6ATL

Exploring Cystine Dense Peptide Space to Open a Unique Molecular Toolbox


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.129 
  • R-Value Observed: 0.131 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Screening, large-scale production and structure-based classification of cystine-dense peptides.

Correnti, C.E.Gewe, M.M.Mehlin, C.Bandaranayake, A.D.Johnsen, W.A.Rupert, P.B.Brusniak, M.Y.Clarke, M.Burke, S.E.De Van Der Schueren, W.Pilat, K.Turnbaugh, S.M.May, D.Watson, A.Chan, M.K.Bahl, C.D.Olson, J.M.Strong, R.K.

(2018) Nat Struct Mol Biol 25: 270-278

  • DOI: 10.1038/s41594-018-0033-9
  • Primary Citation of Related Structures:  
    6ATS, 6AU7, 6ATU, 6ATW, 6ATL, 6ATN, 6AVD, 6AVC, 6AVA, 6AV8, 6AUP

  • PubMed Abstract: 
  • Peptides folded through interwoven disulfides display extreme biochemical properties and unique medicinal potential. However, their exploitation has been hampered by the limited amounts isolatable from natural sources and the expense of chemical synthesis ...

    Peptides folded through interwoven disulfides display extreme biochemical properties and unique medicinal potential. However, their exploitation has been hampered by the limited amounts isolatable from natural sources and the expense of chemical synthesis. We developed reliable biological methods for high-throughput expression, screening and large-scale production of these peptides: 46 were successfully produced in multimilligram quantities, and >600 more were deemed expressible through stringent screening criteria. Many showed extreme resistance to temperature, proteolysis and/or reduction, and all displayed inhibitory activity against at least 1 of 20 ion channels tested, thus confirming their biological functionality. Crystal structures of 12 confirmed proper cystine topology and the utility of crystallography to study these molecules but also highlighted the need for rational classification. Previous categorization attempts have focused on limited subsets featuring distinct motifs. Here we present a global definition, classification and analysis of >700 structures of cystine-dense peptides, providing a unifying framework for these molecules.


    Organizational Affiliation

    Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA. rstrong@fredhutch.org.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Potassium channel toxin alpha-KTx 4.2A, B [auth C]37Tityus serrulatusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P56219 (Tityus serrulatus)
Explore P56219 
Go to UniProtKB:  P56219
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download Ideal Coordinates CCD File 
D [auth A]CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A], E [auth C], F [auth C]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.129 
  • R-Value Observed: 0.131 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 27.758α = 90
b = 23.215β = 94.36
c = 46.308γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-28
    Type: Initial release
  • Version 1.1: 2018-03-14
    Changes: Database references