7AXP

Structural characterisation of WDR5:CS-VIP8 interaction in cis state 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.331 
  • R-Value Work: 0.267 
  • R-Value Observed: 0.270 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 3.0 of the entry. See complete history


Literature

Bistable Photoswitch Allows in Vivo Control of Hematopoiesis.

Albert, L.Nagpal, J.Steinchen, W.Zhang, L.Werel, L.Djokovic, N.Ruzic, D.Hoffarth, M.Xu, J.Kaspareit, J.Abendroth, F.Royant, A.Bange, G.Nikolic, K.Ryu, S.Dou, Y.Essen, L.O.Vazquez, O.

(2022) ACS Cent Sci 8: 57-66

  • DOI: https://doi.org/10.1021/acscentsci.1c00434
  • Primary Citation of Related Structures:  
    7AXP, 7AXQ, 7AXS, 7AXU, 7AXX

  • PubMed Abstract: 

    Optical control has enabled functional modulation in cell culture with unparalleled spatiotemporal resolution. However, current tools for in vivo manipulation are scarce. Here, we design and implement a genuine on-off optochemical probe capable of achieving hematopoietic control in zebrafish. Our photopharmacological approach first developed conformationally strained visible light photoswitches (CS-VIPs) as inhibitors of the histone methyltransferase MLL1 (KMT2A). In blood homeostasis MLL1 plays a crucial yet controversial role. CS-VIP 8 optimally fulfils the requirements of a true bistable functional system in vivo under visible-light irradiation, and with unprecedented stability. These properties are exemplified via hematopoiesis photoinhibition with a single isomer in zebrafish. The present interdisciplinary study uncovers the mechanism of action of CS-VIPs. Upon WDR5 binding, CS-VIP 8 causes MLL1 release with concomitant allosteric rearrangements in the WDR5/RbBP5 interface. Since our tool provides on-demand reversible control without genetic intervention or continuous irradiation, it will foster hematopathology and epigenetic investigations. Furthermore, our workflow will enable exquisite photocontrol over other targets inhibited by macrocycles.


  • Organizational Affiliation

    Department of Chemistry, University of Marburg, 35037 Marburg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
WD repeat-containing protein 5334Homo sapiensMutation(s): 0 
Gene Names: WDR5BIG3
UniProt & NIH Common Fund Data Resources
Find proteins for P61964 (Homo sapiens)
Explore P61964 
Go to UniProtKB:  P61964
PHAROS:  P61964
GTEx:  ENSG00000196363 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61964
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CS-VIP87Homo sapiensMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
ABA
Query on ABA
B
L-PEPTIDE LINKINGC4 H9 N O2ALA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.331 
  • R-Value Work: 0.267 
  • R-Value Observed: 0.270 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.24α = 90
b = 99.24β = 90
c = 98.52γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-15
    Type: Initial release
  • Version 1.1: 2022-02-16
    Changes: Database references
  • Version 2.0: 2023-11-15
    Changes: Advisory, Atomic model, Data collection
  • Version 2.1: 2024-01-31
    Changes: Refinement description
  • Version 3.0: 2024-07-10
    Changes: Data collection, Non-polymer description, Structure summary