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 1.4 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: https://doi.org/10.1038/nature15381
  • Primary Citation of Related Structures:  
    5A9Q

  • 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 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
MoleculeChains Sequence LengthOrganismDetailsImage
NUCLEOPORIN NUP43A [auth 0],
BA [auth R],
J [auth 9],
S [auth I]
380Homo sapiensMutation(s): 0 
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PHAROS:  Q8NFH3
GTEx:  ENSG00000120253 
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UniProt GroupQ8NFH3
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NUCLEAR PORE COMPLEX PROTEIN NUP160B [auth 1],
CA [auth S],
KA [auth a],
T [auth J]
1,436Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000030066 
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UniProt GroupQ12769
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
NUCLEOPORIN NUP37C [auth 2],
DA [auth T],
LA [auth b],
U [auth K]
326Homo sapiensMutation(s): 0 
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PHAROS:  Q8NFH4
GTEx:  ENSG00000075188 
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UniProt GroupQ8NFH4
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
NUCLEAR PORE COMPLEX PROTEIN NUP133D [auth 3],
EA [auth U],
M [auth C],
V [auth L]
1,156Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000069248 
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UniProt GroupQ8WUM0
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
NUCLEAR PORE COMPLEX PROTEIN NUP107E [auth 4],
FA [auth V],
N [auth D],
W [auth M]
925Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000111581 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
NUCLEAR PORE COMPLEX PROTEIN NUP96F [auth 5],
GA [auth W],
O [auth E],
X [auth N]
937Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000110713 
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UniProt GroupP52948
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN SEC13 HOMOLOGG [auth 6],
HA [auth X],
P [auth F],
Y [auth O]
322Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000157020 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
NUCLEOPORIN SEH1H [auth 7],
IA [auth Y],
Q [auth G],
Z [auth P]
360Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000085415 
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UniProt GroupQ96EE3
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
NUCLEAR PORE COMPLEX PROTEIN NUP85AA [auth Q],
I [auth 8],
JA [auth Z],
R [auth H]
656Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125450 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
NUCLEAR PORE COMPLEX PROTEIN NUP155K [auth A],
L [auth B]
1,391Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000113569 
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 23.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: TOMOGRAPHY 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONAV3
RECONSTRUCTIONIMOD
RECONSTRUCTIONTOM Toolbox

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • 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
  • Version 1.4: 2024-05-08
    Changes: Data collection, Database references