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 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 The Human Nuclear Pore Complex as Revealed by Cryo-Electron Tomography

Structure ◽  
2012 ◽  
Vol 20 (6) ◽  
pp. 998-1006 ◽  
Author(s):  
Tal Maimon ◽  
Nadav Elad ◽  
Idit Dahan ◽  
Ohad Medalia
Keyword(s):  
Nuclear Pore Complex ◽  
Electron Tomography ◽  
Nuclear Pore ◽  
Cryo Electron Tomography

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.

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

Cell Research ◽  
2020 ◽  
Vol 30 (6) ◽  
pp. 532-540 ◽  
Author(s):  
Yanqing Zhang ◽  
Sai Li ◽  
Chao Zeng ◽  
Gaoxingyu Huang ◽  
Xuechen Zhu ◽  
...  
Keyword(s):  
Xenopus Laevis ◽  
Nuclear Pore Complex ◽  
Nuclear Pore ◽  
Molecular Architecture

scholarly journals The Structure of the Nuclear Pore Complex (An Update)

2019 ◽  
Vol 88 (1) ◽  
pp. 725-783 ◽  
Author(s):  
Daniel H. Lin ◽  
André Hoelz
Keyword(s):  
Nuclear Pore Complex ◽  
Electron Tomography ◽  
Structure And Function ◽  
Atomic Resolution ◽  
Nuclear Pore ◽  
Structural Studies ◽  
Protein Subunits ◽  
Cryo Electron Tomography ◽  
And Function

The nuclear pore complex (NPC) serves as the sole bidirectional gateway of macromolecules in and out of the nucleus. Owing to its size and complexity (∼1,000 protein subunits, ∼110 MDa in humans), the NPC has remained one of the foremost challenges for structure determination. Structural studies have now provided atomic-resolution crystal structures of most nucleoporins. The acquisition of these structures, combined with biochemical reconstitution experiments, cross-linking mass spectrometry, and cryo–electron tomography, has facilitated the determination of the near-atomic overall architecture of the symmetric core of the human, fungal, and algal NPCs. Here, we discuss the insights gained from these new advances and outstanding issues regarding NPC structure and function. The powerful combination of bottom-up and top-down approaches toward determining the structure of the NPC offers a paradigm for uncovering the architectures of other complex biological machines to near-atomic resolution.

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 Cryo-EM structure of the Inner Ring from Xenopus laevis Nuclear Pore Complex

2021 ◽  
Author(s):  
Gaoxingyu Huang ◽  
Xiechao Zhan ◽  
Chao Zeng ◽  
Ke Liang ◽  
Xuechen Zhu ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Xenopus Laevis ◽  
Nuclear Envelope ◽  
Nuclear Pore Complex ◽  
Single Particle ◽  
Nuclear Pore ◽  
Nucleocytoplasmic Shuttling ◽  
Cryo Electron Microscopy

Nuclear pore complex (NPC) mediates nucleocytoplasmic shuttling. Here we present single-particle cryo-electron microscopy (cryo-EM) structure of the inner ring (IR) subunit from Xenopus laevis NPC at an average resolution of 4.4 Å. The symmetric IR subunit comprises a cytoplasmic half and a nuclear half. A homo-dimer of Nup205 resides at the center of the IR subunit, flanked by two molecules of Nup188. Four molecules of Nup93 each places an extended helix into the axial groove of Nup205 or Nup188, together constituting the central scaffold. The channel nucleoporin heterotrimer (CNT) of Nup54/58/62 is anchored on the central scaffold. Six Nup155 molecules interact with the central scaffold and together with the NDC1-ALADIN hetero-dimers anchor the IR subunit to the nuclear envelope and to outer rings. The scarce inter-subunit contacts may allow sufficient latitude in conformation and diameter of the IR. Our structure of vertebrate IR reveals key insights that are functionally important.

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