6DBV

Cryo-EM structure of RAG in complex with 12-RSS and 23-RSS substrate DNAs

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.29 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.2 of the entry. See complete history. 


Literature

DNA melting initiates the RAG catalytic pathway.

Ru, H., Mi, W., Zhang, P., Alt, F.W., Schatz, D.G., Liao, M., Wu, H.

(2018) Nat Struct Mol Biol 25: 732-742

  • DOI: 10.1038/s41594-018-0098-5
  • Primary Citation of Related Structures:  
    6DBI, 6DBJ, 6DBL, 6DBO, 6DBQ, 6DBR, 6DBT, 6DBU, 6DBV, 6DBW, 6DBX

  • PubMed Abstract: 

    • The mechanism for initiating DNA cleavage by DDE-family enzymes, including the RAG endonuclease, which initiates V(D)J recombination, is not well understood. Here we report six cryo-EM structures of zebrafish RAG in complex with one or two intact recombination signal sequences (RSSs), at up to 3 ...

    The mechanism for initiating DNA cleavage by DDE-family enzymes, including the RAG endonuclease, which initiates V(D)J recombination, is not well understood. Here we report six cryo-EM structures of zebrafish RAG in complex with one or two intact recombination signal sequences (RSSs), at up to 3.9-Å resolution. Unexpectedly, these structures reveal DNA melting at the heptamer of the RSSs, thus resulting in a corkscrew-like rotation of coding-flank DNA and the positioning of the scissile phosphate in the active site. Substrate binding is associated with dimer opening and a piston-like movement in RAG1, first outward to accommodate unmelted DNA and then inward to wedge melted DNA. These precleavage complexes show limited base-specific contacts of RAG at the conserved terminal CAC/GTG sequence of the heptamer, thus suggesting conservation based on a propensity to unwind. CA and TG overwhelmingly dominate terminal sequences in transposons and retrotransposons, thereby implicating a universal mechanism for DNA melting during the initiation of retroviral integration and DNA transposition.

    Organizational Affiliation: 

    Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA. wu@crystal.harvard.edu.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Recombination activating gene 1 - MBP chimeraA1159Escherichia coli K-12, Danio rerio
This entity is chimeric		Mutation(s): 0 
Gene Names: malE, b4034, JW3994, rag1
EC: 2.3.2.27 (PDB Primary Data), 3.1 (UniProt)
UniProt
Find proteins for P0AEX9 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0AEX9
Find proteins for O13033 (Danio rerio)
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Go to UniProtKB:  O13033
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP0AEX9O13033
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Recombination activating gene 2B, D533Danio rerioMutation(s): 0 
Gene Names: rag2, rag-2
UniProt
Find proteins for O13034 (Danio rerio)
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Go to UniProtKB:  O13034
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UniProt GroupO13034
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Recombination activating gene 1 - MBP chimeraC1159Escherichia coli K-12, Danio rerio
This entity is chimeric		Mutation(s): 0 
Gene Names: malE, b4034, JW3994, rag1
EC: 2.3.2.27 (PDB Primary Data), 3.1 (UniProt)
UniProt
Find proteins for P0AEX9 (Escherichia coli (strain K12))
Explore P0AEX9 
Go to UniProtKB:  P0AEX9
Find proteins for O13033 (Danio rerio)
Explore O13033 
Go to UniProtKB:  O13033
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP0AEX9O13033
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Entity ID: 4
MoleculeChainsLengthOrganismImage
Forward strand of 12-RSS substrate DNAE 50Danio rerio
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Entity ID: 5
MoleculeChainsLengthOrganismImage
Reverse strand of 12-RSS substrate DNAF 50Danio rerio
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Entity ID: 6
MoleculeChainsLengthOrganismImage
Forward strand of 23-RSS substrate DNAG 61Danio rerio
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Entity ID: 7
MoleculeChainsLengthOrganismImage
Reverse strand of 23-RSS substrate DNAH 61Danio rerio
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.29 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 Human Genome Research Institute (NIH/NHGRI)United StatesAI125535

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-01
    Type: Initial release
  • Version 1.1: 2018-08-15
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-18
    Changes: Author supporting evidence, Other