Skip to main content
  • Submit
  • About
    • Editorial Board
    • PNAS Staff
    • FAQ
    • Accessibility Statement
    • Rights and Permissions
    • Site Map
  • Contact
  • Journal Club
  • Subscribe
    • Subscription Rates
    • Subscriptions FAQ
    • Open Access
    • Recommend PNAS to Your Librarian
  • Log in
  • Log out
  • My Cart

Main menu

  • Home
  • Articles
    • Current
    • Latest Articles
    • Special Features
    • Colloquia
    • Collected Articles
    • PNAS Classics
    • Archive
  • Front Matter
  • News
    • For the Press
    • Highlights from Latest Articles
    • PNAS in the News
  • Podcasts
  • Authors
    • Information for Authors
    • Purpose and Scope
    • Editorial and Journal Policies
    • Submission Procedures
    • For Reviewers
    • Author FAQ
  • Submit
  • About
    • Editorial Board
    • PNAS Staff
    • FAQ
    • Accessibility Statement
    • Rights and Permissions
    • Site Map
  • Contact
  • Journal Club
  • Subscribe
    • Subscription Rates
    • Subscriptions FAQ
    • Open Access
    • Recommend PNAS to Your Librarian

User menu

  • Log in
  • Log out
  • My Cart

Search

  • Advanced search
Home
Home

Advanced Search

  • Home
  • Articles
    • Current
    • Latest Articles
    • Special Features
    • Colloquia
    • Collected Articles
    • PNAS Classics
    • Archive
  • Front Matter
  • News
    • For the Press
    • Highlights from Latest Articles
    • PNAS in the News
  • Podcasts
  • Authors
    • Information for Authors
    • Purpose and Scope
    • Editorial and Journal Policies
    • Submission Procedures
    • For Reviewers
    • Author FAQ

New Research In

Physical Sciences

Featured Portals

  • Physics
  • Chemistry
  • Sustainability Science

Articles by Topic

  • Applied Mathematics
  • Applied Physical Sciences
  • Astronomy
  • Computer Sciences
  • Earth, Atmospheric, and Planetary Sciences
  • Engineering
  • Environmental Sciences
  • Mathematics
  • Statistics

Social Sciences

Featured Portals

  • Anthropology
  • Sustainability Science

Articles by Topic

  • Economic Sciences
  • Environmental Sciences
  • Political Sciences
  • Psychological and Cognitive Sciences
  • Social Sciences

Biological Sciences

Featured Portals

  • Sustainability Science

Articles by Topic

  • Agricultural Sciences
  • Anthropology
  • Applied Biological Sciences
  • Biochemistry
  • Biophysics and Computational Biology
  • Cell Biology
  • Developmental Biology
  • Ecology
  • Environmental Sciences
  • Evolution
  • Genetics
  • Immunology and Inflammation
  • Medical Sciences
  • Microbiology
  • Neuroscience
  • Pharmacology
  • Physiology
  • Plant Biology
  • Population Biology
  • Psychological and Cognitive Sciences
  • Sustainability Science
  • Systems Biology
Research Article

Structural analysis of the intrinsically disordered splicing factor Spp2 and its binding to the DEAH-box ATPase Prp2

Florian Hamann, Andreas Schmitt, Filippo Favretto, Romina Hofele, Piotr Neumann, ShengQi Xiang, Henning Urlaub, View ORCID ProfileMarkus Zweckstetter, and View ORCID ProfileRalf Ficner
PNAS February 11, 2020 117 (6) 2948-2956; first published January 23, 2020 https://doi.org/10.1073/pnas.1907960117
Florian Hamann
aDepartment of Molecular Structural Biology, Institute of Microbiology and Genetics, Georg-August-University Göttingen, 37077 Göttingen, Germany;
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Andreas Schmitt
aDepartment of Molecular Structural Biology, Institute of Microbiology and Genetics, Georg-August-University Göttingen, 37077 Göttingen, Germany;
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Filippo Favretto
bSenior Research Group of Translational Structural Biology of Dementia, German Center for Neurodegenerative Diseases, 37075 Göttingen, Germany;
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Romina Hofele
cBioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany;
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Piotr Neumann
aDepartment of Molecular Structural Biology, Institute of Microbiology and Genetics, Georg-August-University Göttingen, 37077 Göttingen, Germany;
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
ShengQi Xiang
dDepartment for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany;
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Henning Urlaub
cBioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany;
eBioanalytics, Department of Clinical Chemistry, University Medical Center Göttingen, 37075 Göttingen, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Markus Zweckstetter
bSenior Research Group of Translational Structural Biology of Dementia, German Center for Neurodegenerative Diseases, 37075 Göttingen, Germany;
dDepartment for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany;
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Markus Zweckstetter
  • For correspondence: Markus.Zweckstetter@dzne.de rficner@uni-goettingen.de
Ralf Ficner
aDepartment of Molecular Structural Biology, Institute of Microbiology and Genetics, Georg-August-University Göttingen, 37077 Göttingen, Germany;
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Ralf Ficner
  • For correspondence: Markus.Zweckstetter@dzne.de rficner@uni-goettingen.de
  1. Edited by Michael Sattler, Helmholtz Zentrum München, Neuherberg, Germany, and accepted by Editorial Board Member Axel T. Brunger December 30, 2019 (received for review May 9, 2019)

  • Article
  • Figures & SI
  • Info & Metrics
  • PDF
Loading

Article Figures & SI

Figures

  • Fig. 1.
    • Download figure
    • Open in new tab
    • Download powerpoint
    Fig. 1.

