Biological Assembly 1  

 3D View: Structure | Validation Report

Pseudo Symmetry: Cyclic - C8  (3D View)
Pseudo Stoichiometry: Hetero 304-mer - A128B32C32D32E32F32G16 Global Symmetry: Cyclic - C8  (3D View)
Global Stoichiometry: Hetero 304-mer - A32B32C32D32E32F32G32H32I32J16 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 3243.76 kDa 
• Atom Count: 95884 
• Modelled Residue Count: 19350 
• Deposited Residue Count: 28774 
• Unique protein chains: 10

5A9Q

Human nuclear pore complex

• DOI: 10.2210/pdb5A9Q/pdb
• EMDataResource: EMD-3103

• Classification: TRANSPORT PROTEIN
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2015-07-22 Released: 2015-09-30 
• Deposition Author(s): 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.

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Experimental Data Snapshot

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

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

• PubMed: 26416747 
• DOI: 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NUCLEOPORIN NUP43	A [auth 0], J [auth 9], S [auth I], BA [auth R]	380	Homo sapiens	Mutation(s): 0  Gene Names: NUP43
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NFH3 (Homo sapiens) Explore Q8NFH3  Go to UniProtKB:  Q8NFH3
PHAROS:  Q8NFH3 GTEx:  ENSG00000120253

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NUCLEAR PORE COMPLEX PROTEIN NUP160	B [auth 1], T [auth J], CA [auth S], KA [auth a]	1436	Homo sapiens	Mutation(s): 0  Gene Names: NUP160, KIAA0197, NUP120
UniProt & NIH Common Fund Data Resources
Find proteins for Q12769 (Homo sapiens) Explore Q12769  Go to UniProtKB:  Q12769
PHAROS:  Q12769 GTEx:  ENSG00000030066

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
NUCLEOPORIN NUP37	C [auth 2], U [auth K], DA [auth T], LA [auth b]	326	Homo sapiens	Mutation(s): 0  Gene Names: NUP37
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NFH4 (Homo sapiens) Explore Q8NFH4  Go to UniProtKB:  Q8NFH4
PHAROS:  Q8NFH4 GTEx:  ENSG00000075188

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
NUCLEAR PORE COMPLEX PROTEIN NUP133	D [auth 3], M [auth C], V [auth L], EA [auth U]	1156	Homo sapiens	Mutation(s): 0  Gene Names: NUP133
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WUM0 (Homo sapiens) Explore Q8WUM0  Go to UniProtKB:  Q8WUM0
PHAROS:  Q8WUM0 GTEx:  ENSG00000069248

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
NUCLEAR PORE COMPLEX PROTEIN NUP107	E [auth 4], N [auth D], W [auth M], FA [auth V]	925	Homo sapiens	Mutation(s): 0  Gene Names: NUP107
UniProt & NIH Common Fund Data Resources
Find proteins for P57740 (Homo sapiens) Explore P57740  Go to UniProtKB:  P57740
PHAROS:  P57740 GTEx:  ENSG00000111581

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
NUCLEAR PORE COMPLEX PROTEIN NUP96	F [auth 5], O [auth E], X [auth N], GA [auth W]	937	Homo sapiens	Mutation(s): 0  Gene Names: NUP98, ADAR2 EC: 3.4.21
UniProt & NIH Common Fund Data Resources
Find proteins for P52948 (Homo sapiens) Explore P52948  Go to UniProtKB:  P52948
PHAROS:  P52948 GTEx:  ENSG00000110713

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN SEC13 HOMOLOG	G [auth 6], P [auth F], Y [auth O], HA [auth X]	322	Homo sapiens	Mutation(s): 0  Gene Names: SEC13, D3S1231E, SEC13A, SEC13L1, SEC13R
UniProt & NIH Common Fund Data Resources
Find proteins for P55735 (Homo sapiens) Explore P55735  Go to UniProtKB:  P55735
PHAROS:  P55735 GTEx:  ENSG00000157020

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
NUCLEOPORIN SEH1	H [auth 7], Q [auth G], Z [auth P], IA [auth Y]	360	Homo sapiens	Mutation(s): 0  Gene Names: SEH1L, SEC13L, SEH1
UniProt & NIH Common Fund Data Resources
Find proteins for Q96EE3 (Homo sapiens) Explore Q96EE3  Go to UniProtKB:  Q96EE3
PHAROS:  Q96EE3 GTEx:  ENSG00000085415

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
NUCLEAR PORE COMPLEX PROTEIN NUP85	I [auth 8], R [auth H], AA [auth Q], JA [auth Z]	656	Homo sapiens	Mutation(s): 0  Gene Names: NUP85, NUP75, PCNT1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BW27 (Homo sapiens) Explore Q9BW27  Go to UniProtKB:  Q9BW27
PHAROS:  Q9BW27 GTEx:  ENSG00000125450

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
NUCLEAR PORE COMPLEX PROTEIN NUP155	K [auth A], L [auth B]	1391	Homo sapiens	Mutation(s): 0  Gene Names: NUP155, KIAA0791
UniProt & NIH Common Fund Data Resources
Find proteins for O75694 (Homo sapiens) Explore O75694  Go to UniProtKB:  O75694
PHAROS:  O75694 GTEx:  ENSG00000113569

Experimental Data & Validation

Experimental Data

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-07-22 
• Released Date: 2015-09-30 
Deposition Author(s): 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.

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