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 6OKE | pdb_00006oke

Crystal structure of an apo Transferrin-Receptor-Binding cystine-dense peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 
    0.279 (Depositor), 0.275 (DCC) 
  • R-Value Work: 
    0.221 (Depositor), 0.224 (DCC) 
  • R-Value Observed: 
    0.224 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6OKE

This is version 1.3 of the entry. See complete history. 

Literature

A TfR-Binding Cystine-Dense Peptide Promotes Blood-Brain Barrier Penetration of Bioactive Molecules.

Crook, Z.R., Girard, E., Sevilla, G.P., Merrill, M., Friend, D., Rupert, P.B., Pakiam, F., Nguyen, E., Yin, C., Ruff, R.O., Hopping, G., Strand, A.D., Finton, K.A.K., Coxon, M., Mhyre, A.J., Strong, R.K., Olson, J.M.

(2020) J Mol Biol 432: 3989-4009

  • DOI: https://doi.org/10.1016/j.jmb.2020.04.002
  • Primary Citation Related Structures: 
    6OKD, 6OKE

  • PubMed Abstract: 

    The impenetrability of the blood-brain barrier (BBB) to most conventional drugs impedes the treatment of central nervous system (CNS) disorders. Interventions for diseases like brain cancer, neurodegeneration, or age-associated inflammatory processes require varied approaches to CNS drug delivery. Cystine-dense peptides (CDPs) have drawn recent interest as drugs or drug-delivery vehicles. Found throughout the phylogenetic tree, often in drug-like roles, their size, stability, and protein interaction capabilities make CDPs an attractive mid-size biologic scaffold to complement conventional antibody-based drugs. Here, we describe the identification, maturation, characterization, and utilization of a CDP that binds to the transferrin receptor (TfR), a native receptor and BBB transporter for the iron chaperone transferrin. We developed variants with varying binding affinities (K D as low as 216 pM), co-crystallized it with the receptor, and confirmed murine cross-reactivity. It accumulates in the mouse CNS at ~25% of blood levels (CNS blood content is only ~1%-6%) and delivers neurotensin, an otherwise non-BBB-penetrant neuropeptide, at levels capable of modulating CREB signaling in the mouse brain. Our work highlights the utility of CDPs as a diverse, easy-to-screen scaffold family worthy of inclusion in modern drug discovery strategies, demonstrated by the discovery of a candidate CNS drug delivery vehicle ready for further optimization and preclinical development.


  • Organizational Affiliation: 
    • Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA 98109, USA.

Macromolecule Content 

  • Total Structure Weight: 23.84 kDa 
  • Atom Count: 1,158 
  • Modeled Residue Count: 151 
  • Deposited Residue Count: 204 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Transferrin-Receptor Binding PeptideA [auth C],
B [auth A],
C [auth B],
D
51Monosiga brevicollisMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free:  0.279 (Depositor), 0.275 (DCC) 
  • R-Value Work:  0.221 (Depositor), 0.224 (DCC) 
  • R-Value Observed: 0.224 (Depositor) 
Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.656α = 90
b = 37.656β = 90
c = 190.198γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-15
    Type: Initial release
  • Version 1.1: 2020-05-06
    Changes: Database references
  • Version 1.2: 2020-07-08
    Changes: Database references
  • Version 1.3: 2024-11-20
    Changes: Data collection, Database references, Refinement description, Structure summary