Crystal structure of nucleotide-free dynamin

Faelber, Katja; Posor, York; Gao, Song; Held, Martin; Roske, Yvette; Schulze, Dennis; Haucke, Volker; Noé, Frank; Daumke, Oliver

doi:10.1038/nature10369

Cited by 277 publications

(457 citation statements)

References 55 publications

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“…The PH domains of the outer molecules bind to a conserved surface of the stalk (Fig. 3a, b), to a similar site as in dimeric dynamin 1 2 (Extended Data Fig. 4b).…”

mentioning

confidence: 92%

“…3b), but not at the outer, non-assembled sides of the tetramer. Previous studies have shown that mutation of R399 in loop L2 S completely destroys higher-order assembly and dynamin function 2,3,11 . In our structure, R399 of an outer molecule forms salt bridges to E410 in α2 S and to E345 in L1N S in the outer and inner molecules of the opposite dimer, respectively.…”

mentioning

confidence: 96%

“…1, Extended Data Table 1). Indeed, the asymmetric unit of the crystal lattice contained a dynamin tetramer that did not form the filamentous superstructures seen for dynamin 1 2,3 .…”

mentioning

confidence: 99%

“…oligomerizing mutants led to crystal structures of dynamin 1 2,3 . However, the postulated higher-order assembly interface was not resolved in these structures leaving the oligomerization mechanism unaddressed.…”

mentioning

confidence: 99%

“…Each of the dimers assembles via the previously described interface 2 2,3,[12][13][14] (Fig. 1, Extended Data Fig.…”

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confidence: 99%

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Crystal structure of the dynamin tetramer

Reubold

Faelber

Plattner

et al. 2015

Nature

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The mechano-chemical protein dynamin is the prototype of the dynamin superfamily of large GTPases, which shape and remodel membranes in diverse cellular processes 1 .Dynamin forms predominantly tetramers in the cytosol, which oligomerize at the neck of clathrin-coated vesicles to mediate constriction and subsequent scission of the membrane 1 . Previous studies have described the architecture of dynamin dimers 2,3 , but the molecular determinants for dynamin assembly and its regulation have remained unclear. Here, we present the crystal structure of the nucleotide-free dynamin tetramer.Combining structural data with mutational studies, oligomerization measurements and molecular dynamics simulations, we suggest a mechanism of how oligomerization of dynamin is linked to the release of intramolecular auto-inhibitory interactions. We elucidate how mutations that interfere with tetramer formation and auto-inhibition can lead to the congenital diseases Charcot-Marie-Tooth neuropathy (CMT) 4 and centronuclear myopathy (CNM) 5 , respectively. Strikingly, the bent shape of the tetramer explains how dynamin assembles into a right-handed helical oligomer of defined diameter, which has direct implications for its function in membrane constriction.The three highly conserved vertebrate isoforms of dynamin contain five distinct domains (Extended Data Fig. 1a): an N-terminal GTPase (G) domain mediating nucleotide binding and hydrolysis, a bundle signaling element (BSE), a stalk, a pleckstrin homology (PH) domain involved in lipid binding, and a proline rich domain (PRD) mediating interaction with BAR-and SH3-domain containing scaffolding proteins 6 . To exert its function in clathrinmediated endocytosis (CME), dynamin assembles via the stalks into a helical array surrounding the necks of invaginating clathrin-coated pits (CCP) 7,8 . Dimerization of GTPbound G domains from neighboring helical rungs induces GTP hydrolysis 9 . The ensuing conformational changes are thought to be transmitted from the G domain via the BSE to the stalk resulting in a sliding motion of adjacent helix rungs, concomitant helix constriction 10 , and eventually membrane scission. The inherent tendency to form large assemblies at high protein concentrations has hampered crystallization of dynamin in the past. The use of non-3 oligomerizing mutants led to crystal structures of dynamin 1 2,3 . However, the postulated higher-order assembly interface was not resolved in these structures leaving the oligomerization mechanism unaddressed.We reasoned that an alternative assembly-affecting mutation, such as K361S in dynamin 3 11 , may disturb the oligomerization interface to a lesser extent than the previously used mutants. We obtained crystals of nucleotide-free dynamin 3-K361S lacking the PRD (dynamin 3(∆PRD)-K361S) that diffracted to 3.7 Å (Methods, Extended Data Fig. 1, Extended Data Table 1). Indeed, the asymmetric unit of the crystal lattice contained a dynamin tetramer that did not form the filamentous superstructures seen for dynamin 1 2,3 .The dynamin tetr...

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“…The PH domains of the outer molecules bind to a conserved surface of the stalk (Fig. 3a, b), to a similar site as in dimeric dynamin 1 2 (Extended Data Fig. 4b).…”

mentioning

confidence: 92%

mentioning

confidence: 96%

“…1, Extended Data Table 1). Indeed, the asymmetric unit of the crystal lattice contained a dynamin tetramer that did not form the filamentous superstructures seen for dynamin 1 2,3 .…”

mentioning

confidence: 99%

mentioning

confidence: 99%

“…Each of the dimers assembles via the previously described interface 2 2,3,[12][13][14] (Fig. 1, Extended Data Fig.…”

mentioning

confidence: 99%

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Crystal structure of the dynamin tetramer

Reubold

Faelber

Plattner

et al. 2015

Nature

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121

160

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Molecular mechanisms of force production in clathrin‐mediated endocytosis

et al. 2018

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During clathrin-mediated endocytosis (CME), a flat patch of membrane is invaginated and pinched off to release a vesicle into the cytoplasm. In yeast CME, over 60 proteins—including a dynamic actin meshwork—self-assemble to deform the plasma membrane. Several models have been proposed for how actin and other molecules produce the forces necessary to overcome the mechanical barriers of membrane tension and turgor pressure, but the precise mechanisms and a full picture of their interplay are still not clear. In this review, we discuss the evidence for these force production models from a quantitative perspective and propose future directions for experimental and theoretical work that could clarify their various contributions.

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Autism and mild epilepsy associated with a de novo missense pathogenic variant in the GTPase effector domain of DNM1

Mei

Parrini

Bianchini

et al. 2023

American J of Med Genetics Pt C

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Dynamin 1 is a GTPase protein involved in synaptic vesicle fission, which facilitates the exocytosis of neurotransmitters necessary for normal signaling. Pathogenic variants in the DNM1 gene are associated with intractable epilepsy, often manifested as infantile spasms at onset, developmental delay, and a movement disorder, and are located in the GTPase and middle domains of the protein. We describe a 36‐year‐old man with autism and moderate intellectual disability who experienced only a few generalized seizures between the age 16 and 30 years. Using a whole sequencing approach, we identified the c.1994T>C p.(Leu665Pro) de novo novel missense pathogenic variant in the GTPase effector domain (GED) of the DNM1 protein. Structural analyses suggest that this substitution impairs both the stalk formation and its interactions, known to be important for the dynamin‐1 physiological cellular function. Our data expand the spectrum of phenotypes associated with pathogenic variants in the DNM1 gene, linking a variant in the GED domain with autism and onset in the adolescence of mild epilepsy, a phenotypic presentation remarkably different from the early infantile epileptic encephalopathy associated with pathogenic variants in the GTPase or middle domains.

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Crystal structure of nucleotide-free dynamin

Cited by 277 publications

References 55 publications

Crystal structure of the dynamin tetramer

Crystal structure of the dynamin tetramer

Molecular mechanisms of force production in clathrin‐mediated endocytosis

Autism and mild epilepsy associated with a de novo missense pathogenic variant in the GTPase effector domain of DNM1

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