1.25 Å resolution structure of an RNA 20-mer that binds to the TREX2 complex

Valkov, Eugene; Stewart, Murray

doi:10.1107/s2053230x1501643x

Cited by 4 publications

(5 citation statements)

References 20 publications

(20 reference statements)

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“…Thus, both predictions are within error of the measured value. The average ( n + 2)H8- n H2′/H3′ distance is 5.71 Å for A-form RNA double helixes in crystal structures. − , In MD simulations, both OL3 and ROC-RNA give an average distance of 3.26 Å for C2 extruded structures, providing an estimate of 39% (+54%/–25%) of C2 extruded in NMR.…”

Section: Resultsmentioning

confidence: 99%

“…They average 2.52 Å for r(CAAU), 2.68 Å for r(UCAAUC), 3.13 Å for d(CAAU), and 3.48 Å for d(UCAAUC). Equivalent distances for RNA and DNA double helixes are typically 2.4 Å − and 2.9 Å, respectively.…”

Section: Resultsmentioning

confidence: 99%

“…Because zero quantum coherence effects prohibited using H5–H6 distances for calculating, a H1′–H4′ distance of 3.20 ± 0.06 Å was used as the reference. That distance was measured from RNA/DNA crystal structures with less than 1.5 Å resolution that included hydrogen atoms − (Table S14).…”

Section: Methodsmentioning

confidence: 99%

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Nuclear Magnetic Resonance of Single-Stranded RNAs and DNAs of CAAU and UCAAUC as Benchmarks for Molecular Dynamics Simulations

Zhao

Kennedy

Berger

et al. 2020

J. Chem. Theory Comput.

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RNA and DNA are rapidly emerging as targets for therapeutics and as potential frameworks for nanotechnology. Accurate methods for predicting and designing structures and dynamics of nucleic acids would accelerate progress in these and other applications. Suitable approximations for modeling nucleic acids are being developed but require validation against disparate experimental observations. Here, nuclear magnetic resonance spectra for RNA and DNA single strands, CAAU and UCAAUC, are used as benchmarks to test molecular dynamics simulations with AMBER force fields OL3 and ROC-RNA for RNA and BSC1 for DNA. A detailed scheme for making comparisons is also presented. The results reflect recent progress in approximations and reveal remaining challenges.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

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Nuclear Magnetic Resonance of Single-Stranded RNAs and DNAs of CAAU and UCAAUC as Benchmarks for Molecular Dynamics Simulations

Zhao

Kennedy

Berger

et al. 2020

J. Chem. Theory Comput.

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“…The localization of TREX-2 to NPCs, which appears to be important for all of these functions, appears to derive primarily from the interaction of the CID domain (Sac3 residues 720–805, together with Cdc31 and two Sus1 chains) with Nup1, a component of the NPC nuclear basket ( 10 , 17 , 18 ), whereas the M- and N- regions appear to be important growth, mRNA export, localization of genes such as GAL 7-10-1 cluster and the integration of many of the nuclear steps in the gene expression pathway. Previous work has implicated positively charged residues in the Sac3 M-region with the interaction with both RNAs ( 16 , 38 ) and with the Mediator complex ( 15 ). In the latter case, it is unlikely that one of the Sac3 residues proposed as interacting with the Mediator complex, Arg256, is involved directly because it is inaccessible (Figure 3 and Supplementary Movies 2 and 3 ).…”

Section: Discussionmentioning

confidence: 99%

Structure of the Sac3 RNA-binding M-region in the Saccharomyces cerevisiae TREX-2 complex

Gordon

Aibara

Stewart

2017

Nucleic Acids Research

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Transcription-export complex 2 (TREX-2, or THSC) facilitates localization of actively transcribing genes such as GAL1 to the nuclear periphery, contributes to the generation of export-competent mRNPs and influences gene expression through interactions with Mediator. TREX-2 is based on a Sac3 scaffold to which Thp1, Sem1, Cdc31 and Sus1 bind and consists of three modules: the N-region (Sac3∼1-100), which binds mRNA export factor Mex67:Mtr2; the M-region, in which Thp1 and Sem1 bind to Sac3∼100-550; and the CID region in which Cdc31 and two Sus1 chains bind to Sac3∼720-805. Although the M-region of Sac3 was originally thought to encompass residues ∼250-550, we report here the 2.3Å resolution crystal structure of a complex containing Sac3 residues 60–550 that indicates that the TPR-like repeats of the M-region extend to residue 137 and that residues 90–125 form a novel loop that links Sac3 to Thp1. These new structural elements are important for growth and mRNA export in vivo. Although deleting Sac3 residues 1–90 produced a wild-type phenotype, deletion of the loop as well generated growth defects at 37°C, whereas the deletion of residues 1–250 impaired mRNA export and also generated longer lag times when glucose or raffinose was replaced by galactose as the carbon source.

