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DESCRIPTION:This webinar is part of a series run by the ELIXIR 3D-BioInfo C
 ommunity. There is a complete list of webinars here.  \n			\n				 \n			
 \n		\n	\n\n\nHosts\n\n \n	\n		\n			Dr. Gonzalo Parra\n				Barcelona Super
 computing Center\n		\n	\n\n	\n		\n			Dr Neeladri Sen\n				University Coll
 ege London (UCL)\n		\n	\n\n\nProgramme\n\nImproving validation of nucleic 
 acid structures\n\nProf. Bohdan Schneider (Institute of Biotechnology of t
 he Czech Academy of Sciences\, 252 50\n	Vestec\, Czech Republic)\n\n\n\nTh
 e community of structural biologists and bioinformaticians benefit from th
 e culture of data sharing and generally well-functioning publicly accessib
 le archive\, the PDB. Despite this generally positive situation there rema
 in quality problems. The problems are more serious for nucleic acid than f
 or protein structures because there are many fewer high-quality nucleic ac
 id structures\; in addition\, the evolutionary alignments are limited just
  to a few RNA functional classes [1]. The problems with nucleic acid geome
 try can be divided into three groups:\n\n\n	Inconsistently set and applied
  target values of bond distances and angles for nucleotides\n	Poorly refin
 ed backbone geometries\n	Incompletely and often incorrectly assigned base 
 pairing topologies.\n\n\nIn the talk\, I introduce web-based tools that ad
 dress these problems and offer solution to some. The tools are available f
 rom our web application dnatco.datmos.org [2]. The web leads you from the
  Annotation TAB\, which offers an overview of the analyzed structures acce
 ssible for a non-expert. The Validation TAB enables an in-depth analysis o
 f nucleic acid structures and expert-level judgement of their quality. Thi
 s TAB\n	provides a detailed analysis of NA conformation at the level of di
 nucleotide based on our original system of the dinucleotide NtC classes [3
 ]. This TAB also offers validation of the valence geometry.\n\nSoon\, we w
 ill also provide an integrated tool to analyze base pairs detected in the 
 analyzed structure. Now the web basepairs.datmos.org provides an overview
  of base pairs in the PDB structures. The TAB Refine offers tools to modif
 y structures during the process of their refinement. The last TAB\, Browse
 \, allows the user to view NA structures from various perspectives. Result
 s of most analyses are available for download in several formats.\n\nThis 
 research was funded by Czech Academy of Sciences\, grant RVO86652036 and b
 y grant LM2023055 to ELIXIR CZ from MEYS Czech Republic.\n\n[1] Bohdan Sch
 neider\, Blake Alexander Sweeney\, Alex Bateman\, Jiří Černý\, Tomasz 
 Zok\, &amp\; Marta Szachniuk: When will RNA get its AphaFold moment? Nucle
 ic Acids Research. 51(18): 9522-9532 (2023). doi: 10.1093/nar/gkad726.\n	[
 2] Jiří Černý\, Paulína Božíková\, Michal Malý\, Michal Tykač\, 
 Lada Biedermannová &amp\; Bohdan Schneider: Structural alphabets for conf
 ormational analysis of nucleic acids available at dnatco.datmos.org. Acta
  Crystallographica D76: 805-813 (2020). doi: 10.1107/S2059798320009389.\n	
 [3] Jiří Černý\, Paulína Božíková\, Jakub Svoboda &amp\; Bohdan Sc
 hneider: A unified dinucleotide alphabet describing both RNA and DNA struc
 tures. Nucleic Acids Research. 48(11): 6367-6381 (2020). doi: 10.1093/nar/
 gkaa383.\n\nStructural insight into the mechanism of the SorC protein fami
 ly\n\nMarkéta Šoltysová (Institute of Organic Chemistry and Biochemistr
 y of Czech Academy of Sciences\, Prague\, Czech Republic)\n\nProteins of t
 he SorC family are bacterial transcription regulators involved in carbohyd
 rate metabolism and quorum-sensing control [1\, 2]. They consist of a DNA
 ‑binding domain (DBD) and an effector‑binding domain (EBD)\, though wh
 ich the protomers oligomerize. Based on the sequence similarity of DBDs\, 
 the family is divided into two subfamilies\, SorC/DeoR and SorC/CggR. Prio
 r to our research\, there was no structural information on their complex w
 ith the cognate DNA (operator) and thus neither knowledge of how the prote
 ins recognize their operator targets [3-8].\n	In my talk\, I will present 
 our integrative approach combining Xray crystallography and cryogenic elec
 tron microscopy (cryoEM) to structurally characterize two SorC prototypes 
 in the complex with their operators\, DeoR and CggR from Bacillus subtili
 s. Xray and cryoEM studies of the fulllength repressorDNA complexes provid
 ed lowresolution information revealing the general mechanism of binding. W
 e further complemented these models with  highresolution crystal structur
 es of DeoR and CggR DBDs in complex with halfoperator duplexes. By integra
 ting all this information\, we propose the SorC protein family mechanism\n
 	of the function\, which might be used for further basic and applied resea
 rch.\n	Supported by project 8J23FR035 from Ministry of Education\, Youth a
 nd Sports of the Czech Republic.\n\n[1] Fillinger S et al. J Biol Chem. (2
 000)\, 275\, 14031-7.\n	[2] Taga ME et al. Mol Microbiol. (2001)\, 42\, 77
 7-93.\n	[3] Řezáčová P et al. Mol Microbiol. (2008)\, 69\, 895-910.\n	
 [4] Škerlová J et al. FEBS J. (2014)\, 281\, 4280-92.\n	[5] de Sanctis D
  et al. J Mol Biol. (2009)\, 387\, 759-70.\n	[6] Ha JH et al. J Am Chem So
 c. (2013)\, 135\, 15526-35.\n	[7] Šoltysová M et al. Acta Cryst (2021)\,
  D77\, 1411-1424.\n	[8] Šoltysová M et al. Nucleic Acids Res (2024)\, 52
 \, 7305-7320.\n\nYou can find previous webinars from the 3D-BioInfo Commun
 ity on the Community webinars page.
SUMMARY:3D-BioInfo Webinar: Nucleic Acids Structural Bioinformatics
URL;VALUE=URI:https://www.elixir-europe.org/events/3d-bioinfo-webinar-nucle
 ic-acids-structural-bioinformatics
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