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Open data
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Basic information
Entry | Database: PDB / ID: 6lk8 | |||||||||
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Title | Structure of Xenopus laevis Cytoplasmic Ring subunit. | |||||||||
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![]() | STRUCTURAL PROTEIN / building block of vertebrate NPC. | |||||||||
Function / homology | ![]() macromolecule localization / GATOR2 complex / nephron development / macromolecule metabolic process / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / nuclear pore inner ring / nitrogen compound transport / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore outer ring ...macromolecule localization / GATOR2 complex / nephron development / macromolecule metabolic process / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / nuclear pore inner ring / nitrogen compound transport / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore outer ring / nuclear pore organization / COPII vesicle coat / : / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / attachment of mitotic spindle microtubules to kinetochore / structural constituent of nuclear pore / nucleocytoplasmic transport / poly(A)+ mRNA export from nucleus / mitotic metaphase chromosome alignment / NLS-bearing protein import into nucleus / cellular response to nutrient levels / positive regulation of TOR signaling / mRNA transport / mRNA export from nucleus / nuclear pore / positive regulation of TORC1 signaling / cellular response to amino acid starvation / GTPase activator activity / kinetochore / protein import into nucleus / protein transport / nuclear membrane / cell division / lysosomal membrane / structural molecule activity / positive regulation of DNA-templated transcription / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.5 Å | |||||||||
![]() | Shi, Y. / Huang, G. / Yan, C. / Zhang, Y. | |||||||||
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![]() | ![]() Title: Structure of the cytoplasmic ring of the Xenopus laevis nuclear pore complex by cryo-electron microscopy single particle analysis. Authors: Gaoxingyu Huang / Yanqing Zhang / Xuechen Zhu / Chao Zeng / Qifan Wang / Qiang Zhou / Qinghua Tao / Minhao Liu / Jianlin Lei / Chuangye Yan / Yigong Shi / ![]() Abstract: The 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 ...The 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 neighboring 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. | |||||||||
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Structure visualization
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PDBx/mmCIF format | ![]() | 2.2 MB | Display | ![]() |
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PDB format | ![]() | 1.4 MB | Display | ![]() |
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-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 241.1 KB | Display | |
Data in CIF | ![]() | 442.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 0909MC ![]() 0910C ![]() 0911C ![]() 0982C M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Assembly
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Components
-Protein , 11 types, 23 molecules AaCcDdEeFfHhIiJjSTUVKQR
#1: Protein | Mass: 227854.141 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #3: Protein | Mass: 41744.512 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #4: Protein | Mass: 36037.664 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #5: Protein | Mass: 162658.234 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #6: Protein | Mass: 36588.625 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #8: Protein | Mass: 35315.285 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #9: Protein | Mass: 105398.547 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #10: Protein | Mass: 127551.250 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #11: Protein | Mass: 322784.344 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() #12: Protein | | Mass: 5890.252 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #18: Protein | Mass: 33293.949 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Nuclear pore complex protein ... , 2 types, 4 molecules BbGg
#2: Protein | Mass: 75160.047 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #7: Protein | Mass: 105079.148 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Nup214 complex coiled coil region 1, helix ... , 2 types, 2 molecules LM
#13: Protein | Mass: 6826.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#14: Protein | Mass: 6230.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Nup214 complex Coiled coil region 2, helix ... , 3 types, 3 molecules NOP
#15: Protein/peptide | Mass: 2656.265 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#16: Protein/peptide | Mass: 2996.685 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#17: Protein/peptide | Mass: 2230.741 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Details
Sequence details | Authors know the chains K,L,M and N,O,P come from the coiled-coil region from Nup88,Nup62 and ...Authors know the chains K,L,M and N,O,P come from the coiled-coil region from Nup88,Nup62 and Nup214 (termed Nup214 complex). However, at the current resolution, the three helices of the coiled coil cannot be distinguished a nd there are no crystal structure of the three proteins. (1) Xl_Nup214_Q9PVZ2 MEDDTDLPPE |
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