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“…The TREX-2 complex is based on a Sac3 scaffold to which Thp1, Sem1, Cdc31, and two copies of Sus1 bind ( Fig. 1 A) and broadly speaking, the TREX-2 complex can be subdivided into three regions: the Sac3 N-terminus (Sac3 N ; residues 1–100), which harbors degenerate FG-like repeats similar to those seen in many nuclear pore proteins (FG nucleoporins) ( Fischer et al, 2002 ); the M-subcomplex, consisting of Sac3 residues ∼100–551 bound to Thp1 and Sem1, which forms a nucleic acid binding module as well as docking site for components of the Mediator complex ( Ellisdon et al, 2012 , Schneider et al, 2015 , Valkov and Stewart, 2015 ); and the CID-subcomplex, consisting of Sac3 residues ∼720–805 bound to Cdc31 and two Sus1 chains and which, in Saccharomyces cerevisiae , binds to the nuclear pore complex (NPC) to tether the complex close to the nuclear basket to facilitate localization of genes such as GAL1 ( Jani et al, 2014 , Jani et al, 2009 ).…”

Section: Introductionmentioning

confidence: 99%

The Sac3 TPR-like region in the Saccharomyces cerevisiae TREX-2 complex is more extensive but independent of the CID region

Aibara

Bai

Stewart

2016

Journal of Structural Biology

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Transcription-export complex 2 (TREX-2 complex) facilitates the localization of actively transcribing genes to the nuclear periphery and also functions to contribute to the generation of export-competent mRNPs through interactions with the general mRNA nuclear export factor Mex67:Mtr2. The TREX-2 complex is based on a Sac3 scaffold to which Thp1, Sem1, Cdc31, and Sus1 bind. TREX-2 can be subdivided into two modules: one, in which Thp1 and Sem1 bind to the Sac3M region (residues ∼100–551), and the other in which Cdc31 and two Sus1 chains bind to the Sac3CID region (residues ∼710–805). Complementary structural analyses using X-ray crystallography, electron microscopy, and small-angle X-ray scattering of the Saccharomyces cerevisiae TREX-2 complex, expressed using Baculovirus-infected Sf9 cells, have indicated that the TPR-like repeats of the Sac3M region extend considerably further towards the N-terminus than previously thought, and also indicate that this region and Sac3CID:Sus1:Cdc31 region of the S. cerevisiae complex are structurally independent. Although the density visible accounted for only ∼100 kDa, a 5.3 Å resolution cryo-EM reconstruction was obtained of the M-region of TREX-2 that showed an additional three putative α-helices extending towards the Sac3 N-terminus and these helices were also seen in a 4.9 Å resolution structure obtained by X-ray crystallography.Summary statementWe describe the expression, purification and structural characterization of the S. cerevisiae TREX-2 complex and demonstrate that the Sac3 TPR-like repeats are more extensive than previously thought and that the M- and CID-regions do not appear to have a defined spatial orientation.

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1.25 Å resolution structure of an RNA 20-mer that binds to the TREX2 complex

Cited by 4 publications

References 20 publications

Nuclear Magnetic Resonance of Single-Stranded RNAs and DNAs of CAAU and UCAAUC as Benchmarks for Molecular Dynamics Simulations

Nuclear Magnetic Resonance of Single-Stranded RNAs and DNAs of CAAU and UCAAUC as Benchmarks for Molecular Dynamics Simulations

Structure of the Sac3 RNA-binding M-region in the Saccharomyces cerevisiae TREX-2 complex

The Sac3 TPR-like region in the Saccharomyces cerevisiae TREX-2 complex is more extensive but independent of the CID region

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