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

2022 ◽  
Author(s):  
Linhua Tai ◽  
Yun Zhu ◽  
He Ren ◽  
Xiaojun Huang ◽  
Chuanmao Zhang ◽  
...  
Keyword(s):  
Xenopus Laevis ◽  
Nuclear Pore Complex ◽  
Protein Complexes ◽  
Complex Structure ◽  
Nucleocytoplasmic Transport ◽  
Structural Features ◽  
Nuclear Pore ◽  
Electron Microscopic ◽  
Nuclear Ring ◽  
Great Advance

AbstractThe 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.

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

2021 ◽  
Author(s):  
He Ren ◽  
Linhua Tai ◽  
Yun Zhu ◽  
Xiaojun Huang ◽  
Fei Sun ◽  
...  
Keyword(s):  
Xenopus Laevis ◽  
Nuclear Pore Complex ◽  
Protein Complexes ◽  
Complex Structure ◽  
Nucleocytoplasmic Transport ◽  
Structural Features ◽  
Nuclear Pore ◽  
Electron Microscopic ◽  
Nuclear Ring ◽  
Great Advance

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.

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

2021 ◽  
Author(s):  
Linhua Tai ◽  
Yun Zhu ◽  
He Ren ◽  
Xiaojun Huang ◽  
Chuanmao Zhang ◽  
...  
Keyword(s):  
Xenopus Laevis ◽  
Nuclear Pore Complex ◽  
Protein Complexes ◽  
Complex Structure ◽  
Nucleocytoplasmic Transport ◽  
Structural Features ◽  
Nuclear Pore ◽  
Electron Microscopic ◽  
C Terminus ◽  
Parallel Pattern

As one of the largest protein complexes in eukaryotes, the nuclear pore complex (NPC) forms a conduit regulating nucleocytoplasmic transport. Here, we determined 8 Å resolution cryo-electron microscopic (cryo-EM) structure of the cytoplasmic ring (CR) from the Xenopus laevis NPC. With the aid of AlphaFold2, we managed to build a most comprehensive and accurate pseudoatomic model of the CR to date, including the Y complexes and flanking components of Nup358, Nup214 complexes, Nup205 and Nup93. Comparing with previously reported CR model, the Y complex structure in our model exhibits much tighter interactions in the hub region mediated by α-solenoid domain in Nup160 C-terminus. Five copies of Nup358 are identified in each CR subunit to provide rich interactions with other Nups in stem regions of Y complexes. Two copies of Nup214 complexes lay in a parallel pattern and attach to the short arm region of Y complexes towards the central channel of NPC. Besides, the structural details of two copies of Nup205 on the side of the short arm region and one copy of Nup93 on the stem region of Y complexes in each CR subunit are also revealed. These in-depth novel structural features represent a great advance in understanding the assembly of NPCs.

Structure, assembly and interactions of the nuclear lamina and the nuclear pore complex

1992 ◽  
Vol 50 (1) ◽  
pp. 490-491
Author(s):  
N. Panté ◽  
M. Jarnik ◽  
E. Heitlinger ◽  
U. Aebi
Keyword(s):  
Nuclear Pore Complex ◽  
Divalent Cations ◽  
Nuclear Lamina ◽  
Dynamic Structure ◽  
Nucleocytoplasmic Transport ◽  
Nuclear Pore ◽  
Cytoplasmic Filaments ◽  
Radial Spokes ◽  
Nuclear Ring ◽  
Central Plug

The nuclear pore complex (NPC) is a ∼120 MD supramolecular machine implicated in nucleocytoplasmic transport, that is embedded in the double-membraned nuclear envelope (NE). The basic framework of the ∼120 nm diameter NPC consists of a 32 MD cytoplasmic ring, a 66 MD ‘plug-spoke’ assembly, and a 21 MD nuclear ring. The ‘central plug’ seen in en face views of the NPC reveals a rather variable appearance indicating that it is a dynamic structure. Projecting from the cytoplasmic ring are 8 short, twisted filaments (Fig. 1a), whereas the nuclear ring is topped with a ‘fishtrap’ made of 8 thin filaments that join distally to form a fragile, 30-50 nm distal diameter ring centered above the NPC proper (Fig. 1b). While the cytoplasmic filaments are sensitive to proteases, they as well as the nuclear fishtraps are resistant to RNase treatment. Removal of divalent cations destabilizes the distal rings and thereby opens the fishtraps, addition causes them to reform. Protruding from the tips of the radial spokes into perinuclear space are ‘knobs’ that might represent the large lumenal domain of gp210, a membrane-spanning glycoprotein (Fig. 1c) which, in turn, may play a topogenic role in membrane folding and/or act as a membrane-anchoring site for the NPC. The lectin wheat germ agglutinin (WGA) which is known to recognize the ‘nucleoporins’, a family of glycoproteins having O-linked N-acetyl-glucosamine, is found in two locations on the NPC (Fig. 1. d-f): (i) whereas the cytoplasmic filaments appear unlabelled (Fig. 1d&e), WGA-gold labels sites between the central plug and the cytoplasmic ring (Fig. le; i.e., at a radius of 25-35 nm), and (ii) it decorates the distal ring of the nuclear fishtraps (Fig. 1, d&f; arrowheads).

