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Structural Biology

  • Interconnections between m<sup>6</sup>A RNA modification, RNA structure, and protein–RNA complex assembly
    Open Access
    Interconnections between m6A RNA modification, RNA structure, and protein–RNA complex assembly

    Simone Höfler, Olivier Duss

    Simone Höfler ... Olivier Duss

    Published 7 November 2023

    This review summarizes current knowledge and future directions on the mechanisms that govern the interplay between m6A RNA modification, RNA folding, and protein–RNA interactions, focusing on the mechanisms and available quantitative information.

  • Structural insights into the complex of oncogenic KRas4B<sup>G12V</sup> and Rgl2, a RalA/B activator
    Open Access
    Structural insights into the complex of oncogenic KRas4BG12V and Rgl2, a RalA/B activator

    Mishal Tariq, Teppei Ikeya, Naoyuki Togashi, Louise Fairall, Shun Kamei, Sannojah Mayooramurugan, Lauren R Abbott, Anab Hasan, Carlos Bueno-Alejo, Sakura Sukegawa, Beatriz Romartinez-Alonso, Miguel Angel Muro Campillo, Andrew J Hudson, Yutaka Ito, John WR Schwabe, Cyril Dominguez, Kayoko Tanaka

    Mishal Tariq ... Kayoko Tanaka

    Published 13 October 2023

    The work reports the KRas4BG12V oncogenic mutation alters the binding kinetics with Rgl2, a RalA/B activator, and the V12 resides at the KRas4B(G12V)•Rgl2 complex interface in the crystal structure.

  • Structure shows that the BIR2 domain of E3 ligase XIAP binds across the RIPK2 kinase dimer interface
    Open Access
    Structure shows that the BIR2 domain of E3 ligase XIAP binds across the RIPK2 kinase dimer interface

    Mathilde Lethier, Karine Huard, Michael Hons, Adrien Favier, Bernhard Brutscher, Elisabetta Boeri Erba, Derek W Abbott, Stephen Cusack, Erika Pellegrini

    Mathilde Lethier ... Erika Pellegrini

    Published 6 September 2023

    The structure of RIPK2 kinase bound to the XIAP BIR2 domain reveals the essential role of the RIPK2 dimer in NOD2 signalling and explains the mechanism of anti-inflammatory drugs targeting this complex.

  • Catalytic mechanism of the zinc-dependent MutL endonuclease reaction
    Open Access
    Catalytic mechanism of the zinc-dependent MutL endonuclease reaction

    Kenji Fukui, Tatsuya Yamamoto, Takeshi Murakawa, Seiki Baba, Takashi Kumasaka, Takato Yano

    Kenji Fukui ... Takato Yano

    Published 24 July 2023

    The catalytic mechanism for the DNA cleavage activity of the mismatch repair system endonuclease MutL has been identified, which provides a clue as to how cadmium inhibits its activity.

  • A SAM-key domain required for enzymatic activity of the Fun30 nucleosome remodeler
    Open Access
    A SAM-key domain required for enzymatic activity of the Fun30 nucleosome remodeler

    Leonhard A Karl, Lorenzo Galanti, Susanne CS Bantele, Felix Metzner, Barbara Šafarić, Lional Rajappa, Benjamin Foster, Vanessa Borges Pires, Priyanka Bansal, Erika Chacin, Jerôme Basquin, Karl E Duderstadt, Christoph F Kurat, Till Bartke, Karl-Peter Hopfner, Boris Pfander

    Leonhard A Karl ... Boris Pfander

    Published 19 July 2023

    Biochemical data suggest that the SAM-key domain of the budding yeast remodeler Fun30 is required for its nucleosome remodeling activity by regulating the catalytic ATPase.

  • The C-terminal tail of CSNAP attenuates the CSN complex
    Open Access
    The C-terminal tail of CSNAP attenuates the CSN complex

    Maria G Füzesi-Levi, Gili Ben-Nissan, Dina Listov, Yael Fridmann Sirkis, Zvi Hayouka, Sarel Fleishman, Michal Sharon

    Maria G Füzesi-Levi ... Michal Sharon

    Published 17 July 2023

    The study demonstrates inhibition of the COP9 signalosome (CSN) complex by a peptide derived from CSNAP, the smallest CSN subunit. The peptide displaces the endogenous CSNAP subunit from the complex, leading to a CSNAP null phenotype that attenuates CSN activity.

  • Structural insights into CED-3 activation
    Open Access
    Structural insights into CED-3 activation

    Yini Li, Lu Tian, Ying Zhang, Yigong Shi

    Yini Li ... Yigong Shi

    Published 4 July 2023

    They report cryo-EM structures of CED-4 and three CED-4/CED-3 complexes with multiple oligomeric states. CARD–CARD interaction between CED-4 and CED-3 is essential for CED-3 activation and the newly reported dynamic organization of CED-4 regulates the onset of apoptosis.

  • Disulfide stabilization reveals conserved dynamic features between SARS-CoV-1 and SARS-CoV-2 spikes
    Open Access
    Disulfide stabilization reveals conserved dynamic features between SARS-CoV-1 and SARS-CoV-2 spikes

    Xixi Zhang, Zimu Li, Yanjun Zhang, Yutong Liu, Jingjing Wang, Banghui Liu, Qiuluan Chen, Qian Wang, Lutang Fu, Peiyi Wang, Xiaolin Zhong, Liang Jin, Qihong Yan, Ling Chen, Jun He, Jincun Zhao, Xiaoli Xiong

    Xixi Zhang ... Xiaoli Xiong

    Published 4 July 2023

    SARS-CoV-1 spike protein is stabilized with engineered disulfide bonds, and cryo-EM imaging of these stabilized S-trimers reveals rare spike conformations.

  • Distant sequence regions of JBP1 contribute to J-DNA binding
    Open Access
    Distant sequence regions of JBP1 contribute to J-DNA binding

    Ida de Vries, Danique Ammerlaan, Tatjana Heidebrecht, Patrick HN Celie, Daan P Geerke, Robbie P Joosten, Anastassis Perrakis

    Ida de Vries ... Anastassis Perrakis

    Published 16 June 2023

    Structural modeling and mutagenesis reveal that the N-terminus and DNA-binding domain of JBP1 recognize base-J, enabling replication of this epigenetic marker by JBP1’s thymidine hydroxylase domain.

  • Structural insights into ubiquitin chain cleavage by <em>Legionella</em> ovarian tumor deubiquitinases
    Open Access
    Structural insights into ubiquitin chain cleavage by Legionella ovarian tumor deubiquitinases

    Sangwoo Kang, Gyuhee Kim, Minhyeong Choi, Minwoo Jeong, Gerbrand J van der Heden van Noort, Soung-Hun Roh, Donghyuk Shin

    Sangwoo Kang ... Donghyuk Shin

    Published 26 April 2023

    Legionella possesses OTU deubiquitinases (Lot DUBs), which hinder the host ubiquitin system. We performed structural and biochemical analyses on the Lot DUBs and explained how Lot DUBs are different from other OTU-DUBs.

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