Biological Assembly 1  

 3D View: Structure | Electron Density

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 8-mer - ABCDEFGH Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 8-mer -A2B2CDEF 

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

Macromolecule Content

• Total Structure Weight: 454644.03 
• Atom Count: 26139 
• Residue Count: 4000 
• Unique protein chains: 8

4XMM

Structure of the yeast coat nucleoporin complex, space group C2

• DOI: 10.2210/pdb4XMM/pdb

• Classification: Transport Protein/Immune System
• Organism(s): Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
• Expression System: Escherichia coli


• Deposited: 2015-01-14 Released: 2015-03-25 
• Deposition Author(s): Stuwe, T., Correia, A.R., Lin, D.H., Paduch, M., Lu, V.T., Kossiakoff, A.A., Hoelz, A.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences 

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 7.384 Å
• R-Value Free: 0.353 
• R-Value Work: 0.330 

Literature

Nuclear pores. Architecture of the nuclear pore complex coat.

Stuwe, T., Correia, A.R., Lin, D.H., Paduch, M., Lu, V.T., Kossiakoff, A.A., Hoelz, A.

(2015) Science 347: 1148-1152

• PubMed: 25745173 
• DOI: 10.1126/science.aaa4136
• Primary Citation of Related Structures:  
  4XMN


• PubMed Abstract: 
  

The nuclear pore complex (NPC) constitutes the sole gateway for bidirectional nucleocytoplasmic transport. Despite half a century of structural characterization, the architecture of the NPC remains unknown. Here we present the crystal structure of a reconstituted ~400-kilodalton coat nucleoporin complex (CNC) from Saccharomyces cerevisiae at a 7.4 angstrom resolution. The crystal structure revealed a curved Y-shaped architecture and the molecular details of the coat nucleoporin interactions forming the central "triskelion" of the Y. A structural comparison of the yeast CNC with an electron microscopy reconstruction of its human counterpart suggested the evolutionary conservation of the elucidated architecture. Moreover, 32 copies of the CNC crystal structure docked readily into a cryoelectron tomographic reconstruction of the fully assembled human NPC, thereby accounting for ~16 megadalton of its mass.

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Organizational Affiliation: 

Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA. These authors contributed equally to this work.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Protein transport protein SEC13	A	297	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Gene Names: SEC13 (ANU3)
Find proteins for Q04491 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to Gene View: SEC13 Go to UniProtKB:  Q04491

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Nucleoporin NUP145	B	652	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Gene Names: NUP145 (RAT10) EC: 3.4.21.-
Find proteins for P49687 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P49687

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Nucleoporin SEH1	C	349	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Gene Names: SEH1
Find proteins for P53011 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P53011

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
Nucleoporin NUP85	D	715	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Gene Names: NUP85 (RAT9)
Find proteins for P46673 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to Gene View: NUP85 Go to UniProtKB:  P46673

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details
Nucleoporin NUP120	E	1045	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Gene Names: NUP120 (RAT2)
Find proteins for P35729 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P35729

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details
Nucleoporin NUP84	F	454	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Gene Names: NUP84
Find proteins for P52891 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P52891

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details
Antibody 57 heavy chain	H	271	N/A
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details
Antibody 57 light chain	L	217	N/A
Protein Feature View is not available: No corresponding UniProt sequence found.

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 7.384 Å
• R-Value Free: 0.353 
• R-Value Work: 0.330 
• Space Group: C 1 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 210.645	α = 90.00
b = 186.297	β = 100.85
c = 199.570	γ = 90.00

Software Package:

Software Name	Purpose
XDS	data scaling
PHENIX	refinement
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2015-01-14 
• Released Date: 2015-03-25 
• Deposition Author(s): Stuwe, T., Correia, A.R., Lin, D.H., Paduch, M., Lu, V.T., Kossiakoff, A.A., Hoelz, A.

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Funding Organization	Country	Grant Number
National Institutes of Health/National Institute of General Medical Sciences	United States	5 T32 GM07616
National Institutes of Health/National Institute of General Medical Sciences	United States	U01 GM094588
National Institutes of Health/National Institute of General Medical Sciences	United States	U54 GM087519

Revision History 

• Version 1.0: 2015-03-25
  Type: Initial release
• Version 1.1: 2015-04-01
  Type: Structure summary
• Version 1.2: 2016-02-03
  Type: Database references
• Version 1.3: 2016-07-20
  Type: Data collection
• Version 1.4: 2017-09-20
  Type: Author supporting evidence, Derived calculations