scholarly journals Molecular architecture of the luminal ring of the Xenopus laevis nuclear pore complex

2020 ◽  
Author(s):  
Yanqing Zhang ◽  
Sai Li ◽  
Chao Zeng ◽  
Gaoxingyu Huang ◽  
Xuechen Zhu ◽  
...  
Keyword(s):  
Xenopus Laevis ◽  
Nuclear Pore Complex ◽  
Electron Tomography ◽  
Structural Features ◽  
Rigid Base ◽  
Nuclear Pore ◽  
Molecular Architecture ◽  
Nuclear Membranes ◽  
Cryo Electron Microscopy ◽  
Cryo Electron Tomography

Nuclear pore complex (NPC) mediates the flow of substances between the nucleus and cytoplasm in eukaryotic cells. Here we report the cryo-electron tomography (cryo-ET) structure of the luminal ring (LR) of the NPC from Xenopus laevis oocyte. The observed key structural features of the LR are independently confirmed by single-particle cryo-electron microscopy (cryo-EM) analysis. The LR comprises eight butterfly-shaped subunits, each containing two symmetric wings. Each wing consists of four elongated, tubular protomers. Within the LR subunit, the eight protomers form a Finger domain, which directly contacts the fusion between the inner and outer nuclear membranes, and a Grid domain, which serves as a rigid base for the Finger domain. Two neighbouring LR subunits interact with each other through the lateral edges of their wings to constitute a Bumper domain, which displays two major conformations and appears to cushion neighbouring NPCs. Our study reveals previously unknown features of the LR and potentially explains the elastic property of the NPC.

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

2021 ◽  
Author(s):  
He Ren ◽  
Linhua Tai ◽  
Yun Zhu ◽  
Chun Chan ◽  
Qun Zhao ◽  
...  
Keyword(s):  
Xenopus Laevis ◽  
Nucleocytoplasmic Transport ◽  
Complex Model ◽  
Nuclear Pore ◽  
Xenopus Laevis Oocytes ◽  
Nuclear Pore Complexes ◽  
Cell Experiment ◽  
Nuclear Ring ◽  
Integrated Approaches ◽  
Pore Complexes

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.

scholarly journals Structure of the Cytoplasmic Ring of the Xenopus laevis Nuclear Pore Complex

2020 ◽  
Author(s):  
Gaoxingyu Huang ◽  
Yanqing Zhang ◽  
Xuechen Zhu ◽  
Chao Zeng ◽  
Qifan Wang ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Xenopus Laevis ◽  
Nuclear Pore Complex ◽  
Single Particle ◽  
Coiled Coil ◽  
Structural Features ◽  
Nuclear Pore ◽  
Structural Elements ◽  
Cryo Electron Microscopy ◽  
Secondary Structural Elements

Nuclear pore complex (NPC) exhibits structural plasticity and has only been characterized at local resolutions of up to 15 Å for the cytoplasmic ring (CR). Here we present a single-particle cryo-electron microscopy (cryo-EM) structure of the CR from Xenopus laevis NPC at average resolutions of 5.5-7.9 Å, with local resolutions reaching 4.5 Å. Improved resolutions allow identification and placement of secondary structural elements in the majority of the CR components. The two Y complexes in each CR subunit interact with each other and associate with those from flanking subunits, forming a circular scaffold. Within each CR subunit, the Nup358-containing region wraps around the stems of both Y complexes, likely stabilizing the scaffold. Nup205 connects the short arms of the two Y complexes and associates with the stem of a neighbouring Y complex. The Nup214-containing region uses an extended coiled-coil to link Nup85 of the two Y complexes and protrudes into the axial pore of the NPC. These previously uncharacterized structural features reveal insights into NPC assembly.

scholarly journals Role of the Ndc1 interaction network in yeast nuclear pore complex assembly and maintenance

2009 ◽  
Vol 185 (3) ◽  
pp. 475-491 ◽  
Author(s):  
Evgeny Onischenko ◽  
Leslie H. Stanton ◽  
Alexis S. Madrid ◽  
Thomas Kieselbach ◽  
Karsten Weis
Keyword(s):  
Nuclear Pore Complex ◽  
Structural Integrity ◽  
Fluorescent Protein ◽  
Interaction Network ◽  
Nucleocytoplasmic Transport ◽  
Nuclear Pore ◽  
Binding Partners ◽  
Interaction Partners ◽  
Redundant Functions

