Biological Assembly 1  

 3D View: Structure | Electron Density

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

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

Biological Assembly 2  

 3D View: Structure | Electron Density

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 36.55 kDa 
• Atom Count: 2588 
• Residue Count: 312 
• Unique protein chains: 2

4GPL

Structure of Cbl(TKB) bound to a phosphorylated pentapeptide

• DOI: 10.2210/pdb4GPL/pdb

• Classification: Ligase/ligase inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-08-21 Released: 2013-09-18 
• Deposition Author(s): Borgstahl, G., Natarajan, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.248 
• R-Value Work: 0.182 
• R-Value Observed: 0.185 

Literature

The paradox of conformational constraint in the design of Cbl(TKB)-binding peptides.

Kumar, E.A., Chen, Q., Kizhake, S., Kolar, C., Kang, M., Chang, C.E., Borgstahl, G.E., Natarajan, A.

(2013) Sci Rep 3: 1639-1639

• PubMed: 23572190 
• DOI: 10.1038/srep01639
• Primary Citation of Related Structures:  
  4GPL


• PubMed Abstract: 
  

Solving the crystal structure of Cbl(TKB) in complex with a pentapeptide, pYTPEP, revealed that the PEP region adopted a poly-L-proline type II (PPII) helix. An unnatural amino acid termed a proline-templated glutamic acid (ptE) that constrained both the backbone and sidechain to the bound conformation was synthesized and incorporated into the pYTPXP peptide. We estimated imposing structural constraints onto the backbone and sidechain of the peptide and preorganize it to the bound conformation in solution will yield nearly an order of magnitude improvement in activity. NMR studies confirmed that the ptE-containing peptide adopts the PPII conformation, however, competitive binding studies showed an order of magnitude loss of activity. Given the emphasis that is placed on imposing structural constraints, we provide an example to support the contrary. These results point to conformational flexibility at the interface, which have implications in the design of potent Cbl(TKB)-binding peptides.

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Organizational Affiliation: 

Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska 68022, United States.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ACE-PTR-THR-PRO-GLU-PRO, PEPTIDE INHIBITOR	A	7	N/A	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase CBL	B	309	Homo sapiens	Mutation(s): 0  Gene Names: CBL, CBL2, RNF55 EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
Find proteins for P22681 (Homo sapiens) Explore P22681  Go to UniProtKB:  P22681
NIH Common Fund Data Resources
PHAROS:  P22681 GTEx:  ENSG00000110395

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR	A	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.248 
• R-Value Work: 0.182 
• R-Value Observed: 0.185 
• Space Group: P 6

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.574	α = 90
b = 122.574	β = 90
c = 56.231	γ = 120

Software Package:

Software Name	Purpose
CrystalClear	data collection
MOLREP	phasing
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-08-21 
• Released Date: 2013-09-18 
Deposition Author(s): Borgstahl, G., Natarajan, A.

Revision History 

• Version 1.0: 2013-09-18
  Type: Initial release