High-resolution crystal structures of the solubilized domain of porcine cytochrome<i>b</i><sub>5</sub>

Hirano, Yu; Kimura, Shigenobu; Tamada, Taro

doi:10.1107/s1399004715009438

Cited by 4 publications

(3 citation statements)

References 39 publications

(41 reference statements)

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“…However, the NADPH binding site of RSP5 is absent and filled by two loops (residues 393-414 and 468-484 of RSP5). e , The N-terminal domain of FAP198 closely resembles heme-binding cytochrome b5 (PDB 3X34) 77 . However, no heme is observed bound to FAP198, and the putative heme-binding site is occluded by a loop of FAP198 (residues 89-95).…”

Section: Extended Datamentioning

confidence: 99%

Structures of radial spokes and associated complexes important for ciliary motility

Gui

Sze-Tu

et al. 2020

Nat Struct Mol Biol

104

122

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In motile cilia, a mechanoregulatory network is responsible for converting the action of thousands of dynein motors bound to doublet microtubules into a single propulsive waveform. Here, we use two complementary cryo-EM strategies to determine structures of the major mechanoregulators that bind ciliary doublet microtubules in Chlamydomonas reinhardtii . We determine structures of isolated radial spoke RS1, and the microtubule-bound RS1, RS2, and the nexin-dynein regulatory complex. From these structures, we identify and build atomic models for 30 proteins including 23 radial-spoke subunits. We reveal how mechanoregulatory complexes dock to doublet microtubules with regular 96-nm periodicity and communicate with one another. Additionally, we observe a direct and dynamically coupled association between RS2 and the dynein motor IDA c , providing a molecular basis for the control of motor activity by mechanical signals. These structures advance our understanding of the role of mechanoregulation in defining the ciliary waveform.

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Section: Extended Datamentioning

confidence: 99%

Structures of radial spokes and associated complexes important for ciliary motility

Gui

Sze-Tu

et al. 2020

Nat Struct Mol Biol

104

122

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“…Unfortunately, the information in the PDB does not provide a consistent overview of the application and outcomes of the aforementioned experimental procedures, which is an obstacle from a data-mining perspective. Even when the same publication reports structures in different oxidation states (Hirano et al, 2015), the same residue identifier (HEM) has been used for oxidized and reduced b-type heme cofactors. Indeed, the PDB does not provide distinct residue identifiers for b-type or c-type (HEC) heme containing either iron(II) or iron(III).…”

Section: Discussionmentioning

confidence: 99%

A database overview of metal-coordination distances in metalloproteins

Bazayeva,

Andreini,

Rosato

2024

Acta Crystallogr D Struct Biol

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Metalloproteins are ubiquitous in all living organisms and take part in a very wide range of biological processes. For this reason, their experimental characterization is crucial to obtain improved knowledge of their structure and biological functions. The three-dimensional structure represents highly relevant information since it provides insight into the interaction between the metal ion(s) and the protein fold. Such interactions determine the chemical reactivity of the bound metal. The available PDB structures can contain errors due to experimental factors such as poor resolution and radiation damage. A lack of use of distance restraints during the refinement and validation process also impacts the structure quality. Here, the aim was to obtain a thorough overview of the distribution of the distances between metal ions and their donor atoms through the statistical analysis of a data set based on more than 115 000 metal-binding sites in proteins. This analysis not only produced reference data that can be used by experimentalists to support the structure-determination process, for example as refinement restraints, but also resulted in an improved insight into how protein coordination occurs for different metals and the nature of their binding interactions. In particular, the features of carboxylate coordination were inspected, which is the only type of interaction that is commonly present for nearly all metals.

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“…• 3X2L (Nakamura et al, 2015) • 3X32 (Hirano et al, 2015) • 4TKJ (Matsuoka et al, 2015) • 3X0J (Furuike et al, 2016) • 5WQR (Ohno et al, 2017) • 6EQE (Austin et al, 2018) • 6ETK (Vergara et al, 2018) • 6FJN (Baker et al, 2019) • 6JGJ (Takaba et al, 2019) • 6RYG (Paterson et al, 2019) • 6IIP (Tian et al, 2019) • 6Q01 (Schellenberg et al, 2020) • 6XVM (Plaza-Garrido et al, 2020) • 6Y5S (Wu et al, 2020) • 6YP6 (Franke et al, 2020) • 7A5M (Barone et al, 2020) • 7K4T (Otten et al, 2020) • 6YK4 (Frydenvang et al, 2020) • 6SAY (Glöckner et al, 2020)…”

Section: A Geometric Algebramentioning

confidence: 99%

Geometric Algebra Attention Networks for Small Point Clouds

Spellings¹

2021

Preprint

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Much of the success of deep learning is drawn from building architectures that properly respect underlying symmetry and structure in the data on which they operate-a set of considerations that have been united under the banner of geometric deep learning. Often problems in the physical sciences deal with relatively small sets of points in two-or three-dimensional space wherein translation, rotation, and permutation equivariance are important or even vital for models to be useful in practice. In this work, we present rotation-and permutation-equivariant architectures for deep learning on these small point clouds, composed of a set of products of terms from the geometric algebra and reductions over those products using an attention mechanism. The geometric algebra provides valuable mathematical structure by which to combine vector, scalar, and other types of geometric inputs in a systematic way to account for rotation invariance or covariance, while attention yields a powerful way to impose permutation equivariance. We demonstrate the usefulness of these architectures by training models to solve sample problems relevant to physics, chemistry, and biology.

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High-resolution crystal structures of the solubilized domain of porcine cytochromeb₅

Cited by 4 publications

References 39 publications

Structures of radial spokes and associated complexes important for ciliary motility

Structures of radial spokes and associated complexes important for ciliary motility

A database overview of metal-coordination distances in metalloproteins

Geometric Algebra Attention Networks for Small Point Clouds

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High-resolution crystal structures of the solubilized domain of porcine cytochromeb5

Cited by 4 publications

References 39 publications

Structures of radial spokes and associated complexes important for ciliary motility

Structures of radial spokes and associated complexes important for ciliary motility

A database overview of metal-coordination distances in metalloproteins

Geometric Algebra Attention Networks for Small Point Clouds

Contact Info

Product

Resources

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High-resolution crystal structures of the solubilized domain of porcine cytochromeb₅