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	Structural dynamics of DNA unwinding by a replicative helicase.
Journal, issue, pages	Nature, Year 2025
Publish date	Mar 19, 2025
Authors	Taha Shahid / Ammar U Danazumi / Muhammad Tehseen / Lubna Alhudhali / Alice R Clark / Christos G Savva / Samir M Hamdan / Alfredo De Biasio /
PubMed Abstract	Hexameric helicases are nucleotide-driven molecular machines that unwind DNA to initiate replication across all domains of life. Despite decades of intensive study, several critical aspects of their ...Hexameric helicases are nucleotide-driven molecular machines that unwind DNA to initiate replication across all domains of life. Despite decades of intensive study, several critical aspects of their function remain unresolved: the site and mechanism of DNA strand separation, the mechanics of unwinding propagation, and the dynamic relationship between nucleotide hydrolysis and DNA movement. Here, using cryo-electron microscopy (cryo-EM), we show that the simian virus 40 large tumour antigen (LTag) helicase assembles in the form of head-to-head hexamers at replication origins, melting DNA at two symmetrically positioned sites to establish bidirectional replication forks. Through continuous heterogeneity analysis, we characterize the conformational landscape of LTag on forked DNA under catalytic conditions, demonstrating coordinated motions that drive DNA translocation and unwinding. We show that the helicase pulls the tracking strand through DNA-binding loops lining the central channel, while directing the non-tracking strand out of the rear, in a cyclic process. ATP hydrolysis functions as an 'entropy switch', removing blocks to translocation rather than directly powering DNA movement. Our structures show the allosteric couplings between nucleotide turnover and subunit motions that enable DNA unwinding while maintaining dedicated exit paths for the separated strands. These findings provide a comprehensive model for replication fork establishment and progression that extends from viral to eukaryotic systems. More broadly, they introduce fundamental principles of the mechanism by which ATP-dependent enzymes achieve efficient mechanical work through entropy-driven allostery.
External links	Nature / PubMed:40108462
Methods	EM (single particle)
Resolution	3.0 - 3.7 Å
Structure data	50002 9evh EMDB-50002, PDB-9evh: SV40 large T antigen assembly with DNA in presence of ADP Method: EM (single particle) / Resolution: 3.38 Å 50010 9evp EMDB-50010, PDB-9evp: SV40 LTAg assembly with DNA in presence of AMPPNP and Mg2+. Method: EM (single particle) / Resolution: 3.12 Å 50036 9exd EMDB-50036, PDB-9exd: SV40 LTAg assembly in presence of ATP. Method: EM (single particle) / Resolution: 3.4 Å 50179 9f3t EMDB-50179, PDB-9f3t: Active SV40 LTAg complex with DNA (3D variability component_000, frame_010). Method: EM (single particle) / Resolution: 3.0 Å 50180 9f3u EMDB-50180, PDB-9f3u: Active SV40 LTAg complex with DNA (3D variability component_001, frame_010). Method: EM (single particle) / Resolution: 3.0 Å 50190 9f5i EMDB-50190, PDB-9f5i: Active SV40 LTAg complex with DNA (3D variability component_000, frame_005). Method: EM (single particle) / Resolution: 3.0 Å 50244 9f73 EMDB-50244, PDB-9f73: Active SV40 LTAg complex with DNA (3D variability component_002, frame_015). Method: EM (single particle) / Resolution: 3.0 Å 50245 9f74 EMDB-50245, PDB-9f74: Active SV40 LTAg complex with DNA (3D variability component_000, frame_015). Method: EM (single particle) / Resolution: 3.0 Å 50246 9f75 EMDB-50246, PDB-9f75: Active SV40 LTAg complex with DNA (3D variability component_000, frame_019). Method: EM (single particle) / Resolution: 3.0 Å 50250 9f7n EMDB-50250, PDB-9f7n: Active SV40 LTAg complex with DNA (3D variability component_000, frame_000). Method: EM (single particle) / Resolution: 3.0 Å 50256 9f9n EMDB-50256, PDB-9f9n: Active SV40 LTAg complex with DNA (3D variability component_001, frame_005). Method: EM (single particle) / Resolution: 3.0 Å 50257 9f9o EMDB-50257, PDB-9f9o: Active SV40 LTAg complex with DNA (3D variability component_001, frame_015). Method: EM (single particle) / Resolution: 