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 1.2 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: https://doi.org/10.1038/s41594-019-0366-z
  • Primary Citation of Related Structures:  
    6OES, 6OET

  • 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 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.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
V(D)J recombination-activating protein 1
A, C
1,040Mus 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)
Explore P15919 
Go to UniProtKB:  P15919
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UniProt GroupP15919
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
V(D)J recombination-activating protein 2
B, D
527Mus musculusMutation(s): 0 
Gene Names: Rag2Rag-2
UniProt
Find proteins for P21784 (Mus musculus)
Explore P21784 
Go to UniProtKB:  P21784
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UniProt GroupP21784
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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (50-MER)E [auth F]50Escherichia coli K-12
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Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (5'-D(*CP*CP*TP*GP*GP*AP*TP*CP*TP*GP*GP*CP*CP*TP*G)-3')F [auth I],
G [auth J]
15Escherichia coli K-12
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (59-MER)H [auth G]61Escherichia coli K-12
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (30-MER)I [auth L]30Escherichia coli K-12
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Entity ID: 7
MoleculeChains LengthOrganismImage
DNA (39-MER)J [auth M]41Escherichia coli K-12
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Experimental Data & Validation

Experimental Data

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

Structure Validation

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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  (Full details and data files)

  • Version 1.0: 2020-01-22
    Type: Initial release
  • Version 1.1: 2020-08-05
    Changes: Database references, Derived calculations
  • Version 1.2: 2024-03-20
    Changes: Data collection, Database references