3JRP | pdb_00003jrp

SEC13 with NUP145C (AA109-179) insertion blade

• PDB DOI: https://doi.org/10.2210/pdb3JRP/pdb

• Classification: TRANSPORT PROTEIN, STRUCTURAL PROTEIN
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-09-08 Released: 2009-10-27 
• Deposition Author(s): Brohawn, S.G., Gogola, M., Schwartz, T.U.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.254 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.219 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

Starting Model: experimental

Literature

Molecular architecture of the Nup84-Nup145C-Sec13 edge element in the nuclear pore complex lattice.

Brohawn, S.G., Schwartz, T.U.

(2009) Nat Struct Mol Biol 16: 1173-1177

• PubMed: 19855394 
• DOI: https://doi.org/10.1038/nsmb.1713
• Primary Citation Related Structures: 
  3JRO, 3JRP


• PubMed Abstract: 
  

  Nuclear pore complexes (NPCs) facilitate all nucleocytoplasmic transport. These massive protein assemblies are modular, with a stable structural scaffold supporting more dynamically attached components. The scaffold is made from multiple copies of the heptameric Y complex and the heteromeric Nic96 complex. We previously showed that members of these core subcomplexes specifically share an ACE1 fold with Sec31 of the COPII vesicle coat, and we proposed a lattice model for the NPC based on this commonality. Here we present the crystal structure of the heterotrimeric 134-kDa complex of Nup84-Nup145C-Sec13 of the Y complex. The heterotypic ACE1 interaction of Nup84 and Nup145C is analogous to the homotypic ACE1 interaction of Sec31 that forms COPII lattice edge elements and is inconsistent with the alternative 'fence-like' NPC model. We construct a molecular model of the Y complex and compare the architectural principles of COPII and NPC lattices.

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Organizational Affiliation: 
• Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 41.7 kDa 
• Atom Count: 2,687 
• Modeled Residue Count: 335 
• Deposited Residue Count: 379 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FUSION PROTEIN OF PROTEIN TRANSPORT PROTEIN SEC13 AND NUCLEOPORIN NUP145	A	379	Saccharomyces cerevisiae	Mutation(s): 0  EC: 3.4.21
UniProt
Find proteins for P49687 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P49687  Go to UniProtKB:  P49687
Find proteins for Q04491 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q04491  Go to UniProtKB:  Q04491
UniProt Groups	Q04491P49687

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.254 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.219 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.28	α = 90
b = 93.878	β = 90
c = 55.047	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-27 
Deposition Author(s): Brohawn, S.G., Gogola, M., Schwartz, T.U.

Revision History  

• Version 1.0: 2009-10-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-06-13
  Changes: Other
• Version 1.3: 2017-08-02
  Changes: Source and taxonomy
• Version 1.4: 2023-09-06
  Changes: Data collection, Database references, Refinement description