    Disorder and secondary structure analysis of yeast Spp2 in solution. (A) Analysis of the scSpp2 amino acid sequence by the Genesilico MetaDisorder prediction server. The probability to form disordered regions (y-axis) is shown with respect to the residue number (x-axis). (B) CD spectra of scSpp210–185 (blue line) and scSpp2100–150 (red line). The CD in mdeg (y-axis) is shown with respect to the wavelength (x-axis). (C) Two-dimensional 1H-15N HSQC spectrum of scSpp210–185 at 288 K and pH 6.5.

  • Fig. 2.
    • Download figure
    • Open in new tab
    • Download powerpoint
    Fig. 2.

    Structural overview of the ctSpp2 G-patch bound to ctPrp2. (A) The model of the ctPrp2-ctSpp2211–254 complex depicted as a cartoon model, with ctPrp2 displayed semitransparently. N-terminal residues (270 to 296) of ctPrp2 are shown in black, the RecA1 domain (297 to 476) is shown in orange, the RecA2 domain (477 to 653) is shown in blue, the WH domain (654 to 721) is shown in gray, the HB domain (722 to 840) is shown in wheat, and the OB domain (841 to 921) is shown in green. Two alternative conformations of the ctSpp2 G-patch were found in complex structures obtained from five crystal forms (CFs). ctSpp2211–254 molecules exhibiting conformation 1 are depicted in different shades of red, whereas molecules belonging to conformation 2 are displayed in different shades of yellow. (Right) A zoomed-in view of the alternative conformations at the C-terminal end of the G-patch with one representative for each conformation. (B) Overview of hydrophobic interactions between ctSpp2211–254 and ctPrp2. Hydrophobic residues of ctSpp2 are shown in orange, while hydrophobic residues of ctPrp2 within 8 Å of the conserved ctSpp2211–254 hydrophobic residues are displayed in blue. Glycine residues of ctSpp2211–254 are highlighted as green spheres. (C) Sequence alignment of the G-patch domains of Spp2 from C. thermophilum, S. cerevisiae, and H. sapiens together with Ntr1, Gno1, and Pfa1 from S. cerevisiae. Conserved hydrophobic residues are highlighted in yellow, and glycine residues are shown in red. Secondary structure elements present in any of the five crystal forms are displayed on top of the corresponding segment of the sequence. The N-terminal amphipathic helix, as well as a hydrophobic stretch at the C-terminal end, are highly conserved. (D) Residues identified to cross-link to the lysines K236 and K250 of ctSpp2211–254 are shown as sticks and the cross-linked residues on ctPrp2 are shown in green.

  • Fig. 3.
    • Download figure
    • Open in new tab
    • Download powerpoint
    Fig. 3.

    Transient helical conformations in the G-patch of ctSpp2 before complex formation. (A) Far-UV CD spectrum (mean residue ellipticity vs. wavelength, in nm) of ctSpp2208–254. (Inset) DLS measurements demonstrating that ctSpp2208–254 is predominantly monomeric in solution. (B) Two-dimensional 1H-15N-HSQC spectrum of ctSpp2208–254. The sequence-specific assignment of the backbone resonances is indicated. (C) Residue-specific ΔCα-ΔCβ secondary chemical shifts of ctSpp2208–254 together with S2 parameters derived by TALOS+. Positive values of ΔCα-ΔCβ indicate a propensity for α-helical conformations, while negative values indicate a propensity to form extended structures. The positions of α-helices observed in ctSpp2208–254 when in complex with Prp2 are shown on top. (D) Heteronuclear steady-state {1H,15N} NOE as a function of residue number. Error bars represent the SDs and were calculated as described in Materials and Methods. (E) Ensemble of α-helical conformations populated by residues D213 to F222 of ctSpp2208–254.

  • Fig. 4.
    • Download figure
    • Open in new tab
    • Download powerpoint
    Fig. 4.