The nuclear pore complex (NPC) mediates all nucleocytoplasmic transport, yet its structure and biogenesis remain poorly understood. In this study, we have functionally characterized interaction partners of the yeast transmembrane nucleoporin Ndc1. Ndc1 forms a distinct complex with the transmembrane proteins Pom152 and Pom34 and two alternative complexes with the soluble nucleoporins Nup53 and Nup59, which in turn bind to Nup170 and Nup157. The transmembrane and soluble Ndc1-binding partners have redundant functions at the NPC, and disruption of both groups of interactions causes defects in Ndc1 targeting and in NPC structure accompanied by significant pore dilation. Using photoconvertible fluorescent protein fusions, we further show that the depletion of Pom34 in cells that lack NUP53 and NUP59 blocks new NPC assembly and leads to the reversible accumulation of newly made nucleoporins in cytoplasmic foci. Therefore, Ndc1 together with its interaction partners are collectively essential for the biosynthesis and structural integrity of yeast NPCs.

scholarly journals Structural interaction between the nuclear pore complex and a specific translocating RNP particle.

1995 ◽  
Vol 129 (5) ◽  
pp. 1205-1216 ◽  
Author(s):  
H Mehlin ◽  
B Daneholt ◽  
U Skoglund
Keyword(s):  
Nuclear Pore Complex ◽  
Nuclear Pore ◽  
Initial Contact ◽  
Chironomus Tentans ◽  
Central Channel ◽  
Balbiani Ring ◽  
Salivary Gland Cells ◽  
Larval Salivary Gland ◽  
Nuclear Ring ◽  
Precise Area

The transport of Balbiani ring (BR) premessenger RNP particles in the larval salivary gland cells of the dipteran Chironomus tentans can be followed using electron microscopy. A BR RNP particle consists of an RNP ribbon bent into a ringlike structure. Upon translocation through the nuclear pore complex (NPC), the ribbon is straightened and enters the central channel of the NPC with the 5' end of the transcript in the lead. The translocating ribbon is likely to interact with the central channel but, in addition, the remaining portion of the ribbon ring makes contact with the periphery of the NPC. To determine the nature of this latter interaction, we have now studied the connections between the RNP particle and the border of the NPC during different stages of translocation using electron microscope tomography. It was observed that the 3' terminal domain of the ribbon always touches the nuclear ring of the NPC, but the precise area of contact is variable. Sometimes also a region on the opposite side of the ribbon ring reaches the nuclear ring. The pattern of contacts could be correlated to the stage of translocation, and it was concluded that the particle-nuclear ring interactions reflect a rotation of the ribbon ring in front of the central channel, the rotation being secondary to the successive translocation of the ribbon through the channel. The particle's mode of interaction with the NPC suggests that the initial contact between the 5' end domain of the ribbon and the entrance to the central channel is probably crucial to accomplish the ordered translocation of the premessenger RNP particle through the NPC.

scholarly journals Monoclonal antibodies identify a group of nuclear pore complex glycoproteins.

1987 ◽  
Vol 104 (5) ◽  
pp. 1143-1156 ◽  
Author(s):  
C M Snow ◽  
A Senior ◽  
L Gerace
Keyword(s):  
Monoclonal Antibodies ◽  
Nuclear Envelope ◽  
Nuclear Pore Complex ◽  
Peptide Mapping ◽  
Polyclonal Antibodies ◽  
Integral Membrane Protein ◽  
Nucleocytoplasmic Transport ◽  
Nuclear Pore ◽  
Nuclear Surface ◽  
Punctate Pattern

Using monoclonal antibodies we identified a group of eight polypeptides of rat liver nuclear envelopes that have common epitopes. Most or all of these proteins are structurally distinct, as shown by tryptic peptide mapping and analysis with polyclonal antibodies. While these polypeptides are relatively tightly bound to nuclear membranes, only one is an integral membrane protein. The eight antigens cofractionate with the nuclear pore complex under various conditions of ionic strength and detergent. It can be seen by immunofluorescence microscopy that the monoclonal antibodies reacting with these antigens stain the nuclear surface of interphase cells in a finely punctate pattern. When the nuclear envelope is disassembled and subsequently reformed during mitosis, the proteins are reversibly dispersed throughout the cytoplasm in the form of minute foci. By EM immunogold localization on isolated nuclear envelopes, the monoclonal antibodies label exclusively the nuclear pore complex, at both its nucleoplasmic and cytoplasmic margins. Considered together, our biochemical and localization data indicate that the eight nuclear envelope polypeptides are pore complex components. As shown in the accompanying paper (Holt, G. D., C. M. Snow, A. Senior, R. S. Haltiwanger, L. Gerace, and G. W. Hart, J. Cell Biol., 104:1157-1164) these eight polypeptides contain a novel form of glycosylation, O-linked N-acetylglucosamine. The relative abundance and disposition of these O-linked glycoproteins in the pore complex are consistent with their having a role in nucleocytoplasmic transport.

Sign in / Sign up

Export Citation Format

Share Document