RIBFIND2: Identifying rigid bodies in protein and nucleic acid structures

Author:

Malhotra Sony1,Mulvaney Thomas234ORCID,Cragnolini Tristan25,Sidhu Haneesh5,Joseph Agnel P1ORCID,Beton Joseph G23,Topf Maya234ORCID

Affiliation:

1. Science and Technology Facilities Council, Scientific Computing, Research Complex at Harwell , Didcot OX11 0FA , UK

2. Leibniz Institute of Virology , Hamburg 20251 , Germany

3. Centre for Structural Systems Biology , Hamburg D-22607 , Germany

4. Universitätsklinikum Hamburg Eppendorf (UKE) , Hamburg 20246 , Germany

5. Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, University of London , London WC1E 7HX , UK

Abstract

Abstract Molecular structures are often fitted into cryo-EM maps by flexible fitting. When this requires large conformational changes, identifying rigid bodies can help optimize the model-map fit. Tools for identifying rigid bodies in protein structures exist, however an equivalent for nucleic acid structures is lacking. With the increase in cryo-EM maps containing RNA and progress in RNA structure prediction, there is a need for such tools. We previously developed RIBFIND, a program for clustering protein secondary structures into rigid bodies. In RIBFIND2, this approach is extended to nucleic acid structures. RIBFIND2 can identify biologically relevant rigid bodies in important groups of complex RNA structures, capturing a wide range of dynamics, including large rigid-body movements. The usefulness of RIBFIND2-assigned rigid bodies in cryo-EM model refinement was demonstrated on three examples, with two conformations each: Group II Intron complexed IEP, Internal Ribosome Entry Site and the Processome, using cryo-EM maps at 2.7–5 Å resolution. A hierarchical refinement approach, performed on progressively smaller sets of RIBFIND2 rigid bodies, was clearly shown to have an advantage over classical all-atom refinement. RIBFIND2 is available via a web server with structure visualization and as a standalone tool.

Funder

Wellcome Trust

Leibniz Institute of Virology

Universitätsklinikum Hamburg Eppendorf

Landesforschungsförderung Hamburg

Publisher

Oxford University Press (OUP)

Subject

Genetics

Reference30 articles.

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