Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	DNA melting initiates the RAG catalytic pathway.
Journal, issue, pages	Nat Struct Mol Biol, Vol. 25, Issue 8, Page 732-742, Year 2018
Publish date	Jul 30, 2018
Authors	Heng Ru / Wei Mi / Pengfei Zhang / Frederick W Alt / David G Schatz / Maofu Liao / Hao Wu /
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 ...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.
External links	Nat Struct Mol Biol / PubMed:30061602 / PubMed Central
Methods	EM (single particle)
Resolution	3.0 - 5.0 Å
Structure data	7843 6dbi EMDB-7843, PDB-6dbi: Cryo-EM structure of RAG in complex with 12-RSS and 23-RSS nicked DNA intermediates Method: EM (single particle) / Resolution: 3.4 Å 7844 6dbj EMDB-7844, PDB-6dbj: Cryo-EM structure of RAG in complex with 12-RSS and 23-RSS nicked DNA intermediates Method: EM (single particle) / Resolution: 3.0 Å 7845 6dbl EMDB-7845, PDB-6dbl: Cryo-EM structure of RAG in complex with 12-RSS and 23-RSS substrate DNAs Method: EM (single particle) / Resolution: 5.0 Å 7846 6dbo EMDB-7846, PDB-6dbo: Cryo-EM structure of RAG in complex with 12-RSS and 23-RSS substrate DNAs Method: EM (single particle) / Resolution: 4.4 Å 7847 6dbq EMDB-7847, PDB-6dbq: Cryo-EM structure of RAG in complex with 12-RSS and 23-RSS substrate DNAs Method: EM (single particle) / Resolution: 4.22 Å 7848 6dbr EMDB-7848, PDB-6dbr: Cryo-EM structure of RAG in complex with one melted RSS and one unmelted RSS Method: EM (single particle) / Resolution: 4.0 Å 7849 6dbt EMDB-7849, PDB-6dbt: Cryo-EM structure of RAG in complex with 12-RSS and 23-RSS substrate DNAs Method: EM (single particle) / Resolution: 4.3 Å 7850 6dbu EMDB-7850, PDB-6dbu: Cryo-EM structure of RAG in complex with 12-RSS and 23-RSS substrate DNAs Method: EM (single particle) / Resolution: 3.9 Å 7851 6dbv EMDB-7851, PDB-6dbv: Cryo-EM structure of RAG in complex with 12-RSS and 23-RSS substrate DNAs Method: EM (single particle) / Resolution: 4.29 Å 7852 6dbw EMDB-7852, PDB-6dbw: Cryo-EM structure of RAG in complex with 12-RSS substrate DNA Method: EM (single particle) / Resolution: 4.7 Å 7853 6dbx EMDB-7853, PDB-6dbx: Cryo-EM structure of RAG in complex with 12-RSS substrate DNA Method: EM (single particle) / Resolution: 4.2 Å
Chemicals	ChemComp-ZN: Unknown entry ChemComp-CA: Unknown entry
Source	danio rerio (zebrafish) escherichia coli (E. coli)
Keywords	RECOMBINATION/DNA / V(D)J recombination / synaptic RAG complex / nicked RSS intermediates / paired complex / RECOMBINATION-DNA complex / RSS / RAG complex / melted DNA / Pre-cleavage complex / Pre-cleveage complex / RSS substrate DNA / Pre-cleveaage complex / Melted RSS / Unmelted RSS / unmelted DNA substrates / melted RSS substrate / singly-bound complex / unmelted RSS substrate / singly bound complex