1LDK

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.331 
  • R-Value Work: 0.289 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


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

  • DOI: 10.1038/416703a
  • Structures With Same Primary Citation

  • 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 Cul ...

    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.


    Organizational Affiliation

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



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CULLIN HOMOLOG
A
396Homo sapiensMutation(s): 0 
Gene Names: CUL1
Find proteins for Q13616 (Homo sapiens)
Go to UniProtKB:  Q13616
NIH Common Fund Data Resources
PHAROS  Q13616

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
ring-box protein 1
C
90Homo sapiensMutation(s): 0 
Gene Names: RBX1RNF75ROC1
EC: 2.3.2.27 (UniProt), 2.3.2.32 (UniProt)
Find proteins for P62877 (Homo sapiens)
Go to UniProtKB:  P62877
NIH Common Fund Data Resources
PHAROS  P62877

Find similar proteins by: Sequence  |  Structure

Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
CYCLIN A/CDK2-ASSOCIATED PROTEIN P19
D
133Homo sapiensMutation(s): 0 
Gene Names: SKP1EMC19OCP2SKP1ATCEB1L
Find proteins for P63208 (Homo sapiens)
Go to UniProtKB:  P63208
NIH Common Fund Data Resources
PHAROS  P63208

Find similar proteins by: Sequence  |  Structure

Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
SKP2-like protein type gamma
E
41Homo sapiensMutation(s): 0 
Gene Names: SKP2FBXL1
Find proteins for Q13309 (Homo sapiens)
Go to UniProtKB:  Q13309
NIH Common Fund Data Resources
PHAROS  Q13309

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CULLIN HOMOLOG
B
366Homo sapiensMutation(s): 0 
Gene Names: CUL1
Find proteins for Q13616 (Homo sapiens)
Go to UniProtKB:  Q13616
NIH Common Fund Data Resources
PHAROS  Q13616
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.331 
  • R-Value Work: 0.289 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 219.378α = 90
b = 50.529β = 90
c = 158.61γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

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: 2019-11-20
    Changes: Advisory, Database references, Derived calculations