5FR6 | pdb_00005fr6

The structure of polycomb ULD complex

• PDB DOI: https://doi.org/10.2210/pdb5FR6/pdb

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


• Deposited: 2015-12-15 Released: 2016-11-16 
• Deposition Author(s): Gray, F., Cho, H.J., Cierpicki, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free: 
  0.328 (Depositor), 0.328 (DCC) 
• R-Value Work: 
  0.233 (Depositor), 0.236 (DCC) 
• R-Value Observed: 
  0.237 (Depositor) 

Starting Model: experimental

Literature

Bmi1 Regulates Prc1 Architecture and Activity Through Homo-and Hetero-Oligomerization

Gray, F., Cho, H.J., Shihan, S., Harris, A., Boytsov, B., Jaremko, L., Jaremko, M., Demeler, B., Lawlor, E.R., Grembecka, J., Cierpicki, T.

(2016) Nat Commun 7: 13343

• PubMed: 27827373 
• DOI: https://doi.org/10.1038/ncomms13343
• Primary Citation Related Structures: 
  2NA1, 5FR6


• PubMed Abstract: 
  

  BMI1 is a core component of the polycomb repressive complex 1 (PRC1) and emerging data support a role of BMI1 in cancer. The central domain of BMI1 is involved in protein-protein interactions and is essential for its oncogenic activity. Here, we present the structure of BMI1 bound to the polyhomeotic protein PHC2 illustrating that the central domain of BMI1 adopts an ubiquitin-like (UBL) fold and binds PHC2 in a β-hairpin conformation. Unexpectedly, we find that the UBL domain is involved in homo-oligomerization of BMI1. We demonstrate that both the interaction of BMI1 with polyhomeotic proteins and homo-oligomerization via UBL domain are necessary for H2A ubiquitination activity of PRC1 and for clonogenic potential of U2OS cells. Here, we also emphasize need for joint application of NMR spectroscopy and X-ray crystallography to determine the overall structure of the BMI1-PHC2 complex.

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Organizational Affiliation: 
• Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA.
Translational Oncology Program, University of Michigan, Ann Arbor, Michigan 48109, USA.
Department of Pediatrics and Communicable Diseases, University of Michigan, Ann Arbor, Michigan 48109, USA.
Deutsches Zentrum fur Neurodegenerative Erkrankungen (DZNE), Am Fassberg 11, 37077 Goettingen, Germany.
Max-Planck Institute of Biophysical Chemistry, NMR-based Department for Structural Biology, Am Fassberg 11, 37077 Goettingen, Germany.
Department of Biochemistry, The University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 14.1 kDa 
• Atom Count: 724 
• Modeled Residue Count: 83 
• Deposited Residue Count: 115 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
POLYCOMB COMPLEX PROTEIN BMI-1	A	115	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P35226 (Homo sapiens) Explore P35226  Go to UniProtKB:  P35226
PHAROS:  P35226 GTEx:  ENSG00000168283

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free:  0.328 (Depositor), 0.328 (DCC) 
• R-Value Work:  0.233 (Depositor), 0.236 (DCC) 
• R-Value Observed: 0.237 (Depositor) 

Space Group: P 3₂ 1 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.275	α = 90
b = 78.275	β = 90
c = 43.119	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-11-16 
Deposition Author(s): Gray, F., Cho, H.J., Cierpicki, T.

Revision History  

• Version 1.0: 2016-11-16
  Type: Initial release
  
• Version 1.1: 2016-11-23
  Changes: Database references
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Other, Refinement description