6SWU

Crystal structure of the TPR domain of KLC1 in complex with an engineered high-affinity cargo peptide.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.202 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Fragment-linking peptide design yields a high-affinity ligand for microtubule-based transport.

Cross, J.A.Chegkazi, M.S.Steiner, R.A.Woolfson, D.N.Dodding, M.P.

(2021) Cell Chem Biol 28: 1347

  • DOI: 10.1016/j.chembiol.2021.03.010
  • Primary Citation of Related Structures:  
    6SWU

  • PubMed Abstract: 
  • Synthetic peptides are attractive candidates to manipulate protein-protein interactions inside the cell as they mimic natural interactions to compete for binding. However, protein-peptide interactions are often dynamic and weak. A challenge is to design peptides that make improved interactions with the target ...

    Synthetic peptides are attractive candidates to manipulate protein-protein interactions inside the cell as they mimic natural interactions to compete for binding. However, protein-peptide interactions are often dynamic and weak. A challenge is to design peptides that make improved interactions with the target. Here, we devise a fragment-linking strategy-"mash-up" design-to deliver a high-affinity ligand, KinTag, for the kinesin-1 motor. Using structural insights from natural micromolar-affinity cargo-adaptor ligands, we have identified and combined key binding features in a single, high-affinity ligand. An X-ray crystal structure demonstrates interactions as designed and reveals only a modest increase in interface area. Moreover, when genetically encoded, KinTag promotes transport of lysosomes with higher efficiency than natural sequences, revealing a direct link between motor-adaptor binding affinity and organelle transport. Together, these data demonstrate a fragment-linking strategy for peptide design and its application in a synthetic motor ligand to direct cellular cargo transport.


    Organizational Affiliation

    School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK. Electronic address: mark.dodding@bristol.ac.uk.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Kinesin light chain 1,Kinesin light chain 1,TPR domain of kinesin light chain 1 in complex with an engineered high-affinity cargo peptide of sequence TVFTTEDIYEWDDSAI
A, B, C, D, E, F
A, B, C, D, E, F
343Mus musculusMutation(s): 0 
Gene Names: Klc1Kns2
UniProt
Find proteins for Q5UE59 (Mus musculus)
Explore Q5UE59 
Go to UniProtKB:  Q5UE59
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5UE59
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.202 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.732α = 90
b = 107.532β = 90
c = 222.65γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
DIALSdata scaling
REFMACphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/S000828/1, BB/S000917/1

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-30
    Type: Initial release
  • Version 2.0: 2021-08-18
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Other, Polymer sequence, Refinement description, Structure summary
  • Version 2.1: 2021-09-29
    Changes: Data collection, Database references