6OET

Cryo-EM structure of mouse RAG1/2 STC complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

How mouse RAG recombinase avoids DNA transposition.

Chen, X.Cui, Y.Wang, H.Zhou, Z.H.Gellert, M.Yang, W.

(2020) Nat Struct Mol Biol 27: 127-133

  • DOI: 10.1038/s41594-019-0366-z
  • Primary Citation of Related Structures:  
    6OET, 6OES

  • PubMed Abstract: 
  • The RAG1-RAG2 recombinase (RAG) cleaves DNA to initiate V(D)J recombination, but RAG also belongs to the RNH-type transposase family. To learn how RAG-catalyzed transposition is inhibited in developing lymphocytes, we determined the structure of a DN ...

    The RAG1-RAG2 recombinase (RAG) cleaves DNA to initiate V(D)J recombination, but RAG also belongs to the RNH-type transposase family. To learn how RAG-catalyzed transposition is inhibited in developing lymphocytes, we determined the structure of a DNA-strand transfer complex of mouse RAG at 3.1-Å resolution. The target DNA is a T form (T for transpositional target), which contains two >80° kinks towards the minor groove, only 3 bp apart. RAG2, a late evolutionary addition in V(D)J recombination, appears to enforce the sharp kinks and additional inter-segment twisting in target DNA and thus attenuates unwanted transposition. In contrast to strand transfer complexes of genuine transposases, where severe kinks occur at the integration sites of target DNA and thus prevent the reverse reaction, the sharp kink with RAG is 1 bp away from the integration site. As a result, RAG efficiently catalyzes the disintegration reaction that restores the RSS (donor) and target DNA.


    Organizational Affiliation

    Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD, USA. weiy@niddk.nih.gov.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
V(D)J recombination-activating protein 2BD527Mus musculusMutation(s): 0 
Gene Names: Rag2Rag-2
Find proteins for P21784 (Mus musculus)
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Go to UniProtKB:  P21784
Protein Feature View
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  • Reference Sequence
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
V(D)J recombination-activating protein 1AC1040Mus musculusMutation(s): 1 
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
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA (50-MER)F50Escherichia coli K-12
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Entity ID: 6
MoleculeChainsLengthOrganismImage
DNA (30-MER)L30Escherichia coli K-12
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Entity ID: 7
MoleculeChainsLengthOrganismImage
DNA (39-MER)M41Escherichia coli K-12
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  • Entity ID: 4
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*CP*CP*TP*GP*GP*AP*TP*CP*TP*GP*GP*CP*CP*TP*G)-3')I, J15Escherichia coli K-12
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    (by identity cutoff)  |  Structure
    Entity ID: 5
    MoleculeChainsLengthOrganismImage
    DNA (59-MER)G61Escherichia coli K-12
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    ZN
    Query on ZN

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

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    A, C
    CALCIUM ION
    Ca
    BHPQYMZQTOCNFJ-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 3.40 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 StatesDK036167

    Revision History 

    • Version 1.0: 2020-01-22
      Type: Initial release
    • Version 1.1: 2020-08-05
      Changes: Database references, Derived calculations