5A9Q

Human nuclear pore complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 23.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: TOMOGRAPHY 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

In Situ Structural Analysis of the Human Nuclear Pore Complex

Von Appen, A.Kosinski, J.Sparks, L.Ori, A.Diguilio, A.Vollmer, B.Mackmull, M.Banterle, N.Parca, L.Kastritis, P.Buczak, K.Mosalaganti, S.Hagen, W.Andres-Pons, A.Lemke, E.A.Bork, P.Antonin, W.Glavy, J.S.Bui, K.H.Beck, M.

(2015) Nature 526: 140

  • DOI: 10.1038/nature15381
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Nuclear pore complexes are fundamental components of all eukaryotic cells that mediate nucleocytoplasmic exchange. Determining their 110-megadalton structure imposes a formidable challenge and requires in situ structural biology approaches. Of approx ...

    Nuclear pore complexes are fundamental components of all eukaryotic cells that mediate nucleocytoplasmic exchange. Determining their 110-megadalton structure imposes a formidable challenge and requires in situ structural biology approaches. Of approximately 30 nucleoporins (Nups), 15 are structured and form the Y and inner-ring complexes. These two major scaffolding modules assemble in multiple copies into an eight-fold rotationally symmetric structure that fuses the inner and outer nuclear membranes to form a central channel of ~60 nm in diameter. The scaffold is decorated with transport-channel Nups that often contain phenylalanine-repeat sequences and mediate the interaction with cargo complexes. Although the architectural arrangement of parts of the Y complex has been elucidated, it is unclear how exactly it oligomerizes in situ. Here we combine cryo-electron tomography with mass spectrometry, biochemical analysis, perturbation experiments and structural modelling to generate, to our knowledge, the most comprehensive architectural model of the human nuclear pore complex to date. Our data suggest previously unknown protein interfaces across Y complexes and to inner-ring complex members. We show that the transport-channel Nup358 (also known as Ranbp2) has a previously unanticipated role in Y-complex oligomerization. Our findings blur the established boundaries between scaffold and transport-channel Nups. We conclude that, similar to coated vesicles, several copies of the same structural building block--although compositionally identical--engage in different local sets of interactions and conformations.


    Organizational Affiliation

    European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NUCLEOPORIN NUP43
0, 9, I, R
380Homo sapiensMutation(s): 0 
Gene Names: NUP43
Find proteins for Q8NFH3 (Homo sapiens)
Go to UniProtKB:  Q8NFH3
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PHAROS  Q8NFH3
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
NUCLEOPORIN NUP37
2, K, T, b
326Homo sapiensMutation(s): 0 
Gene Names: NUP37
Find proteins for Q8NFH4 (Homo sapiens)
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PHAROS  Q8NFH4
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
NUCLEAR PORE COMPLEX PROTEIN NUP107
4, D, M, V
925Homo sapiensMutation(s): 0 
Gene Names: NUP107
Find proteins for P57740 (Homo sapiens)
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PHAROS  P57740
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
NUCLEAR PORE COMPLEX PROTEIN NUP96
5, E, N, W
937Homo sapiensMutation(s): 0 
Gene Names: NUP98ADAR2
EC: 3.4.21
Find proteins for P52948 (Homo sapiens)
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PHAROS  P52948
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
PROTEIN SEC13 HOMOLOG
6, F, O, X
322Homo sapiensMutation(s): 0 
Gene Names: SEC13D3S1231ESEC13ASEC13L1SEC13R
Find proteins for P55735 (Homo sapiens)
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PHAROS  P55735
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
NUCLEOPORIN SEH1
7, G, P, Y
360Homo sapiensMutation(s): 0 
Gene Names: SEH1LSEC13LSEH1
Find proteins for Q96EE3 (Homo sapiens)
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PHAROS  Q96EE3
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
NUCLEAR PORE COMPLEX PROTEIN NUP155
A, B
1391Homo sapiensMutation(s): 0 
Gene Names: NUP155KIAA0791
Find proteins for O75694 (Homo sapiens)
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PHAROS  O75694
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
NUCLEAR PORE COMPLEX PROTEIN NUP160
1, J, S, a
1436Homo sapiensMutation(s): 0 
Gene Names: NUP160KIAA0197NUP120
Find proteins for Q12769 (Homo sapiens)
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PHAROS  Q12769
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
NUCLEAR PORE COMPLEX PROTEIN NUP133
3, C, L, U
1156Homo sapiensMutation(s): 0 
Gene Names: NUP133
Find proteins for Q8WUM0 (Homo sapiens)
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PHAROS  Q8WUM0
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
NUCLEAR PORE COMPLEX PROTEIN NUP85
8, H, Q, Z
656Homo sapiensMutation(s): 0 
Gene Names: NUP85NUP75PCNT1
Find proteins for Q9BW27 (Homo sapiens)
Go to UniProtKB:  Q9BW27
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PHAROS  Q9BW27
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 23.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: TOMOGRAPHY 

Structure Validation

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Entry History 

Revision History 

  • Version 1.0: 2015-09-30
    Type: Initial release
  • Version 1.1: 2015-10-07
    Changes: Database references
  • Version 1.2: 2015-10-14
    Changes: Database references
  • Version 1.3: 2017-08-23
    Changes: Data collection