Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 14.92 kDa 
• Atom Count: 1109 
• Residue Count: 125 
• Unique protein chains: 2

2BZ8

N-terminal Sh3 domain of CIN85 bound to Cbl-b peptide

• DOI: 10.2210/pdb2BZ8/pdb

• Classification: SH3 DOMAIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-08-12 Released: 2005-10-05 
• Deposition Author(s): Cardenes, N., Moncalian, G., Bravo, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.271 
• R-Value Work: 0.221 
• R-Value Observed: 0.221 

Literature

Cbl Promotes Clustering of Endocytic Adaptor Proteins

Jozic, D., Cardenes, N., Lissanu-Deribe, Y., Moncalian, G., Hoeller, D., Groemping, Y., Dikic, I., Rittinger, K., Bravo, J.

(2005) Nat Struct Mol Biol 12: 972

• PubMed: 16228008 
• DOI: 10.1038/nsmb1000
• Primary Citation of Related Structures:  
  2AK5, 2BZ8


• PubMed Abstract: 
  

The ubiquitin ligases c-Cbl and Cbl-b play a crucial role in receptor downregulation by mediating multiple monoubiquitination of receptors and promoting their sorting for lysosomal degradation. Their function is modulated through interactions with regulatory proteins including CIN85 and PIX, which recognize a proline-arginine motif in Cbl and thus promote or inhibit receptor endocytosis. We report the structures of SH3 domains of CIN85 and beta-PIX in complex with a proline-arginine peptide from Cbl-b. Both structures reveal a heterotrimeric complex containing two SH3 domains held together by a single peptide. Trimerization also occurs in solution and is facilitated by the pseudo-symmetrical peptide sequence. Moreover, ternary complexes of CIN85 and Cbl are formed in vivo and are important for the ability of Cbl to promote epidermal growth factor receptor (EGFR) downregulation. These results provide molecular explanations for a novel mechanism by which Cbl controls receptor downregulation.

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Organizational Affiliation: 

Division of Protein Structure, National Institute for Medical Research, The Ridgeway, London NW7 1AA, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SH3-DOMAIN KINASE BINDING PROTEIN 1	A, B	58	Homo sapiens	Mutation(s): 0  Gene Names: SH3KBP1, CIN85
Find proteins for Q96B97 (Homo sapiens) Explore Q96B97  Go to UniProtKB:  Q96B97
NIH Common Fund Data Resources
PHAROS  Q96B97 GTEx  ENSG00000147010

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SIGNAL TRANSDUCTION PROTEIN CBL-B SH3-BINDING PROTEIN CBL-B, RING FINGER PROTEIN 56, CBL-B	C	11	Homo sapiens	Mutation(s): 0  Gene Names: CBLB, RNF56, Nbla00127 EC: 2.3.2.27
Find proteins for Q13191 (Homo sapiens) Explore Q13191  Go to UniProtKB:  Q13191
NIH Common Fund Data Resources
PHAROS  Q13191 GTEx  ENSG00000114423

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	A, B	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.271 
• R-Value Work: 0.221 
• R-Value Observed: 0.221 
• Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.158	α = 90
b = 51.158	β = 90
c = 97.472	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-08-12 
• Released Date: 2005-10-05 
Deposition Author(s): Cardenes, N., Moncalian, G., Bravo, J.

Revision History 

• Version 1.0: 2005-10-05
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-04-04
  Changes: Data collection