Crystal Structures of Tropomyosin: Flexible Coiled-Coil

AbstractAlthough the Ub-binding domain in ABIN proteins and NEMO (UBAN) is highly conserved, UBAN-containing proteins exhibit different Ub-binding properties, resulting in their diverse biological roles. Post-translational modifications further control UBAN domain specificity for poly-Ub chains. However, precisely, how the UBAN domain structurally confers such functional diversity remains poorly understood. Here we report crystal structures of ABIN-1 alone and in complex with one or two M1-linked di-Ub chains. ABIN-1 UBAN forms a homo-dimer that provides two symmetrical Ub-binding sites on either side of the coiled-coil structure. Moreover, crystal structures of ABIN1 UBAN in complex with di-Ub chains reveal a concentration-dependency of UBAN/di-Ub binding stoichiometry. Analysis of UBAN/M1-linked di-Ub binding characteristics indicates that phosphorylated S473 in OPTN and its corresponding phospho-mimetic residue in ABIN-1 (E484) are essential for high affinity interactions with M1-linked Ub chains. Also, a phospho-mimetic mutation of A303 in NEMO, corresponding to S473 of OPTN, increases binding affinity for M1-linked Ub chains. These findings are in line with the diverse physiological roles of UBAN domains, as phosphorylation of OPTN UBAN is required to enhance its binding to Ub during mitophagy.

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Molecular architecture of a dynamin adaptor: implications for assembly of mitochondrial fission complexes

The Journal of Cell Biology ◽

10.1083/jcb.201005046 ◽

2010 ◽

Vol 191 (6) ◽

pp. 1127-1139 ◽

Cited By ~ 33

Author(s):

Sajjan Koirala ◽

Huyen T. Bui ◽

Heidi L. Schubert ◽

Debra M. Eckert ◽

Christopher P. Hill ◽

...

Keyword(s):

Membrane Protein ◽

Crystal Structures ◽

Binding Sites ◽

Mitochondrial Fission ◽

Coiled Coil ◽

Adaptor Proteins ◽

Molecular Architecture ◽

Cellular Membranes ◽

Membrane Scission ◽

Antiparallel Coiled Coil

Recruitment and assembly of some dynamin-related guanosine triphosphatases depends on adaptor proteins restricted to distinct cellular membranes. The yeast Mdv1 adaptor localizes to mitochondria by binding to the membrane protein Fis1. Subsequent Mdv1 binding to the mitochondrial dynamin Dnm1 stimulates Dnm1 assembly into spirals, which encircle and divide the mitochondrial compartment. In this study, we report that dimeric Mdv1 is joined at its center by a 92-Å antiparallel coiled coil (CC). Modeling of the Fis1–Mdv1 complex using available crystal structures suggests that the Mdv1 CC lies parallel to the bilayer with N termini at opposite ends bound to Fis1 and C-terminal β-propeller domains (Dnm1-binding sites) extending into the cytoplasm. A CC length of appropriate length and sequence is necessary for optimal Mdv1 interaction with Fis1 and Dnm1 and is important for proper Dnm1 assembly before membrane scission. Our results provide a framework for understanding how adaptors act as scaffolds to orient and stabilize the assembly of dynamins on membranes.

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Crystal Structure of the Marburg Virus VP35 Oligomerization Domain

Journal of Virology ◽

10.1128/jvi.01085-16 ◽

2016 ◽

Vol 91 (2) ◽

Cited By ~ 22

Author(s):

Jessica F. Bruhn ◽

Robert N. Kirchdoerfer ◽

Sarah M. Urata ◽

Sheng Li ◽

Ian J. Tickle ◽

...

