Structure insights of the human peroxisomal ABC transporter ALDP

Adrenoleukodystrophy protein (ALDP) is responsible for the transport of free very-long-chain fatty acids (VLCFAs) and corresponding CoA-esters across the peroxisomal membrane. ALDP belongs to the ATP-binding cassette sub-family D, which is also named as ABCD1. Dysfunction of ALDP leads to peroxisomal metabolic disorder exemplified by X-linked adrenoleukodystrophy (ALD). Hundreds of ALD-causing mutations are identified on ALDP. However, the pathogenic mechanisms of these mutations are restricted to clinical description due to limited structural information. Furthermore, ALDP plays a role in myelin maintenance, which is tightly associated with axon regeneration. Here we report the cryo-electron microscopy (cryo-EM) structure of human ALDP with nominal resolution of 3.4 angstrom in nucleotide free state. The structure of ALDP exhibits a typical assembly of ABC transporters. The nucleotide binding domains (NBDs) displays a ligand free state. ALDP exhibits an inward-open conformation to the cytosol. A short helix is located at the peroxisomal side, which is different from other three members of ABCD transporters. The two transmembrane domains (TMDs) of ALDP form a cavity, in which two lipid-like densities can be recognized as the head group of an coenzyme-A ester of a lipid. This structure provides a framework for understanding the working mechanism of ALDP and classification of the disease-causing mutations.

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Vestibular Migraine with Visual Aura and Olfactory Hallucination in Children: Two Case Reports

Neuropediatrics ◽

10.1055/s-0038-1673642 ◽

2018 ◽

Vol 49 (06) ◽

pp. 414-416 ◽

Cited By ~ 1

Author(s):

T.R. Villa ◽

L.M. Agessi

Keyword(s):

Case Reports ◽

International Classification ◽

Vestibular Migraine ◽

Migraine Aura ◽

Headache Disorders ◽

Visual Aura ◽

Clinical Description ◽

Olfactory Hallucination

Background Approximately 3.9% children with migraine have olfactory hallucination which was defined as a perception of a smell without the substantial existence of any physical odor. Case We described the first two cases of children with vestibular migraine, presenting visual aura and olfactory hallucination. We reported two children with vertigo, visual aura, and olfactory hallucination before the headache who were responsive to topiramate. Conclusion The clinical description of olfactory hallucination presented some characteristics of migraine aura. Olfactory hallucinations could be inserted as a migraine aura in International Classification of Headache Disorders.

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Examining the structure of the mature amyloid fibril

Biochemical Society Transactions ◽

10.1042/bst0300521 ◽

2002 ◽

Vol 30 (4) ◽

pp. 521-525 ◽

Cited By ~ 43

Author(s):

O. S. Makin ◽

L. C. Serpell

Keyword(s):

Self Assembly ◽

Rational Design ◽

Amyloid Fibrils ◽

Structural Information ◽

X Ray ◽

X Ray Crystallography ◽

Cryo Electron Microscopy ◽

Fibre Diffraction ◽

Complementary Techniques ◽

Mature Fibril

The pathogenesis of the group of diseases known collectively as the amyloidoses is characterized by the deposition of insoluble amyloid fibrils. These are straight, unbranching structures about 70–120 å (1 å = 0.1 nm) in diameter and of indeterminate length formed by the self-assembly of a diverse group of normally soluble proteins. Knowledge of the structure of these fibrils is necessary for the understanding of their abnormal assembly and deposition, possibly leading to the rational design of therapeutic agents for their prevention or disaggregation. Structural elucidation is impeded by fibril insolubility and inability to crystallize, thus preventing the use of X-ray crystallography and solution NMR. CD, Fourier-transform infrared spectroscopy and light scattering have been used in the study of the mechanism of fibril formation. This review concentrates on the structural information about the final, mature fibril and in particular the complementary techniques of cryo-electron microscopy, solid-state NMR and X-ray fibre diffraction.

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Accurate geometrical restraints for Watson–Crick base pairs

Acta Crystallographica Section B Structural Science Crystal Engineering and Materials ◽

10.1107/s2052520619002002 ◽

2019 ◽

Vol 75 (2) ◽

pp. 235-245 ◽

Cited By ~ 3

Author(s):

Miroslaw Gilski ◽

Jianbo Zhao ◽

Marcin Kowiel ◽

Dariusz Brzezinski ◽

Douglas H. Turner ◽

...

