Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 33.34 kDa 
• Atom Count: 1804 
• Modelled Residue Count: 213 
• Deposited Residue Count: 288 
• Unique protein chains: 1

3KFO

Crystal structure of the C-terminal domain from the nuclear pore complex component NUP133 from Saccharomyces cerevisiae

• PDB DOI: 10.2210/pdb3KFO/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-10-27 Released: 2010-01-26 
• Deposition Author(s): Sampathkumar, P., Bonanno, J.B., Miller, S., Bain, K., Dickey, M., Gheyi, T., Almo, S.C., Rout, M., Sali, A., Phillips, J., Pieper, U., Fernandez-Martinez, J., Franke, J.D., Atwell, S., Thompson, D.A., Emtage, J.S., Wasserman, S., Sauder, J.M., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.245 
• R-Value Work: 0.191 
• R-Value Observed: 0.193 

Literature

Structure of the C-terminal domain of Saccharomyces cerevisiae Nup133, a component of the nuclear pore complex.

Sampathkumar, P., Gheyi, T., Miller, S.A., Bain, K.T., Dickey, M., Bonanno, J.B., Kim, S.J., Phillips, J., Pieper, U., Fernandez-Martinez, J., Franke, J.D., Martel, A., Tsuruta, H., Atwell, S., Thompson, D.A., Emtage, J.S., Wasserman, S.R., Rout, M.P., Sali, A., Sauder, J.M., Burley, S.K.

(2011) Proteins 79: 1672-1677

• PubMed: 21365675 
• DOI: 10.1002/prot.22973
• Primary Citation of Related Structures:  
  3KFO

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoporin NUP133	A	288	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: NUP133, RAT3, YKR082W, YKR402
UniProt
Find proteins for P36161 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P36161  Go to UniProtKB:  P36161

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.245 
• R-Value Work: 0.191 
• R-Value Observed: 0.193 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.433	α = 90
b = 52.678	β = 90
c = 76.674	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SCALA	data scaling
SHELX	phasing
SHELXD	phasing
SHELXE	model building

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-10-27 
• Released Date: 2010-01-26 
Deposition Author(s): Sampathkumar, P., Bonanno, J.B., Miller, S., Bain, K., Dickey, M., Gheyi, T., Almo, S.C., Rout, M., Sali, A., Phillips, J., Pieper, U., Fernandez-Martinez, J., Franke, J.D., Atwell, S., Thompson, D.A., Emtage, J.S., Wasserman, S., Sauder, J.M., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2010-01-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2018-11-21
  Changes: Data collection, Structure summary
• Version 1.4: 2020-07-29
  Changes: Derived calculations, Structure summary
• Version 1.5: 2021-02-10
  Changes: Database references, Structure summary