Names: Rag2Rag-2
UniProt
Find proteins for P21784 (Mus musculus)
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Go to UniProtKB:  P21784
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
High mobility group protein B1E [auth N]163Homo sapiensMutation(s): 0 
Gene Names: HMGB1HMG1
UniProt & NIH Common Fund Data Resources
Find proteins for P09429 (Homo sapiens)
Explore P09429 
Go to UniProtKB:  P09429
PHAROS:  P09429
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsLengthOrganismImage
Nicked 12RSS intermediate reverse strandF40Homo sapiens
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 5
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*GP*CP*CP*TP*GP*TP*CP*TP*TP*A)-3')G [auth I]10Homo sapiens
    Protein Feature View
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    Entity ID: 6
    MoleculeChainsLengthOrganismImage
    Nicked 12RSS intermediate forward strandH [auth L]30Homo sapiens
    Protein Feature View
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    • Reference Sequence
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    Entity ID: 7
    MoleculeChainsLengthOrganismImage
    Intact 23RSS substrate reverse strandI [auth G]56Homo sapiens
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    Entity ID: 8
    MoleculeChainsLengthOrganismImage
    Intact 23RSS substrate forward strandJ56Homo sapiens
    Protein Feature View
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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 
    K [auth A], M [auth C]ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    MN
    Query on MN

    Download Ideal Coordinates CCD File 
    L [auth A], N [auth C]MANGANESE (II) ION
    Mn
    WAEMQWOKJMHJLA-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 3.60 Å
    • R-Value Free: 0.254 
    • R-Value Work: 0.214 
    • R-Value Observed: 0.216 
    • Space Group: C 1 2 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 156.678α = 90
    b = 123.562β = 105.6
    c = 186.286γ = 90
    Software Package:
    Software NamePurpose
    HKL-2000data reduction
    SCALAdata scaling
    PHENIXphasing
    PHENIXrefinement
    PDB_EXTRACTdata extraction

    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 StatesDK036147, DK036144, DK036167
    National Institutes of Health Intramural AIDS targeted Anti-viral ProgramUnited 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
    • Version 1.2: 2019-02-20
      Changes: Author supporting evidence, Data collection
    • Version 1.3: 2019-12-25
      Changes: Author supporting evidence