3.0 Å 50261 9f9w EMDB-50261, PDB-9f9w: Active SV40 LTAg complex with DNA (3D variability component_001, frame_019). Method: EM (single particle) / Resolution: 3.0 Å 50262 9f9x EMDB-50262, PDB-9f9x: Active SV40 LTAg complex with DNA (3D variability component_001, frame_000). Method: EM (single particle) / Resolution: 3.0 Å 50264 9fa1 EMDB-50264, PDB-9fa1: Active SV40 LTAg complex with DNA (3D variability component_002, frame_010). Method: EM (single particle) / Resolution: 3.0 Å 50265 9fa2 EMDB-50265, PDB-9fa2: Active SV40 LTAg complex with DNA (3D variability component_002, frame_005). Method: EM (single particle) / Resolution: 3.0 Å 50286 9fb0 EMDB-50286, PDB-9fb0: Active SV40 LTAg complex with DNA (3D variability component_002, frame_019). Method: EM (single particle) / Resolution: 3.0 Å 50287 9fb4 EMDB-50287, PDB-9fb4: SV40 large T antigen assembly with DNA in presence of ATP. Method: EM (single particle) / Resolution: 3.13 Å 50288 9fb5 EMDB-50288, PDB-9fb5: Active SV40 LTAg complex with DNA (3D variability component_002, frame_000). Method: EM (single particle) / Resolution: 3.0 Å 50289 9fb6 EMDB-50289, PDB-9fb6: SV40 large T antigen assembly with DNA in presence of ATP. Method: EM (single particle) / Resolution: 3.13 Å EMDB-50290: Active SV40 LTAg complex with DNA (Consensus reconstruction). Method: EM (single particle) / Resolution: 3.0 Å EMDB-52108: SV40 LTAg complex with ADP and DNA (3D variability component_000, frame_000). Method: EM (single particle) / Resolution: 3.4 Å EMDB-52109: SV40 LTAg complex with ADP and DNA (3D variability component_000, frame_019). Method: EM (single particle) / Resolution: 3.4 Å EMDB-52110: SV40 LTAg complex with ADP and DNA (3D variability component_001, frame_000). Method: EM (single particle) / Resolution: 3.4 Å EMDB-52111: SV40 LTAg complex with ADP and DNA (3D variability component_001, frame_019). Method: EM (single particle) / Resolution: 3.4 Å EMDB-52112: SV40 LTAg complex with ADP and DNA (3D variability component_002, frame_000). Method: EM (single particle) / Resolution: 3.4 Å EMDB-52113: SV40 LTAg complex with ADP and DNA (3D variability component_002, frame_019). Method: EM (single particle) / Resolution: 3.4 Å EMDB-52176: SV40 large T antigen assembly with DNA in presence of ATP (3D variability component_000, frame_019). Method: EM (single particle) / Resolution: 3.13 Å EMDB-52180: SV40 large T antigen assembly with DNA in presence of ATP (3D variability component_000, frame_000). Method: EM (single particle) / Resolution: 3.13 Å EMDB-52181: SV40 large T antigen assembly with DNA in presence of ATP (3D variability component_001, frame_019). Method: EM (single particle) / Resolution: 3.13 Å EMDB-52182: SV40 large T antigen assembly with DNA in presence of ATP (3D variability component_001, frame_000). Method: EM (single particle) / Resolution: 3.13 Å EMDB-52183: SV40 large T antigen assembly with DNA in presence of ATP (3D variability component_002, frame_000). Method: EM (single particle) / Resolution: 3.13 Å EMDB-52184: SV40 large T antigen assembly with DNA in presence of ATP (3D variability component_002, frame_019). Method: EM (single particle) / Resolution: 3.13 Å 62206 9kae EMDB-62206, PDB-9kae: CryoEM structure of LTag bound to SV40 EP half origin DNA Method: EM (single particle) / Resolution: 3.1 Å 62209 9kak EMDB-62209, PDB-9kak: CryoEM structure of LTag bound to SV40 AT half origin DNA Method: EM (single particle) / Resolution: 3.1 Å EMDB-62502: CryoEM structure of SV40 LTag bound to SV40 origin DNA Method: EM (single particle) / Resolution: 3.7 Å
Chemicals	ChemComp-ADP: ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying moleculeYM ChemComp-ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogueYM ChemComp-MG: Unknown entry ChemComp-ATP: ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM
Source	betapolyomavirus macacae synthetic construct (others)
Keywords	DNA BINDING PROTEIN / AAA+ superfamily Helicase Substrate translocation DNA unwinding / AAA+ superfamily; Helicase; Substrate translocation; DNA unwinding; DNA BINDING PROTEIN / TRANSLOCASE / Helicase / ATPase / EP half origin / AMP-PNP / DNA replication / AT half origin