Crystal Structure of a Coiled-Coil Domain from Human ROCK I

Tu, Daqi; Li, Yiqun; Song, Hyun Kyu; Toms, A.V.; Gould, Christopher J.; Ficarro, Scott B.; Marto, Jarrod A.; Goode, Bruce L.; Eck, Michael J.

doi:10.1371/journal.pone.0018080

Cited by 34 publications

(35 citation statements)

References 49 publications

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“…1c) was generated as follows. The putative CC region of NDP52 was based on the structure of the ROCK-I CC region (PDB accession code: 3O0Z) 43 and the structurally uncharacterized SKICH and UBZ domains were shown as ovals. The monomeric forms of LC3C and GAL8 were drawn with the Atg8 structure (PDB accession code: 3RUI) 44 and this study (PDB accession code: 4HAN), respectively.…”

Section: Methodsmentioning

confidence: 99%

Structural basis for recognition of autophagic receptor NDP52 by the sugar receptor galectin-8

et al. 2013

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Infectious bacteria are cleared from mammalian cells by host autophagy in combination with other upstream cellular components, such as the autophagic receptor NDP52 and sugar receptor galectin-8. However, the detailed molecular basis of the interaction between these two receptors remains to be elucidated. Here, we report the biochemical characterization of both NDP52 and galectin-8 as well as the crystal structure of galectin-8 complexed with an NDP52 peptide. The unexpected observation of nicotinamide adenine dinucleotide located at the carbohydrate-binding site expands our knowledge of the sugar-binding specificity of galectin-8. The NDP52-galectin-8 complex structure explains the key determinants for recognition on both receptors and defines a special orientation of N-and C-terminal carbohydrate recognition domains of galectin-8. Dimeric NDP52 forms a ternary complex with two monomeric galectin-8 molecules as well as two LC3C molecules. These results lay the groundwork for understanding how host cells target bacterial pathogens for autophagy.

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Section: Methodsmentioning

confidence: 99%

Structural basis for recognition of autophagic receptor NDP52 by the sugar receptor galectin-8

et al. 2013

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“…Notable dimers include a tropomyocin fragment (PDB entry 2efr; S. Minakata, Y. Nitanai, K. Maeda, N. Oda, K. Wakabayashi & Y. Maeda, unpublished work) and the central domain of a Rho-associated kinase (PDB entry 3o0z; Tu et al, 2011). These proteins have R g > 65 Å , while other dimers with a similar number of residues have an R g of 18-30 Å (Fig.…”

Section: Highly Elongated Proteins Deviate From Power-law Behaviormentioning

confidence: 99%

Empirical power laws for the radii of gyration of protein oligomers

Tanner

2016

Acta Crystallogr D Struct Biol

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The radius of gyration is a fundamental structural parameter that is particularly useful for describing polymers. It has been known since Flory's seminal work in the mid-20th century that polymers show a power-law dependence, where the radius of gyration is proportional to the number of residues raised to a power. The power-law exponent has been measured experimentally for denatured proteins and derived empirically for folded monomeric proteins using crystal structures. Here, the biological assemblies in the Protein Data Bank are surveyed to derive the power-law parameters for protein oligomers having degrees of oligomerization of 2–6 and 8. The power-law exponents for oligomers span a narrow range of 0.38–0.41, which is close to the value of 0.40 obtained for monomers. This result shows that protein oligomers exhibit essentially the same power-law behavior as monomers. A simple power-law formula is provided for estimating the oligomeric state from an experimental measurement of the radius of gyration. Several proteins in the Protein Data Bank are found to deviate substantially from power-law behavior by having an atypically large radius of gyration. Some of the outliers have highly elongated structures, such as coiled coils. For coiled coils, the radius of gyration does not follow a power law and instead scales linearly with the number of residues in the oligomer. Other outliers are proteins whose oligomeric state or quaternary structure is incorrectly annotated in the Protein Data Bank. The power laws could be used to identify such errors and help prevent them in future depositions.

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“…All crystal forms showed strong off-origin peaks in self-Patterson maps with a distance of 5.15 Å from the origin (22,23). These peaks correspond to the length of one full turn of an ␣-helix and result from intrahelical vectors of long helices all oriented in the same direction (24) and are strongly suggestive of an inherent coiled-coil structure (25).…”

mentioning

confidence: 97%

Crystal Structure of the Nipah Virus Phosphoprotein Tetramerization Domain

Bruhn

Barnett

Bibby

et al. 2014

J Virol

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eThe Nipah virus phosphoprotein (P) is multimeric and tethers the viral polymerase to the nucleocapsid. We present the crystal structure of the multimerization domain of Nipah virus P: a long, parallel, tetrameric, coiled coil with a small, ␣-helical cap structure. Across the paramyxoviruses, these domains share little sequence identity yet are similar in length and structural organization, suggesting a common requirement for scaffolding or spatial organization of the functions of P in the virus life cycle.

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Crystal Structure of a Coiled-Coil Domain from Human ROCK I

Cited by 34 publications

References 49 publications

Structural basis for recognition of autophagic receptor NDP52 by the sugar receptor galectin-8

Structural basis for recognition of autophagic receptor NDP52 by the sugar receptor galectin-8

Empirical power laws for the radii of gyration of protein oligomers

Crystal Structure of the Nipah Virus Phosphoprotein Tetramerization Domain

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