8 Å structure of the outer rings of the Xenopus laevis nuclear pore complex obtained by cryo-EM and AI

The nuclear pore complex (NPC), one of the largest protein complexes in eukaryotes, serves as a physical gate to regulate nucleocytoplasmic transport. Here, we determined the 8 Å resolution cryo-electron microscopic (cryo-EM) structure of the outer rings containing nuclear ring (NR) and cytoplasmic ring (CR) from the Xenopus laevis NPC, with local resolutions reaching 4.9 Å. With the aid of AlphaFold2, we managed to build a pseudoatomic model of the outer rings, including the Y complexes and flanking components. In this most comprehensive and accurate model of outer rings to date, the almost complete Y complex structure exhibits much tighter interaction in the hub region. In addition to two copies of Y complexes, each asymmetric subunit in CR contains five copies of Nup358, two copies of the Nup214 complex, two copies of Nup205 and one copy of newly identified Nup93, while that in NR contains one copy of Nup205, one copy of ELYS and one copy of Nup93. These in-depth structural features represent a great advance in understanding the assembly of NPCs.

Extragalactic Magnetism with SOFIA (Legacy Program) - II: A Magnetically Driven Flow in the Starburst Ring of NGC 1097*

Galactic bars are frequent in disk galaxies and they may support the transfer of matter toward the central engine of active nuclei. The barred galaxy NGC 1097 has magnetic forces controlling the gas flow at several kpc scales, which suggest that magnetic fields (B-fields) are dynamically important along the bar and nuclear ring. However, the effect of the B-field on the gas flows in the central kpc scale has not been characterized. Using thermal polarized emission at 89 μm with HAWC+/SOFIA, here, we measure that the polarized flux is spatially located at the contact regions of the outer bar with the starburst ring. The linear polarization decomposition analysis shows that the 89 μm and radio (3.5 and 6.2 cm) polarization traces two different modes, m, of the B-field: a constant B-field orientation and dominated by m = 0 at 89 μm, and a spiral B-field dominated by m = 2 at radio. We show that the B-field at 89 μm is concentrated in the warmest region of a shock driven by the galactic-bar dynamics in the contact regions between the outer bar with the starburst ring. Radio polarization traces a superposition of the spiral B-field outside and within the starburst ring. According to Faraday rotation measures between 3.5 and 6.2 cm, the radial component of the B-field along the contact regions points toward the galaxy's center on both sides. We conclude that gas streams outside and within the starburst ring follow the B-field, which feeds the black hole with matter from the host galaxy.

8 Å structure of the nuclear ring of the Xenopus laevis nuclear pore complex solved by cryo-EM and AI

The nuclear pore complex (NPC), one of the largest protein complexes in eukaryotes, serves as a physical gate to regulate nucleocytoplasmic transport. Here, we determined the 8 Å resolution cryo-electron microscopic (cryo-EM) structure of the nuclear ring (NR) from the Xenopus laevis NPC, with local resolutions reaching 4.9 Å. With the aid of AlphaFold2, we managed to build a pseudoatomic model of the NR, including the Y complexes and flanking components. In this most comprehensive and accurate model to date, the almost complete Y complex structure exhibits much tighter interaction in the hub region. Each NR asymmetric subunit contains two copies of Y complexes, one copy of Nup205 that connects the Y complexes to the neighbouring complex, one copy of ELYS that stabilizes the long arm region of the inner Y complex, and one copy of newly identified Nup93 that forms a bridge across the stems of Y complexes. These in-depth structural features represent a great advance in understanding the assembly of NPCs.

Determining the architecture of nuclear ring of Xenopus laevis nuclear pore complex using integrated approaches

The nuclear pore complexes (NPCs) are large protein assemblies as a physical gate to regulate nucleocytoplasmic transport. Here, using integrated approaches including cryo-electron microscopy, hybrid homology modeling and cell experiment, we determined the architecture of the nuclear ring (NR) from Xenopus laevis oocytes NPC at subnanometer resolution. In addition to the improvement of the Y complex model, eight copies of Nup205 and ELYS were assigned in NR. Nup205 connects the inner and outer Y complexes and contributes to the assembly and stability of the NR. By interacting with both the inner Nup160 and the nuclear envelope (NE), the N-terminal β-propeller and α-solenoid domains of ELYS were found to be essential for accurate assembly of the NPC on the NE.

3D super-resolution fluorescence microscopy maps the variable molecular architecture of the Nuclear Pore Complex

Nuclear pore complexes (NPCs) are large macromolecular machines that mediate the traffic between the nucleus and the cytoplasm. In vertebrates, each NPC consists of ∼1000 proteins, termed nucleoporins, and has a mass of over 100 MDa. While a pseudo-atomic static model of the central scaffold of the NPC has recently been assembled by integrating data from isolated proteins and complexes, many structural components still remain elusive due to the enormous size and flexibility of the NPC. Here, we explored the power of 3D super-resolution microscopy combined with computational classification and averaging to explore the 3D structure of the NPC in single human cells. We show that this approach can build the first integrated 3D structural map containing both central as well as peripheral NPC subunits with molecular specificity and nanoscale resolution. Our unbiased classification of over ten thousand individual NPCs indicates that the nuclear ring and the nuclear basket can adopt different conformations. Our approach opens up the exciting possibility to relate different structural states of the NPC to function in situ.