Keyword(s):

Crystal Structures ◽

Immune Evasion ◽

Ebola Virus ◽

Severe Disease ◽

Coiled Coil ◽

Marburg Virus ◽

Oligomeric State ◽

Homologous Proteins ◽

Content Type ◽

Oligomerization Domain

ABSTRACT Marburg virus (MARV) is a highly pathogenic filovirus that is classified in a genus distinct from that of Ebola virus (EBOV) (genera Marburgvirus and Ebolavirus, respectively). Both viruses produce a multifunctional protein termed VP35, which acts as a polymerase cofactor, a viral protein chaperone, and an antagonist of the innate immune response. VP35 contains a central oligomerization domain with a predicted coiled-coil motif. This domain has been shown to be essential for RNA polymerase function. Here we present crystal structures of the MARV VP35 oligomerization domain. These structures and accompanying biophysical characterization suggest that MARV VP35 is a trimer. In contrast, EBOV VP35 is likely a tetramer in solution. Differences in the oligomeric state of this protein may explain mechanistic differences in replication and immune evasion observed for MARV and EBOV. IMPORTANCE Marburg virus can cause severe disease, with up to 90% human lethality. Its genome is concise, only producing seven proteins. One of the proteins, VP35, is essential for replication of the viral genome and for evasion of host immune responses. VP35 oligomerizes (self-assembles) in order to function, yet the structure by which it assembles has not been visualized. Here we present two crystal structures of this oligomerization domain. In both structures, three copies of VP35 twist about each other to form a coiled coil. This trimeric assembly is in contrast to tetrameric predictions for VP35 of Ebola virus and to known structures of homologous proteins in the measles, mumps, and Nipah viruses. Distinct oligomeric states of the Marburg and Ebola virus VP35 proteins may explain differences between them in polymerase function and immune evasion. These findings may provide a more accurate understanding of the mechanisms governing VP35's functions and inform the design of therapeutics.

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Complexes of Fabs with a mimetic of the HIV-1 gp41 trimeric coiled-coil.

Acta Crystallographica Section A Foundations and Advances ◽

10.1107/s2053273314081911 ◽

2014 ◽

Vol 70 (a1) ◽

pp. C1809-C1809

Author(s):

Mi Li ◽

Elena Gustchina ◽

Alla Gustchina ◽

Marius Clore ◽

Alexander Wlodawer

Keyword(s):

Crystal Structures ◽

Neutralizing Antibodies ◽

Body Movement ◽

Coiled Coil ◽

Structural Data ◽

Biological Properties ◽

Heptad Repeat ◽

X Ray Crystallography ◽

Subtype B ◽

Hiv 1

A series of mini-antibodies (monovalent and bivalent Fabs) targeting the conserved internal trimeric coiled-coil of the N-heptad repeat (N-HR) of HIV-1 gp41 has been previously constructed and reported. Crystal structures of two closely related monovalent Fabs, one (Fab 8066) broadly neutralizing across a wide panel of HIV-1 subtype B and C viruses, and the other (Fab 8062) non-neutralizing, representing the extremes of this series, were previously solved as complexes with 5-Helix, a gp41 pre-hairpin intermediate mimetic. Binding of these Fabs to covalently stabilized chimeric trimers of N-peptides of HIV-1 gp41 (named (CCIZN36)3 or 3-H) has now been investigated using X-ray crystallography, cryo-electron microscopy, and a variety of biophysical methods. Crystal structures of the complexes between 3-H and Fab 8066 and Fab 8062 were determined at 2.8 and 3.0 Å resolution, respectively. Although the structures of the complexes with the neutralizing Fab 8066 and its non-neutralizing counterpart Fab 8062 were generally similar, small differences between them could be correlated with the biological properties of these antibodies. The conformations of the corresponding CDRs of each antibody in the complexes with 3-H and 5-Helix are very similar. The adaptation to a different target upon complex formation is predominantly achieved by changes in the structure of the trimer of N-HR helices, as well as by adjustment of the orientation of the Fab molecule relative to the N-HR in the complex, via rigid-body movement. The structural data presented here indicate that binding of three Fabs 8062 with high affinity requires more significant changes in the structure of the N-HR trimer compared to binding of Fab 8066. A comparative analysis of the structures of Fabs complexed to different gp41 intermediate mimetics allows further evaluation of biological relevance for generation of neutralizing antibodies, as well as provides novel structural insights into immunogen design.