Keyword(s):

Structural Information ◽

Data Bank ◽

Base Pairs ◽

Acta Cryst ◽

Ultrahigh Resolution ◽

Cryo Electron Microscopy ◽

Structural Database ◽

Different Sources ◽

Best Parameters

Geometrical restraints provide key structural information for the determination of biomolecular structures at lower resolution by experimental methods such as crystallography or cryo-electron microscopy. In this work, restraint targets for nucleic acids bases are derived from three different sources and compared: small-molecule crystal structures in the Cambridge Structural Database (CSD), ultrahigh-resolution structures in the Protein Data Bank (PDB) and quantum-mechanical (QM) calculations. The best parameters are those based on CSD structures. After over two decades, the standard library of Parkinson et al. [(1996), Acta Cryst. D52, 57–64] is still valid, but improvements are possible with the use of the current CSD database. The CSD-derived geometry is fully compatible with Watson–Crick base pairs, as comparisons with QM results for isolated and paired bases clearly show that the CSD targets closely correspond to proper base pairing. While the QM results are capable of distinguishing between single and paired bases, their level of accuracy is, on average, nearly two times lower than for the CSD-derived targets when gauged by root-mean-square deviations from ultrahigh-resolution structures in the PDB. Nevertheless, the accuracy of QM results appears sufficient to provide stereochemical targets for synthetic base pairs where no reliable experimental structural information is available. To enable future tests for this approach, QM calculations are provided for isocytosine, isoguanine and the iCiG base pair.

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A resolution record for cryoEM

Faculty Reviews ◽

10.12703/r-01-000002 ◽

2021 ◽

Vol 10 ◽

Author(s):

Jonathan Ashmore ◽

Bridget Carragher ◽

Peter B Rosenthal ◽

William Weis

Keyword(s):

Electron Microscopy ◽

Image Analysis ◽

Structure Determination ◽

Test Specimen ◽

Structural Information ◽

Atomic Resolution ◽

Fast Growing ◽

Cryo Electron Microscopy ◽

New Instrument ◽

Resolution Structure

Cryo electron microscopy (cryoEM) is a fast-growing technique for structure determination. Two recent papers report the first atomic resolution structure of a protein obtained by averaging images of frozen-hydrated biomolecules. They both describe maps of symmetric apoferritin assemblies, a common test specimen, in unprecedented detail. New instrument improvements, different in the two studies, have contributed better images, and image analysis can extract structural information sufficient to resolve individual atomic positions. While true atomic resolution maps will not be routine for most proteins, the studies suggest structures determined by cryoEM will continue to improve, increasing their impact on biology and medicine.

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Structural insight into TPX2-stimulated microtubule assembly

eLife ◽

10.7554/elife.30959 ◽

2017 ◽

Vol 6 ◽

Cited By ~ 49

Author(s):

Rui Zhang ◽

Johanna Roostalu ◽

Thomas Surrey ◽

Eva Nogales

Keyword(s):

Molecular Mechanism ◽

Structural Information ◽

Microtubule Assembly ◽

Cryo Electron Microscopy ◽

Interaction Mode ◽

In Vitro Reconstitution ◽

Assembly Factor ◽

Ran Gtp ◽

Mitosis And Meiosis

During mitosis and meiosis, microtubule (MT) assembly is locally upregulated by the chromatin-dependent Ran-GTP pathway. One of its key targets is the MT-associated spindle assembly factor TPX2. The molecular mechanism of how TPX2 stimulates MT assembly remains unknown because structural information about the interaction of TPX2 with MTs is lacking. Here, we determine the cryo-electron microscopy structure of a central region of TPX2 bound to the MT surface. TPX2 uses two flexibly linked elements (’ridge’ and ‘wedge’) in a novel interaction mode to simultaneously bind across longitudinal and lateral tubulin interfaces. These MT-interacting elements overlap with the binding site of importins on TPX2. Fluorescence microscopy-based in vitro reconstitution assays reveal that this interaction mode is critical for MT binding and facilitates MT nucleation. Together, our results suggest a molecular mechanism of how the Ran-GTP gradient can regulate TPX2-dependent MT formation.

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Structure of the Infective Getah Virus at 2.8 Å-resolution Determined by Cryo-electron Microscopy

10.1101/2021.07.16.452580 ◽

2021 ◽

Author(s):

Aojie Wang ◽

Feng Zhou ◽

Congcong Liu ◽

Dongsheng Gao ◽

Ruxi Qi ◽

...