Morphological and Kinematical Analysis of the Double-barred Galaxy NGC 3504 Using ALMA CO (2–1) Data

We present results obtained from ALMA CO (2–1) data of the double-barred galaxy NGC 3504. With three times higher angular resolution (∼ 0.″8) than previous studies, our observations reveal an inner molecular gas bar, a nuclear ring, and four inner spiral arm-like structures in the central 1 kpc region. Furthermore, the CO emission is clearly aligned with the two dust lanes in the outer bar region, with differences in shape and intensity between them. The total molecular gas mass in the observed region (50″ × 57″) is estimated to be ∼3.1 × 109 M⊙, which is 17 per cent of the stellar mass. We used the Kinemetry package to fit the velocity field and found that circular motion strongly dominates at R = 0.3 − 0.8 kpc, but radial motion becomes important at R < 0.3 kpc and R = 1.0 − 2.5 kpc, which is expected due to the presence of the inner and outer bars. Finally, assuming that the gas moves along the dust lanes in the bar rotating frame, we derived the pattern speed of the outer bar to be 18 ± 5 km s−1 kpc−1, the average streaming velocities on each of the two dust lanes to be 165 and 221 km s−1, and the total mass inflow rate along the dust lanes to be 12 M⊙ yr−1. Our results give a new example of an inner gas bar within a gas-rich double-barred galaxy and suggest that the formation of double-barred galaxies could be associated with the existence of such gas structures.

3D super-resolution fluorescence microscopy maps the variable molecular architecture of the Nuclear Pore Complex

Nuclear pore complexes (NPCs) are large macromolecular machines that mediate the traffic between the nucleus and the cytoplasm. In vertebrates, each NPC consists of ∼1000 proteins, termed nucleoporins, and has a mass of over 100 MDa. While a pseudo-atomic static model of the central scaffold of the NPC has recently been assembled by integrating data from isolated proteins and complexes, many structural components still remain elusive due to the enormous size and flexibility of the NPC. Here, we explored the power of 3D super-resolution microscopy combined with computational classification and averaging to explore the 3D structure of the NPC in single human cells. We show that this approach can build the first integrated 3D structural map containing both central as well as peripheral NPC subunits with molecular specificity and nanoscale resolution. Our unbiased classification of over ten thousand individual NPCs indicates that the nuclear ring and the nuclear basket can adopt different conformations. Our approach opens up the exciting possibility to relate different structural states of the NPC to function in situ.

Inside-out formation of nuclear discs and the absence of old central spheroids in barred galaxies of the TIMER survey

The centres of disc galaxies host a variety of structures built via both internal and external processes. In this study, we constrain the formation and evolution of these central structures, in particular, nuclear rings and nuclear discs, by deriving maps of mean stellar ages, metallicities, and [α/Fe] abundances. We use observations obtained with the MUSE integral-field spectrograph for the TIMER sample of 21 massive barred galaxies. Our results indicate that nuclear discs and nuclear rings are part of the same physical component, with nuclear rings constituting the outer edge of nuclear discs. All nuclear discs in the sample are clearly distinguished based on their stellar population properties. As expected in the picture of bar-driven secular evolution, nuclear discs are younger, more metal-rich, and exhibit lower [α/Fe] enhancements, as compared to their immediate surroundings. Moreover, nuclear discs exhibit well-defined radial gradients, with ages and metallicities decreasing, and [α/Fe] abundances increasing with radius out to the nuclear ring. Often, these gradients show no breaks from the edge of the nuclear disc up through the centre, suggesting that these structures extend to the very centres of galaxies. We argue that continuous (stellar) nuclear discs may form from a series of bar-built (initially gas-rich) nuclear rings that expand in their radius as the bar evolves. In this picture, nuclear rings are simply the (often) star-forming outer edge of nuclear discs. Finally, by combining our results with those taken from a accompanying kinematic study, we do not find evidence for the presence of large, dispersion-dominated components in the centres of these galaxies. This could be a result of quiet merger histories, despite the large galaxy masses, or, perhaps, due to high angular momentum and strong feedback processes preventing the formation of these kinematically hot components.

The Nuclear Pore Complex: A Target for NS3 Protease of Dengue and Zika Viruses

During flavivirus infection, some viral proteins move to the nucleus and cellular components are relocated from the nucleus to the cytoplasm. Thus, the integrity of the main regulator of the nuclear-cytoplasmic transport, the nuclear pore complex (NPC), was evaluated during infection with dengue virus (DENV) and Zika virus (ZIKV). We found that while during DENV infection the integrity and distribution of at least three nucleoporins (Nup), Nup153, Nup98, and Nup62 were altered, during ZIKV infection, the integrity of TPR, Nup153, and Nup98 were modified. In this work, several lines of evidence indicate that the viral serine protease NS2B3 is involved in Nups cleavage. First, the serine protease inhibitors, TLCK and Leupeptin, prevented Nup98 and Nup62 cleavage. Second, the transfection of DENV and ZIKV NS2B3 protease was sufficient to inhibit the nuclear ring recognition detected in mock-infected cells with the Mab414 antibody. Third, the mutant but not the active (WT) protease was unable to cleave Nups in transfected cells. Thus, here we describe for the first time that the NS3 protein from flavivirus plays novel functions hijacking the nuclear pore complex, the main controller of the nuclear-cytoplasmic transport.