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1,068,577
Computed Structure Models (CSM)
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 3UVK|pdb_00003uvk

Crystal structure of WDR5 in complex with the WDR5-interacting motif of MLL2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 
    0.192 (Depositor), 0.200 (DCC) 
  • R-Value Work: 
    0.151 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 
    0.153 (Depositor) 

Starting Model:experimental
View more details

wwPDB Validation  3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The plasticity of WDR5 peptide-binding cleft enables the binding of the SET1 family of histone methyltransferases.

Zhang, P.Lee, H.Brunzelle, J.S.Couture, J.F.

(2012) Nucleic Acids Res 40: 4237-4246

  • PubMed22266653 Search on PubMedSearch on PubMed Central
  • DOI: https://doi.org/10.1093/nar/gkr1235
  • Primary Citation of Related Structures:  
    3UVK,3UVL,3UVM,3UVN,3UVO

  • PubMed Abstract: 

    In mammals, the SET1 family of lysine methyltransferases (KMTs), which includes MLL1-5, SET1A and SET1B, catalyzes the methylation of lysine-4 (Lys-4) on histone H3. Recent reports have demonstrated that a three-subunit complex composed of WD-repeat protein-5 (WDR5), retinoblastoma-binding protein-5 (RbBP5) and absent, small, homeotic disks-2-like (ASH2L) stimulates the methyltransferase activity of MLL1. On the basis of studies showing that this stimulation is in part controlled by an interaction between WDR5 and a small region located in close proximity of the MLL1 catalytic domain [referred to as the WDR5-interacting motif (Win)], it has been suggested that WDR5 might play an analogous role in scaffolding the other SET1 complexes. We herein provide biochemical and structural evidence showing that WDR5 binds the Win motifs of MLL2-4, SET1A and SET1B. Comparative analysis of WDR5-Win complexes reveals that binding of the Win motifs is achieved by the plasticity of WDR5 peptidyl-arginine-binding cleft allowing the C-terminal ends of the Win motifs to be maintained in structurally divergent conformations. Consistently, enzymatic assays reveal that WDR5 plays an important role in the optimal stimulation of MLL2-4, SET1A and SET1B methyltransferase activity by the RbBP5-ASH2L heterodimer. Overall, our findings illustrate the function of WDR5 in scaffolding the SET1 family of KMTs and further emphasize on the important role of WDR5 in regulating global histone H3 Lys-4 methylation.


  • Organizational Affiliation
    • Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada.
Biological Assembly 1  

 Explore in 3DStructure |Sequence Annotations |Electron Density |Validation Report |Ligand Interaction (BTB)


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


Find Similar Assemblies

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

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Macromolecule Content 

  • Total Structure Weight: 36.28 kDa 
  • Atom Count: 2,650 
  • Modeled Residue Count: 310 
  • Deposited Residue Count: 329 
  • Unique protein chains: 2

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
WD repeat-containing protein 5318Homo 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
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase MLL211Homo sapiensMutation(s): 0 
EC: 2.1.1.43 (PDB Primary Data), 2.1.1.364 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O14686 (Homo sapiens)
Explore O14686 
Go to UniProtKB:  O14686
PHAROS:  O14686
GTEx:  ENSG00000167548 
Entity Groups 
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14686
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BTB
Query on BTB

Download Ideal Coordinates CCD File 
C [auth A]2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C8 H19 N O5
OWMVSZAMULFTJU-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.192 (Depositor), 0.200 (DCC) 
  • R-Value Work: 0.151 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 0.153 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.827α = 90
b = 68.496β = 90
c = 87.815γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASESphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-12-14
    Type: Initial release
  • Version 1.1: 2012-02-08
    Changes: Database references
  • Version 1.2: 2012-05-30
    Changes: Database references
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description
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RCSB PDB Core Operations are funded by theU.S. National Science Foundation (DBI-2321666), theUS Department of Energy (DE-SC0019749), and theNational Cancer Institute,National Institute of Allergy and Infectious Diseases, andNational Institute of General Medical Sciences of theNational Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.


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