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 Biology 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 

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