Structure of human translin at 2.2 Å resolution

Sugiura, Ikuko; Sasaki, Chizuko; Hasegawa, Tsukasa; Kohno, Toshiyuki; Sugio, Shigetoshi; Moriyama, Hideaki; Kasai, Masataka; Matsuzaki, Takao

doi:10.1107/s0907444904002549

Cited by 32 publications

(59 citation statements)

References 15 publications

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“…2a, open interface). Whereas three of the interfaces between dimeric units (A/B, A/D, and B/C) were preserved in a closed conformation similar to that seen in the previously reported, closed-barrel structure of human translin 1J1J [23] (RMSD of~0.5 Å, buried area of~720 Å 2 , and interactions at the interface of~80), the fourth interface (C/D) is dramatically different and widely open (~100 Å 2 buried area and~7 interactions) providing a large entryway into the interior cavity of the barrel (Fig. 2a and d).…”

supporting

confidence: 59%

“…Translin barrel structures comprise a large inner cavity that can encapsulate single-stranded oligonucleotides of 11-30 bases in length [22,23]. In the closed-barrel form, the oligonucleotide binding surfaces map to this inner cavity and appear inaccessibly caged [26,27].…”

mentioning

confidence: 99%

“…Translin binds 5′-and 3′-ends with almost identical affinities [8], suggesting no polarity in binding. TRAX, which forms similar seven-α-helical bundles, assembles with translin into hetero-octameric complexes with almost identical structures that can also bind nucleic acids [11,[17][18][19][22][23][24][25].…”

mentioning

confidence: 99%

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A Novel Open-Barrel Structure of Octameric Translin Reveals a Potential RNA Entryway

Eliahoo

Marx

Manor

et al. 2015

Journal of Molecular Biology

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supporting

confidence: 59%

mentioning

confidence: 99%

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A Novel Open-Barrel Structure of Octameric Translin Reveals a Potential RNA Entryway

Eliahoo

Marx

Manor

et al. 2015

Journal of Molecular Biology

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“…The 1J1J structure of human translin was downloaded from the PDB repository (29). A single monomer was analyzed with the GRID program, using eight different probes (DRY, C3, OH, O, N, N:, N2, NH).…”

Section: Immunoprecipitation and Rt-pcrmentioning

confidence: 99%

Dendritic trafficking of BDNF mRNA is mediated by translin and blocked by the G196A (Val66Met) mutation

Chiaruttini

Vicario

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

203

229

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Alternatively spliced brain-derived neurotrophic factor (BDNF) transcripts are targeted to distinct cellular compartments in neurons but the mechanisms underlying this sorting are unknown. Although only some BDNF isoforms are targeted to dendrites, we have found that the coding region common to all BDNF transcripts contains a constitutively active dendritic targeting signal and that this signal is suppressed in transcripts containing exons 1 or 4, which are restricted to the cell soma and proximal dendrites. This dendritic targeting signal is mediated by translin, an RNA-binding protein implicated in RNA trafficking, and is disrupted by the G196A mutation associated with memory deficits and psychiatric disorders. Molecular modeling and mutational studies indicate that the G196A mutation blocks dendritic targeting of BDNF mRNA by disrupting its interaction with translin. These findings implicate abnormal dendritic trafficking of BDNF mRNA in the pathophysiology of neuropsychiatric disorders linked to the G196A mutation.neuropsychiatric disorders ͉ neurotrophins S everal lines of evidence indicate that targeting of BDNF mRNA to dendrites plays a key role in mediating synaptic plasticity (1-4). However, the molecular mechanisms regulating this process and the differential subcellular localization of alternatively spliced BDNF transcripts, remain to be clarified.Multiple BDNF transcripts are generated by alternative splicing of one 5Ј exon with a shared 3Ј exon containing the entire BDNF coding region and either a short or long 3Ј UTR sequence (5, 6). In recent studies, we have demonstrated that BDNF transcripts differ in their subcellular localization (7). Exon 1 and 4 transcripts are localized in the cell soma, while exon 2 and 6 transcripts show a somato-dendritic localization. Thus, splice variants appear to encode spatial localization signals used to preferentially regulate BDNF expression in different subcellular domains (2, 3). A recent study has suggested that the long 3Ј UTR contains signals necessary for dendritic targeting of BDNF transcripts (4). However, it is unlikely that this mechanism can fully account for the differential dendritic targeting displayed by BDNF transcripts because more than one-third of exon 4 transcripts, which are retained in the soma, contain the long 3Ј UTR. Conversely, more than one-half of exon 6 transcripts, an isoform that displays targeting to dendrites, contain the short 3Ј UTR. To help define the mechanisms underlying differential localization of BDNF transcripts, we have tested the hypothesis that additional signals might be encoded by other BDNF mRNA regions.

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“…(d) Ala82, chain A, PDB entry 1v6i (Kundhavai Natchiar et al, 2004), 2.15 Å resolution. (e) Pro55, chain B, PDB entry 1j1j (Sugiura et al, 2004), 2.2 Å resolution. The PDB_REDO program pepflip (Joosten et al, 2011) performs tt+ peptide-plane flips, which are a combination of both a C O flip and an N-H flip.…”

Section: Introductionmentioning

confidence: 99%

Detection oftrans–cisflips and peptide-plane flips in protein structures

Touw

Joosten

Vriend

2015

Acta Crystallogr D Biol Crystallogr

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A coordinate-based method is presented to detect peptide bonds that need correction either by a peptide-plane flip or by a trans-cis inversion of the peptide bond. When applied to the whole Protein Data Bank, the method predicts 4617 trans-cis flips and many thousands of hitherto unknown peptide-plane flips. A few examples are highlighted for which a correction of the peptide-plane geometry leads to a correction of the understanding of the structure-function relation. All data, including 1088 manually validated cases, are freely available and the method is available from a web server, a web-service interface and through WHAT_CHECK.

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Structure of human translin at 2.2 Å resolution

Cited by 32 publications

References 15 publications

A Novel Open-Barrel Structure of Octameric Translin Reveals a Potential RNA Entryway

A Novel Open-Barrel Structure of Octameric Translin Reveals a Potential RNA Entryway

Dendritic trafficking of BDNF mRNA is mediated by translin and blocked by the G196A (Val66Met) mutation

Detection oftrans–cisflips and peptide-plane flips in protein structures

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