7WB4

Cryo-EM structure of the NR subunit from X. laevis NPC


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Cryo-EM structure of the nuclear ring from Xenopus laevis nuclear pore complex.

Huang, G.Zhan, X.Zeng, C.Zhu, X.Liang, K.Zhao, Y.Wang, P.Wang, Q.Zhou, Q.Tao, Q.Liu, M.Lei, J.Yan, C.Shi, Y.

(2022) Cell Res 32: 349-358

  • DOI: 10.1038/s41422-021-00610-w
  • Primary Citation of Related Structures:  
    7WB4

  • PubMed Abstract: 
  • Nuclear pore complex (NPC) shuttles cargo across the nuclear envelope. Here we present single-particle cryo-EM structure of the nuclear ring (NR) subunit from Xenopus laevis NPC at an average resolution of 5.6 Å. The NR subunit comprises two 10-membered Y complexes, each with the nucleoporin ELYS closely associating with Nup160 and Nup37 of the long arm ...

    Nuclear pore complex (NPC) shuttles cargo across the nuclear envelope. Here we present single-particle cryo-EM structure of the nuclear ring (NR) subunit from Xenopus laevis NPC at an average resolution of 5.6 Å. The NR subunit comprises two 10-membered Y complexes, each with the nucleoporin ELYS closely associating with Nup160 and Nup37 of the long arm. Unlike the cytoplasmic ring (CR) or inner ring (IR), the NR subunit contains only one molecule each of Nup205 and Nup93. Nup205 binds both arms of the Y complexes and interacts with the stem of inner Y complex from the neighboring subunit. Nup93 connects the stems of inner and outer Y complexes within the same NR subunit, and places its N-terminal extended helix into the axial groove of Nup205 from the neighboring subunit. Together with other structural information, we have generated a composite atomic model of the central ring scaffold that includes the NR, IR, and CR. The IR is connected to the two outer rings mainly through Nup155. This model facilitates functional understanding of vertebrate NPC.


    Organizational Affiliation

    Tsinghua University-Peking University Joint Center for Life Sciences; School of Life Sciences, Tsinghua University, Beijing, China. syg@westlake.edu.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
outer Nup133A [auth J],
Y [auth P],
X [auth j],
W [auth p]
1,140Xenopus laevisMutation(s): 0 
Gene Names: nup133.L
UniProt
Find proteins for A0A1L8H1I9 (Xenopus laevis)
Explore A0A1L8H1I9 
Go to UniProtKB:  A0A1L8H1I9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1L8H1I9
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear pore complex protein Nup85B,
F [auth b]
653Xenopus laevisMutation(s): 0 
Gene Names: nup85
UniProt
Find proteins for Q68FJ0 (Xenopus laevis)
Explore Q68FJ0 
Go to UniProtKB:  Q68FJ0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ68FJ0
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
MGC154553 proteinC,
G [auth c]
375Xenopus laevisMutation(s): 0 
Gene Names: nup43.SMGC154553nup43
UniProt
Find proteins for Q05AW3 (Xenopus laevis)
Explore Q05AW3 
Go to UniProtKB:  Q05AW3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ05AW3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
MGC83926 proteinD [auth F],
J [auth f]
326Xenopus laevisMutation(s): 0 
Gene Names: nup37.LMGC83926nup37
UniProt
Find proteins for Q66IZ6 (Xenopus laevis)
Explore Q66IZ6 
Go to UniProtKB:  Q66IZ6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ66IZ6
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleoporin SEH1-BT [auth D],
E [auth d]
360Xenopus laevisMutation(s): 0 
Gene Names: seh1l-b
UniProt
Find proteins for Q6GNF1 (Xenopus laevis)
Explore Q6GNF1 
Go to UniProtKB:  Q6GNF1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6GNF1
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
outer Nup160H [auth E],
I [auth e]
1,435Xenopus laevisMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Nup155-prov proteinK1,388Xenopus laevisMutation(s): 0 
Gene Names: nup155.Lnup155
UniProt
Find proteins for Q7ZWL0 (Xenopus laevis)
Explore Q7ZWL0 
Go to UniProtKB:  Q7ZWL0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7ZWL0
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
GATOR complex protein SEC13L [auth H],
N [auth h]
320Xenopus laevisMutation(s): 0 
Gene Names: sec13.Ssec13sec13l1
UniProt
Find proteins for Q7ZYJ8 (Xenopus laevis)
Explore Q7ZYJ8 
Go to UniProtKB:  Q7ZYJ8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7ZYJ8
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear pore complex protein Nup96M [auth G],
O [auth g]
923Xenopus laevisMutation(s): 0 
Gene Names: nup98l.S
UniProt
Find proteins for A0A8J1MFV7 (Xenopus laevis)
Explore A0A8J1MFV7 
Go to UniProtKB:  A0A8J1MFV7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A8J1MFV7
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear pore complex proteinP [auth I],
V [auth M],
Q [auth i]
916Xenopus laevisMutation(s): 0 
Gene Names: nup107.Snup107
UniProt
Find proteins for A0A8J0UTW4 (Xenopus laevis)
Explore A0A8J0UTW4 
Go to UniProtKB:  A0A8J0UTW4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A8J0UTW4
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear pore complex protein Nup93R [auth L],
U [auth O]
820Xenopus laevisMutation(s): 0 
Gene Names: nup93
UniProt
Find proteins for Q7ZX96 (Xenopus laevis)
Explore Q7ZX96 
Go to UniProtKB:  Q7ZX96
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7ZX96
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
MGC83295 proteinS [auth A]2,011Xenopus laevisMutation(s): 0 
Gene Names: nup205.SMGC83295nup205nup205.Lxnup205
UniProt
Find proteins for Q642R6 (Xenopus laevis)
Explore Q642R6 
Go to UniProtKB:  Q642R6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ642R6
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Protein ELYSAA [auth N],
Z [auth n]
2,408Xenopus laevisMutation(s): 0 
Gene Names: ahctf1elys
UniProt
Find proteins for Q5U249 (Xenopus laevis)
Explore Q5U249 
Go to UniProtKB:  Q5U249
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5U249
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-02
    Type: Initial release
  • Version 1.1: 2022-04-20
    Changes: Database references