    Spp2 in the spliceosome and its conformational adaptability to different DEAH-box ATPase conformations. Using a combination of the ctPrp2-ctSpp2211–254 complex structure together with the cryo-EM and cross-linking data from Rauhut et al. (27), how Spp2 interacts with the spliceosome can be estimated. All spliceosomal factors are depicted as cartoon models, and cross-links of Spp2 are highlighted as pink spheres. The estimated path of Spp2 is displayed as a pink dashed line, and main contact sites are numbered starting from the most N-terminal cross-linked residue. (A) N-terminally from the G-patch, Spp2 cross-links with Brr2 and Rse1, as well as with Prp2. (B) The C-terminal end of the Spp2 G-patch cross-links with the OB-fold domain of Prp2 and parts of Bud13 and Pml1. Cross-linked regions of Bud13 and Pml1 are not part of the cryo-EM model and are symbolically depicted as dashed lines. C-terminally from the G-patch, Spp2 contacts another part of the RecA2 domain. (C) Overview of Spp2 cross-links numbered as in A and B. (D) Schematic representation of the catalytic states of Prp2 during one translocation cycle. The RecA2 domain is the most mobile domain during this process, and due to the versatile conformations of the conserved C-terminal stretch together with the flexible linker region, the Spp2 G-patch is able to adapt to the individual conformations of the RecA2 domain.

Data supplements

  • Supporting Information

    • Download Appendix (PDF)
PreviousNext
Back to top
Article Alerts
Email Article

Thank you for your interest in spreading the word on PNAS.

NOTE: We only request your email address so that the person you are recommending the page to knows that you wanted them to see it, and that it is not junk mail. We do not capture any email address.

Enter multiple addresses on separate lines or separate them with commas.
Structural analysis of the intrinsically disordered splicing factor Spp2 and its binding to the DEAH-box ATPase Prp2
(Your Name) has sent you a message from PNAS
(Your Name) thought you would like to see the PNAS web site.
Citation Tools
Structural analysis of the intrinsically disordered splicing factor Spp2 and its binding to the DEAH-box ATPase Prp2
Florian Hamann, Andreas Schmitt, Filippo Favretto, Romina Hofele, Piotr Neumann, ShengQi Xiang, Henning Urlaub, Markus Zweckstetter, Ralf Ficner
Proceedings of the National Academy of Sciences Feb 2020, 117 (6) 2948-2956; DOI: 10.1073/pnas.1907960117

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
Request Permissions
Share
Structural analysis of the intrinsically disordered splicing factor Spp2 and its binding to the DEAH-box ATPase Prp2
Florian Hamann, Andreas Schmitt, Filippo Favretto, Romina Hofele, Piotr Neumann, ShengQi Xiang, Henning Urlaub, Markus Zweckstetter, Ralf Ficner
Proceedings of the National Academy of Sciences Feb 2020, 117 (6) 2948-2956; DOI: 10.1073/pnas.1907960117
del.icio.us logo Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
  • Tweet Widget
  • Facebook Like
  • Mendeley logo Mendeley
Proceedings of the National Academy of Sciences: 117 (6)
Table of Contents

Submit

Sign up for Article Alerts

Article Classifications

  • Biological Sciences
  • Biophysics and Computational Biology

Jump to section

  • Article
    • Abstract
    • Results
    • Discussion
    • Materials and Methods
    • Acknowledgments
    • Footnotes
    • References
  • Figures & SI
  • Info & Metrics
  • PDF

You May Also be Interested in

QnAs with NAS member and bioengineer Sangeeta Bhatia. Image courtesy of Howard Hughes Medical Institute/Scott Eisen.
Featured QnAs
QnAs with NAS member and bioengineer Sangeeta Bhatia.
Image courtesy of Howard Hughes Medical Institute/Scott Eisen.
An ancient bead-making settlement on a Florida coastal island was crucial to pre-Columbian economies.
Bead-making complex off Florida coast
An ancient bead-making settlement on a Florida coastal island was crucial to pre-Columbian economies.
Image courtesy of Terry E. Barbour and Kenneth E. Sassaman.
Amber piece showing the tumbling flower beetle Angimordella burmitina.
Insect pollination of flowering plants
A beetle preserved in Burmese amber suggests early evidence of insect pollination of flowering plants.
Image courtesy of Bo Wang.
Numerous larval flying fish sampled in surface slicks off Hawaii Island were found to have ingested plastics.
Prey-size plastics in fish nurseries
A study explores the pervasiveness of plastics in fish nurseries and suggests plastic accumulation in larval fish nurseries may affect marine ecosystems.
Image courtesy of Jonathan L. Whitney.
Thus far, researchers have mostly just monitored the body’s microbiome. Now they’re starting to modify it to treat disease. Image credit: Science Source/Paul Gunning.
News Feature: Editing the microbiome
Thus far, researchers have mostly just monitored the body’s microbiome. Now they’re starting to modify it to treat disease.
Image credit: Science Source/Paul Gunning.

Similar Articles

Site Logo
Powered by HighWire
  • Submit Manuscript
  • Twitter
  • Facebook
  • RSS Feeds
  • Email Alerts

Articles

  • Current Issue
  • Latest Articles
  • Archive

PNAS Portals

  • Classics
  • Front Matter
  • Teaching Resources
  • Anthropology
  • Chemistry
  • Physics
  • Sustainability Science

Information

  • Authors
  • Editorial Board
  • Reviewers
  • Press
  • Site Map
  • PNAS Updates

Feedback    Privacy/Legal

Copyright © 2020 National Academy of Sciences. Online ISSN 1091-6490