6WNX

FBXW11-SKP1 in complex with a pSer33/pSer37 Beta-Catenin peptide

• PDB DOI: https://doi.org/10.2210/pdb6WNX/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2020-04-23 Released: 2020-05-06 
• Deposition Author(s): Ivanochko, D., Edwards, A.M., Bountra, C., Arrowsmith, C.H., Boettcher, J., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.251 
• R-Value Work: 0.206 
• R-Value Observed: 0.208 

Starting Model: experimental

Literature

FBXW11-SKP1 in complex with a pSer33/pSer37 Beta-Catenin peptide

Ivanochko, D., Edwards, A.M., Bountra, C., Arrowsmith, C.H., Boettcher, J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Biological Assembly Evidence: surface plasmon resonance, gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: surface plasmon resonance, gel filtration

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: surface plasmon resonance, gel filtration

Macromolecule Content

• Total Structure Weight: 201.11 kDa 
• Atom Count: 13,651 
• Modelled Residue Count: 1,659 
• Deposited Residue Count: 1,749 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
F-box/WD repeat-containing protein 11	A, D, G	429	Homo sapiens	Mutation(s): 0  Gene Names: FBXW11, BTRCP2, FBW1B, FBXW1B, KIAA0696
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UKB1 (Homo sapiens) Explore Q9UKB1  Go to UniProtKB:  Q9UKB1
PHAROS:  Q9UKB1 GTEx:  ENSG00000072803

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
S-phase kinase-associated protein 1	B, E, H	145	Homo sapiens	Mutation(s): 0  Gene Names: SKP1, EMC19, OCP2, SKP1A, TCEB1L
UniProt & NIH Common Fund Data Resources
Find proteins for P63208 (Homo sapiens) Explore P63208  Go to UniProtKB:  P63208
PHAROS:  P63208 GTEx:  ENSG00000113558

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Catenin beta-1	C, F, I	9	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P35222 (Homo sapiens) Explore P35222  Go to UniProtKB:  P35222
PHAROS:  P35222 GTEx:  ENSG00000168036

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	J [auth A], K [auth A], L [auth A], N [auth B], O [auth D], Q [auth G]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	M [auth A], P [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	C, F, I	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.251 
• R-Value Work: 0.206 
• R-Value Observed: 0.208 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.732	α = 90
b = 81.866	β = 92.92
c = 133.198	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-05-06 
Deposition Author(s): Ivanochko, D., Edwards, A.M., Bountra, C., Arrowsmith, C.H., Boettcher, J., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2020-05-06
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-30
  Changes: Structure summary