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	Structures of 9-1-1 DNA checkpoint clamp loading at gaps from start to finish and ramification to biology.
Journal, issue, pages	bioRxiv, Year 2023
Publish date	May 3, 2023
Authors	Fengwei Zheng / Roxana E Georgescu / Nina Y Yao / Michael E O'Donnell / Huilin Li /
PubMed Abstract	Recent structural studies show the Rad24-RFC loads the 9-1-1 checkpoint clamp onto a recessed 5' end by binding the 5' DNA on Rad24 at an external surface site and threading the 3' ssDNA into the ...Recent structural studies show the Rad24-RFC loads the 9-1-1 checkpoint clamp onto a recessed 5' end by binding the 5' DNA on Rad24 at an external surface site and threading the 3' ssDNA into the well-established internal chamber and into 9-1-1. We find here that Rad24-RFC loads 9-1-1 onto DNA gaps in preference to a recessed 5' DNA end, thus presumably leaving 9-1-1 on a 3' ss/ds DNA after Rad24-RFC ejects from the 5' gap end and may explain reports of 9-1-1 directly functioning in DNA repair with various TLS polymerases, in addition to signaling the ATR kinase. To gain a deeper understanding of 9-1-1 loading at gaps we report high-resolution structures of Rad24-RFC during loading of 9-1-1 onto 10-nt and 5-nt gapped DNAs. At a 10-nt gap we captured five Rad24-RFC-9-1-1 loading intermediates in which the 9-1-1 DNA entry gate varies from fully open to fully closed around DNA using ATPγS, supporting the emerging view that ATP hydrolysis is not needed for clamp opening/closing, but instead for dissociation of the loader from the clamp encircling DNA. The structure of Rad24-RFC-9-1-1 at a 5-nt gap shows a 180° axially rotated 3'-dsDNA which orients the template strand to bridge the 3'- and 5'- junctions with a minimum 5-nt ssDNA. The structures reveal a unique loop on Rad24 that limits the length of dsDNA in the inner chamber, and inability to melt DNA ends unlike RFC, thereby explaining Rad24-RFC's preference for a preexisting ssDNA gap and suggesting a direct role in gap repair in addition to its checkpoint role.
External links	bioRxiv / PubMed:37205533 / PubMed Central
Methods	EM (single particle)
Resolution	2.76 - 3.04 Å
Structure data	29412 8fs3 EMDB-29412: EM map of S. cerevisiae Rad24-RFC loading the 9-1-1 clamp onto a 10-nt gapped DNA in step 1 (open 9-1-1 and shoulder bound DNA only) PDB-8fs3: Structure of S. cerevisiae Rad24-RFC loading the 9-1-1 clamp onto a 10-nt gapped DNA in step 1 (open 9-1-1 and shoulder bound DNA only) Method: EM (single particle) / Resolution: 2.93 Å 29413 8fs4 EMDB-29413: EM map of S. cerevisiae Rad24-RFC loading the 9-1-1 clamp onto a 10-nt gapped DNA in step 2 (open 9-1-1 ring and flexibly bound chamber DNA) PDB-8fs4: Structure of S. cerevisiae Rad24-RFC loading the 9-1-1 clamp onto a 10-nt gapped DNA in step 2 (open 9-1-1 ring and flexibly bound chamber DNA) Method: EM (single particle) / Resolution: 2.94 Å 29414 8fs5 EMDB-29414: EM map of S. cerevisiae Rad24-RFC loading the 9-1-1 clamp onto a 10-nt gapped DNA in step 3 (open 9-1-1 and stably bound chamber DNA) PDB-8fs5: Structure of S. cerevisiae Rad24-RFC loading the 9-1-1 clamp onto a 10-nt gapped DNA in step 3 (open 9-1-1 and stably bound chamber DNA) Method: EM (single particle) / Resolution: 2.76 Å 29415 8fs6 EMDB-29415: EM map of S. cerevisiae Rad24-RFC loading the 9-1-1 clamp onto a 10-nt gapped DNA in step 4 (partially closed 9-1-1 and stably bound chamber DNA) PDB-8fs6: Structure of S. cerevisiae Rad24-RFC loading the 9-1-1 clamp onto a 10-nt gapped DNA in step 4 (partially closed 9-1-1 and stably bound chamber DNA) Method: EM (single particle) / Resolution: 2.9 Å 29416 8fs7 EMDB-29416: EM map of S. cerevisiae Rad24-RFC loading the 9-1-1 clamp onto a 10-nt gapped DNA in step 5 (closed 9-1-1 and stably bound chamber DNA) PDB-8fs7: Structure of S. cerevisiae Rad24-RFC loading the 9-1-1 clamp onto a 10-nt gapped DNA in step 5 (closed 9-1-1 and stably bound chamber DNA) Method: EM (single particle) / Resolution: 2.85 Å 29417 8fs8 EMDB-29417: EM map of S. cerevisiae Rad24-RFC loading the 9-1-1 clamp onto a 5-nt gapped DNA (9-1-1 encircling fully bound DNA) PDB-8fs8: Structure of S. cerevisiae Rad24-RFC loading the 9-1-1 clamp onto a 5-nt gapped DNA (9-1-1 encircling fully bound DNA) Method: EM (single particle) / Resolution: 3.04 Å
Chemicals	ChemComp-MG: Unknown entry ChemComp-AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogueYM ChemComp-ADP: ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying moleculeYM
Source	synthetic construct (others) saccharomyces cerevisiae (brewer's yeast)
Keywords	CELL CYCLE/DNA / DNA damage repair / Rad24-RFC / 9-1-1 clamp / DNA clamp / alternative clamp loader / DNA damage signaling / DNA BINDING PROTEIN-DNA complex / CELL CYCLE-DNA complex