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A complete compendium of crystal structures for the human SEPT3 subgroup reveals functional plasticity at a specific septin interface

IUCrJ ◽

10.1107/s2052252520002973 ◽

2020 ◽

Vol 7 (3) ◽

pp. 462-479 ◽

Cited By ~ 6

Author(s):

Danielle Karoline Silva do Vale Castro ◽

Sabrina Matos de Oliveira da Silva ◽

Humberto D'Muniz Pereira ◽

Joci Neuby Alves Macedo ◽

Diego Antonio Leonardo ◽

...

Keyword(s):

Crystal Structures ◽

Coiled Coil ◽

Amino Acid Residues ◽

Binding Domains ◽

Cellular Events ◽

Gtp Binding ◽

Wide Range ◽

Specific Subgroup ◽

Order Complexes ◽

Polybasic Region

Human septins 3, 9 and 12 are the only members of a specific subgroup of septins that display several unusual features, including the absence of a C-terminal coiled coil. This particular subgroup (the SEPT3 septins) are present in rod-like octameric protofilaments but are lacking in similar hexameric assemblies, which only contain representatives of the three remaining subgroups. Both hexamers and octamers can self-assemble into mixed filaments by end-to-end association, implying that the SEPT3 septins may facilitate polymerization but not necessarily function. These filaments frequently associate into higher order complexes which associate with biological membranes, triggering a wide range of cellular events. In the present work, a complete compendium of crystal structures for the GTP-binding domains of all of the SEPT3 subgroup members when bound to either GDP or to a GTP analogue is provided. The structures reveal a unique degree of plasticity at one of the filamentous interfaces (dubbed NC). Specifically, structures of the GDP and GTPγS complexes of SEPT9 reveal a squeezing mechanism at the NC interface which would expel a polybasic region from its binding site and render it free to interact with negatively charged membranes. On the other hand, a polyacidic region associated with helix α5′, the orientation of which is particular to this subgroup, provides a safe haven for the polybasic region when retracted within the interface. Together, these results suggest a mechanism which couples GTP binding and hydrolysis to membrane association and implies a unique role for the SEPT3 subgroup in this process. These observations can be accounted for by constellations of specific amino-acid residues that are found only in this subgroup and by the absence of the C-terminal coiled coil. Such conclusions can only be reached owing to the completeness of the structural studies presented here.

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Routine phasing of coiled-coil protein crystal structures withAMPLE

IUCrJ ◽

10.1107/s2052252515002080 ◽

2015 ◽

Vol 2 (2) ◽

pp. 198-206 ◽

Cited By ~ 16

Author(s):

Jens M. H. Thomas ◽

Ronan M. Keegan ◽

Jaclyn Bibby ◽

Martyn D. Winn ◽

Olga Mayans ◽

...

Keyword(s):

Ab Initio ◽

Crystal Structures ◽

Coiled Coil ◽

Protein Crystal ◽

Molecular Replacement ◽

Search Models ◽

Homologous Protein ◽

Coil Structure ◽

Convenient Route ◽

Chain Lengths

Coiled-coil protein folds are among the most abundant in nature. These folds consist of long wound α-helices and are architecturally simple, but paradoxically their crystallographic structures are notoriously difficult to solve with molecular-replacement techniques. The programAMPLEcan solve crystal structures by molecular replacement usingab initiosearch models in the absence of an existent homologous protein structure.AMPLEhas been benchmarked on a large and diverse test set of coiled-coil crystal structures and has been found to solve 80% of all cases. Successes included structures with chain lengths of up to 253 residues and resolutions down to 2.9 Å, considerably extending the limits on size and resolution that are typically tractable byab initiomethodologies. The structures of two macromolecular complexes, one including DNA, were also successfully solved using their coiled-coil components. It is demonstrated that both theab initiomodelling and the use of ensemble search models contribute to the success ofAMPLEby comparison with phasing attempts using single structures or ideal polyalanine helices. These successes suggest that molecular replacement withAMPLEshould be the method of choice for the crystallographic elucidation of a coiled-coil structure. Furthermore,AMPLEmay be able to exploit the presence of a coiled coil in a complex to provide a convenient route for phasing.

