7O6W

Crystal structure of (the) VEL1 VEL polymerising domain (I664D mutant)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.64 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.215 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Head-to-tail polymerization by VEL proteins underpins cold-induced Polycomb silencing in flowering control.

Fiedler, M.Franco-Echevarria, E.Schulten, A.Nielsen, M.Rutherford, T.J.Yeates, A.Ahsan, B.Dean, C.Bienz, M.

(2022) Cell Rep 41: 111607-111607

  • DOI: https://doi.org/10.1016/j.celrep.2022.111607
  • Primary Citation of Related Structures:  
    7O6T, 7O6U, 7O6V, 7O6W, 7OQV

  • PubMed Abstract: 

    Transcriptional silencing through the Polycomb silencing machinery utilizes a "read-write" mechanism involving histone tail modifications. However, nucleation of silencing and long-term stable transmission of the silenced state also requires P-olycomb Repressive Complex 2 (PRC2) accessory proteins, whose molecular role is poorly understood. The Arabidopsis VEL proteins are accessory proteins that interact with PRC2 to nucleate and propagate silencing at the FLOWERING LOCUS C (FLC) locus, enabling early flowering in spring. Here, we report that VEL proteins contain a domain related to an atypical four-helix bundle that engages in spontaneous concentration-dependent head-to-tail polymerization to assemble dynamic biomolecular condensates. Mutations blocking polymerization of this VEL domain prevent Polycomb silencing at FLC. Plant VEL proteins thus facilitate assembly of dynamic multivalent Polycomb complexes required for inheritance of the silenced state.


  • Organizational Affiliation

    MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
VIN3-like protein 2
A, B
69Arabidopsis thalianaMutation(s): 1 
Gene Names: VIL2VEL1At4g30200F9N11.50
UniProt
Find proteins for Q9SUM4 (Arabidopsis thaliana)
Explore Q9SUM4 
Go to UniProtKB:  Q9SUM4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9SUM4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download Ideal Coordinates CCD File 
C [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.64 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.215 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.259α = 90
b = 79.259β = 90
c = 59.957γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
CRANK2phasing
Cootmodel building
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomU105192713
Royal SocietyUnited KingdomRP/R1/180002

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-09
    Type: Initial release
  • Version 1.1: 2022-11-23
    Changes: Database references