1LDD | pdb_00001ldd

Structure of the Cul1-Rbx1-Skp1-F boxSkp2 SCF Ubiquitin Ligase Complex

• PDB DOI: https://doi.org/10.2210/pdb1LDD/pdb

• Classification: LIGASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2002-04-08 Released: 2002-05-08 
• Deposition Author(s): Zheng, N., Schulman, B.A., Song, L., Miller, J.J., Jeffrey, P.D., Wang, P., Chu, C., Koepp, D.M., Elledge, S.J., Pagano, M., Conaway, R.C., Conaway, J.W., Harper, J.W., Pavletich, N.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.266 (Depositor) 
• R-Value Work: 
  0.205 (Depositor) 

Literature

Structure of the Cul1-Rbx1-Skp1-F boxSkp2 SCF ubiquitin ligase complex.

Zheng, N., Schulman, B.A., Song, L., Miller, J.J., Jeffrey, P.D., Wang, P., Chu, C., Koepp, D.M., Elledge, S.J., Pagano, M., Conaway, R.C., Conaway, J.W., Harper, J.W., Pavletich, N.P.

(2002) Nature 416: 703-709

• PubMed: 11961546 
• DOI: https://doi.org/10.1038/416703a
• Primary Citation Related Structures: 
  1LDD, 1LDJ, 1LDK


• PubMed Abstract: 
  

  SCF complexes are the largest family of E3 ubiquitin-protein ligases and mediate the ubiquitination of diverse regulatory and signalling proteins. Here we present the crystal structure of the Cul1-Rbx1-Skp1-F boxSkp2 SCF complex, which shows that Cul1 is an elongated protein that consists of a long stalk and a globular domain. The globular domain binds the RING finger protein Rbx1 through an intermolecular beta-sheet, forming a two-subunit catalytic core that recruits the ubiquitin-conjugating enzyme. The long stalk, which consists of three repeats of a novel five-helix motif, binds the Skp1-F boxSkp2 protein substrate-recognition complex at its tip. Cul1 serves as a rigid scaffold that organizes the Skp1-F boxSkp2 and Rbx1 subunits, holding them over 100 A apart. The structure suggests that Cul1 may contribute to catalysis through the positioning of the substrate and the ubiquitin-conjugating enzyme, and this model is supported by Cul1 mutations designed to eliminate the rigidity of the scaffold.

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Organizational Affiliation: 
• Cellular Biochemistry and Biophysics Program, Memorial Sloan-Kettering Cancer Center, New York 10021, USA.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 34.27 kDa 
• Atom Count: 2,416 
• Modeled Residue Count: 296 
• Deposited Residue Count: 296 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Anaphase Promoting Complex	A, B, C, D	74	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for Q12440 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12440  Go to UniProtKB:  Q12440

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.266 (Depositor) 
• R-Value Work:  0.205 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.7	α = 90
b = 72.9	β = 90
c = 79.8	γ = 90

Software Package:

Software Name	Purpose
SHELXS	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-05-08 
Deposition Author(s): Zheng, N., Schulman, B.A., Song, L., Miller, J.J., Jeffrey, P.D., Wang, P., Chu, C., Koepp, D.M., Elledge, S.J., Pagano, M., Conaway, R.C., Conaway, J.W., Harper, J.W., Pavletich, N.P.

Revision History  

• Version 1.0: 2002-05-08
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references