3C99 | pdb_00003c99

Structural Basis of Histone H4 Recognition by p55

• PDB DOI: https://doi.org/10.2210/pdb3C99/pdb

• Classification: TRANSCRIPTION REPRESSOR
• Organism(s): Drosophila melanogaster
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2008-02-15 Released: 2008-05-13 
• Deposition Author(s): Song, J.J., Garlick, J.D., Kingston, R.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.256 (Depositor), 0.257 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.219 (DCC) 

Starting Model: experimental

Literature

Structural basis of histone H4 recognition by p55.

Song, J.J., Garlick, J.D., Kingston, R.E.

(2008) Genes Dev 22: 1313-1318

• PubMed: 18443147 
• DOI: https://doi.org/10.1101/gad.1653308
• Primary Citation Related Structures: 
  3C99, 3C9C


• PubMed Abstract: 
  

  p55 is a common component of many chromatin-modifying complexes and has been shown to bind to histones. Here, we present a crystal structure of Drosophila p55 bound to a histone H4 peptide. p55, a predicted WD40 repeat protein, recognizes the first helix of histone H4 via a binding pocket located on the side of a beta-propeller structure. The pocket cannot accommodate the histone fold of H4, which must be altered to allow p55 binding. Reconstitution experiments show that the binding pocket is important to the function of p55-containing complexes. These data demonstrate that WD40 repeat proteins use various surfaces to direct the modification of histones.

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Organizational Affiliation: 
• Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 49.83 kDa 
• Atom Count: 3,063 
• Modeled Residue Count: 380 
• Deposited Residue Count: 432 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chromatin assembly factor 1 p55 subunit	A	432	Drosophila melanogaster	Mutation(s): 0  Gene Names: Caf1
UniProt
Find proteins for Q24572 (Drosophila melanogaster) Explore Q24572  Go to UniProtKB:  Q24572

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CD	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.256 (Depositor), 0.257 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.219 (DCC) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 151.121	α = 90
b = 151.121	β = 90
c = 98.013	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASES	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-05-13 
Deposition Author(s): Song, J.J., Garlick, J.D., Kingston, R.E.

Revision History  

• Version 1.0: 2008-05-13
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations
• Version 1.3: 2024-04-03
  Changes: Refinement description