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Coiled coils 9-to-5: Rational de novo design of α-helical barrels with tunable oligomeric states

10.1101/2021.01.20.427391 ◽

2021 ◽

Author(s):

William M. Dawson ◽

Freddie J.O. Martin ◽

Guto G. Rhys ◽

Kathryn L. Shelley ◽

R. Leo Brady ◽

...

Keyword(s):

Crystal Structures ◽

Rational Design ◽

De Novo ◽

Coiled Coil ◽

De Novo Design ◽

Coiled Coils ◽

Alternative States ◽

X Ray ◽

Amphipathic Helices ◽

Made In

ABSTRACTThe rational design of linear peptides that assemble controllably and predictably in water is challenging. Sequences must encode unique target structures and avoid alternative states. However, the stabilizing and discriminating non-covalent forces available are weak in water. Nonetheless, for α-helical coiled-coil assemblies considerable progress has been made in rational de novo design. In these, sequence repeats of nominally hydrophobic (h) and polar (p) residues, hpphppp, direct the assembly of amphipathic helices into dimeric to tetrameric bundles. Expanding this pattern to hpphhph can produce larger α-helical barrels. Here, we show that pentamers to nonamers are achieved simply by varying the residue at one of these h sites. In L/I-K-E-I-A-x-Z repeats, decreasing the size of Z from threonine to serine to alanine to glycine gives progressively larger oligomers. X-ray crystal structures of the resulting α-helical barrels rationalize this: side chains at Z point directly into the helical interfaces, and smaller residues allow closer helix contacts and larger assemblies.

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Crystal structures of a single coiled-coil peptide in two oligomeric states reveal the basis for structural polymorphism

Natural Structural Biology ◽

10.1038/nsb1296-1002 ◽

1996 ◽

Vol 3 (12) ◽

pp. 1002-1010 ◽

Cited By ~ 67

Author(s):

Lino Gonzalez ◽

Russell A. Brown ◽

Diane Richardson ◽

Tom Alber

Keyword(s):

Crystal Structures ◽

Coiled Coil ◽

Structural Polymorphism

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Pollutant Identification by Selected Area Electron Diffraction

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100052675 ◽

1974 ◽

Vol 32 ◽

pp. 532-533

Author(s):

R. E. Ferrell ◽

G. G. Paulson ◽

C. W. Walker

Keyword(s):

Thermal Treatment ◽

Electron Diffraction ◽

Sample Preparation ◽

Crystal Structures ◽

Water Samples ◽

Environmental Samples ◽

Short Review ◽

Selected Area Electron Diffraction ◽

Multiple Component

Selected area electron diffraction (SAD) has been used successfully to determine crystal structures, identify traces of minerals in rocks, and characterize the phases formed during thermal treatment of micron-sized particles. There is an increased interest in the method because it has the potential capability of identifying micron-sized pollutants in air and water samples. This paper is a short review of the theory behind SAD and a discussion of the sample preparation employed for the analysis of multiple component environmental samples.

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The Imaging of Crystal Structures and Crystal Defects

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100069995 ◽

1978 ◽

Vol 36 (3) ◽

pp. 207-217

Author(s):

J.M. Cowley

Keyword(s):

Electron Microscope ◽

Crystal Structures ◽

Phase Contrast ◽

Crystal Defects ◽

Atom Density ◽

Lack Of Information ◽

Spatial Frequencies

The problem of "understandinq" electron microscope imaqes becomes more acute as the resolution is improved. The naive interpretation of an imaqe as representinq the projection of an atom density becomes less and less appropriate. We are increasinqly forced to face the complexities of coherent imaqinq of what are essentially phase objects. Most electron microscopists are now aware that, for very thin weakly scatterinq objects such as thin unstained bioloqical specimens, hiqh resolution imaqes are best obtained near the optimum defocus, as prescribed by Scherzer, where the phase contrast imaqe qives a qood representation of the projected potential, apart from a lack of information on the lower spatial frequencies. But phase contrast imaqinq is never simple except in idealized limitinq cases.

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