8Q1N | pdb_00008q1n

Cyclic peptide binder of the WBM-site of WDR5

• PDB DOI: https://doi.org/10.2210/pdb8Q1N/pdb

• Classification: GENE REGULATION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-08-01 Released: 2023-09-06 
• Deposition Author(s): Schmeing, S., Chang, J.Y., t Hart, P., Gasper, R.
• Funding Organization(s): Other private, Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free: 
  0.243 (Depositor), 0.243 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: in silico

Literature

Macrocyclic peptides as inhibitors of WDR5-lncRNA interactions.

Chang, J.Y., Neugebauer, C., Schmeing, S., Amrahova, G., 't Hart, P.

(2023) Chem Commun (Camb) 59: 10656-10659

• PubMed: 37581220 
• DOI: https://doi.org/10.1039/d3cc03221c
• Primary Citation Related Structures: 
  8Q1N


• PubMed Abstract: 
  

  WDR5 is an adaptor protein involved in the regulation of various epigenetic modifier complexes. Various inhibitors have been described but only as inhibitors of its protein-protein interactions. Here we describe peptidic macrocycles that act as inhibitors of the interaction between WDR5 and long non-coding RNAs. The findings provide a new strategy to modulate the biological function of WDR5 as an RNA binding epigenetic regulator.

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Organizational Affiliation: 
• Chemical Genomics Centre of the Max Planck, Society Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: assay for oligomerization

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: assay for oligomerization

Macromolecule Content 

• Total Structure Weight: 73.11 kDa 
• Atom Count: 5,614 
• Modeled Residue Count: 659 
• Deposited Residue Count: 664 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
WD repeat-containing protein 5	A, B	321	Homo sapiens	Mutation(s): 0  Gene Names: WDR5
UniProt & NIH Common Fund Data Resources
Find proteins for P61964 (Homo sapiens) Explore P61964  Go to UniProtKB:  P61964
PHAROS:  P61964 GTEx:  ENSG00000196363

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclic peptide inhibitor	C [auth a], D [auth b]	11	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P01106 (Homo sapiens) Explore P01106  Go to UniProtKB:  P01106
PHAROS:  P01106 GTEx:  ENSG00000136997

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DAB	C [auth a], D [auth b]	L-PEPTIDE LINKING	C4 H10 N2 O2		ALA

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free:  0.243 (Depositor), 0.243 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.174	α = 90
b = 82.174	β = 90
c = 201.707	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data scaling
xia2	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-09-06 
Deposition Author(s): Schmeing, S., Chang, J.Y., t Hart, P., Gasper, R.

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Funding Organization	Location	Grant Number
Other private	Germany	--
Other government	Taiwan	--

Revision History  

• Version 1.0: 2023-09-06
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Database references
• Version 1.2: 2024-11-13
  Changes: Structure summary