Keyword(s):

Electron Microscopy ◽

Immune Evasion ◽

Cell Invasion ◽

Structural Information ◽

Host Cell Invasion ◽

Hydrophobic Pocket ◽

Viral Immune Evasion ◽

Cryo Electron Microscopy ◽

Reproductive Losses ◽

Getah Virus

Getah virus (GETV) is a mosquito-borne pathogen that can cause a mild illness and reproductive losses in animals. Although antibodies to GETV have been found in humans, there are no reports of clinical symptom associated with GETV. However, antivirals or vaccine against GETV is still unavailable due to lack of knowledge of the structure of GETV virion. Here, we present the structure of mature GETV at a resolution of 2.8 Å with capsid protein, envelope glycoproteins E1 and E2. Glycosylation and S-acylation sites in E1 and E2 are identified. The surface-exposed glycans demonstrated their impact on the viral immune evasion and host cell invasion. The S-acylation sites strongly stabilize the virion. In addition, a cholesterol and phospholipid molecule are observed in transmembrane hydrophobic pocket, together with two more cholesterols surround the pocket. These structural information are helpful for structure-based antivirals and vaccine design.

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Diversity and evolution of B-family DNA polymerases

Nucleic Acids Research ◽

10.1093/nar/gkaa760 ◽

2020 ◽

Vol 48 (18) ◽

pp. 10142-10156 ◽

Cited By ~ 4

Author(s):

Darius Kazlauskas ◽

Mart Krupovic ◽

Julien Guglielmini ◽

Patrick Forterre ◽

Česlovas Venclovas

Keyword(s):

Structural Information ◽

Dna Polymerases ◽

Comprehensive Analysis ◽

Metagenomic Data ◽

Dna Viruses ◽

Taxonomic Distribution ◽

Binding Domains ◽

Catalytically Active ◽

Domains Of Life ◽

Massive Accumulation

Abstract B-family DNA polymerases (PolBs) represent the most common replicases. PolB enzymes that require RNA (or DNA) primed templates for DNA synthesis are found in all domains of life and many DNA viruses. Despite extensive research on PolBs, their origins and evolution remain enigmatic. Massive accumulation of new genomic and metagenomic data from diverse habitats as well as availability of new structural information prompted us to conduct a comprehensive analysis of the PolB sequences, structures, domain organizations, taxonomic distribution and co-occurrence in genomes. Based on phylogenetic analysis, we identified a new, widespread group of bacterial PolBs that are more closely related to the catalytically active N-terminal half of the eukaryotic PolEpsilon (PolEpsilonN) than to Escherichia coli Pol II. In Archaea, we characterized six new groups of PolBs. Two of them show close relationships with eukaryotic PolBs, the first one with PolEpsilonN, and the second one with PolAlpha, PolDelta and PolZeta. In addition, structure comparisons suggested common origin of the catalytically inactive C-terminal half of PolEpsilon (PolEpsilonC) and PolAlpha. Finally, in certain archaeal PolBs we discovered C-terminal Zn-binding domains closely related to those of PolAlpha and PolEpsilonC. Collectively, the obtained results allowed us to propose a scenario for the evolution of eukaryotic PolBs.

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Ultrapotent human antibodies protect against SARS-CoV-2 challenge via multiple mechanisms

Science ◽

10.1126/science.abe3354 ◽

2020 ◽

Vol 370 (6519) ◽

pp. 950-957 ◽

Cited By ~ 21

Author(s):

M. Alejandra Tortorici ◽

Martina Beltramello ◽

Florian A. Lempp ◽

Dora Pinto ◽

Ha V. Dang ◽

...

Keyword(s):

Neutralizing Antibodies ◽

Viral Escape ◽

Angiotensin Converting Enzyme 2 ◽

Effector Functions ◽

Human Antibodies ◽

Binding Domains ◽

Isolation And Characterization ◽

Cryo Electron Microscopy ◽

Escape Mutants

Efficient therapeutic options are needed to control the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that has caused more than 922,000 fatalities as of 13 September 2020. We report the isolation and characterization of two ultrapotent SARS-CoV-2 human neutralizing antibodies (S2E12 and S2M11) that protect hamsters against SARS-CoV-2 challenge. Cryo–electron microscopy structures show that S2E12 and S2M11 competitively block angiotensin-converting enzyme 2 (ACE2) attachment and that S2M11 also locks the spike in a closed conformation by recognition of a quaternary epitope spanning two adjacent receptor-binding domains. Antibody cocktails that include S2M11, S2E12, or the previously identified S309 antibody broadly neutralize a panel of circulating SARS-CoV-2 isolates and activate effector functions. Our results pave the way to implement antibody cocktails for prophylaxis or therapy, circumventing or limiting the emergence of viral escape mutants.

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