2MG9 | pdb_00002mg9

Truncated EGF-A

• PDB DOI: https://doi.org/10.2210/pdb2MG9/pdb
• BMRB: 19593

• Classification: METAL BINDING PROTEIN
• Organism(s): Homo sapiens
• Mutation(s): Yes 


• Deposited: 2013-10-30 Released: 2014-04-02 
• Deposition Author(s): Schroeder, C.I., Rosengren, K.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

Design and Synthesis of Truncated EGF-A Peptides that Restore LDL-R Recycling in the Presence of PCSK9 In Vitro.

Schroeder, C.I., Swedberg, J.E., Withka, J.M., Rosengren, K.J., Akcan, M., Clayton, D.J., Daly, N.L., Cheneval, O., Borzilleri, K.A., Griffor, M., Stock, I., Colless, B., Walsh, P., Sunderland, P., Reyes, A., Dullea, R., Ammirati, M., Liu, S., McClure, K.F., Tu, M., Bhattacharya, S.K., Liras, S., Price, D.A., Craik, D.J.

(2014) Chem Biol 21: 284-294

• PubMed: 24440079 
• DOI: https://doi.org/10.1016/j.chembiol.2013.11.014
• Primary Citation Related Structures: 
  2MG9, 4NE9


• PubMed Abstract: 
  

  Disrupting the binding interaction between proprotein convertase (PCSK9) and the epidermal growth factor-like domain A (EGF-A domain) in the low-density lipoprotein receptor (LDL-R) is a promising strategy to promote LDL-R recycling and thereby lower circulating cholesterol levels. In this study, truncated 26 amino acid EGF-A analogs were designed and synthesized, and their structures were analyzed in solution and in complex with PCSK9. The most potent peptide had an increased binding affinity for PCSK9 (KD = 0.6 μM) compared with wild-type EGF-A (KD = 1.2 μM), and the ability to increase LDL-R recycling in the presence of PCSK9 in a cell-based assay.

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Organizational Affiliation: 
• Institute for Molecular Bioscience, The University of Queensland, Brisbane, 4072 QLD, Australia.
Structural Biology and Biophysics, Pfizer Global Research and Development, Eastern Point Road, Groton, CT 06340, USA.
School of Biomedical Sciences, The University of Queensland, Brisbane, 4072 QLD, Australia.
PDM-NCE, Pfizer Global Research and Development, Eastern Point Road, Groton, CT 06340, USA.
CVMED, Pfizer Global Research and Development, 620 Memorial Drive, Cambridge, MA 02139, USA.
Institute for Molecular Bioscience, The University of Queensland, Brisbane, 4072 QLD, Australia. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 2.81 kDa 
• Atom Count: 191 
• Modeled Residue Count: 27 
• Deposited Residue Count: 27 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Low-density lipoprotein receptor	A	27	Homo sapiens	Mutation(s): 1
UniProt & NIH Common Fund Data Resources
Find proteins for P01130 (Homo sapiens) Explore P01130  Go to UniProtKB:  P01130
PHAROS:  P01130 GTEx:  ENSG00000130164

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-04-02 
Deposition Author(s): Schroeder, C.I., Rosengren, K.

Revision History  

• Version 1.0: 2014-04-02
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary