3CFS

Structural basis of the interaction of RbAp46/RbAp48 with histone H4

• PDB DOI:  https://doi.org/10.2210/pdb3CFS/pdb

• Classification: HISTONE/CHAPERONE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda, Escherichia coli
• Mutation(s): No 


• Deposited: 2008-03-04 Released: 2008-06-10 
• Deposition Author(s): Murzina, N.V., Pei, X.-Y., Pratap, J.V., Sparkes, M., Vicente-Garcia, J., Ben-Shahar, T.R., Verreault, A., Luisi, B.F., Laue, E.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.249 
• R-Value Work: 0.184 
• R-Value Observed: 0.187 

Literature

Structural Basis for the Recognition of Histone H4 by the Histone-Chaperone RbAp46.

Murzina, N.V., Pei, X.Y., Zhang, W., Sparkes, M., Vicente-Garcia, J., Pratap, J.V., McLaughlin, S.H., Ben-Shahar, T.R., Verreault, A., Luisi, B.F., Laue, E.D.

(2008) Structure 16: 1077-1085

• PubMed: 18571423 
• DOI: https://doi.org/10.1016/j.str.2008.05.006
• Primary Citation of Related Structures:  
  3CFS, 3CFV


• PubMed Abstract: 
  

RbAp46 and RbAp48 (pRB-associated proteins p46 and p48, also known as RBBP7 and RBBP4, respectively) are highly homologous histone chaperones that play key roles in establishing and maintaining chromatin structure. We report here the crystal structure of human RbAp46 bound to histone H4. RbAp46 folds into a seven-bladed beta propeller structure and binds histone H4 in a groove formed between an N-terminal alpha helix and an extended loop inserted into blade six. Surprisingly, histone H4 adopts a different conformation when interacting with RbAp46 than it does in either the nucleosome or in the complex with ASF1, another histone chaperone. Our structural and biochemical results suggest that when a histone H3/H4 dimer (or tetramer) binds to RbAp46 or RbAp48, helix 1 of histone H4 unfolds to interact with the histone chaperone. We discuss the implications of our findings for the assembly and function of RbAp46 and RbAp48 complexes.

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Organizational Affiliation: 

Department of Biochemistry, 80 Tennis Court Road, Cambridge CB2 1GA, UK. [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)

Macromolecule Content

• Total Structure Weight: 48.71 kDa 
• Atom Count: 3,397 
• Modelled Residue Count: 398 
• Deposited Residue Count: 429 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone-binding protein RBBP7	A [auth B]	414	Homo sapiens	Mutation(s): 0  Gene Names: RBBP7, RBAP46
UniProt & NIH Common Fund Data Resources
Find proteins for Q16576 (Homo sapiens) Explore Q16576  Go to UniProtKB:  Q16576
PHAROS:  Q16576

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	B [auth E]	15	Homo sapiens	Mutation(s): 0  Gene Names:  HIST1H4A, H4C1, H4/A, H4FA, H4C2, H4/I, H4FI, HIST1H4B, H4C3, H4/G, H4FG, HIST1H4C, H4C4, H4/B, H4FB, HIST1H4D, H4C5, H4/J, H4FJ, HIST1H4E, H4C6, H4/C, H4FC, HIST1H4F, H4C8, H4/H, H4FH, HIST1H4H, H4C9, H4/M, H4FM, HIST1H4I, H4C11, H4/E, H4FE, HIST1H4J, H4C12, H4/D, H4FD, HIST1H4K, H4C13, H4/K, H4FK, HIST1H4L, H4C14, H4/N, H4F2, H4FN, HIST2H4, HIST2H4A, H4C15, H4/O, H4FO, HIST2H4B, H4-16, HIST4H4
UniProt & NIH Common Fund Data Resources
Find proteins for P62805 (Homo sapiens) Explore P62805  Go to UniProtKB:  P62805
PHAROS:  P62805

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ARS	C [auth B]	ARSENIC As RBFQJDQYXXHULB-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A [auth B]	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.249 
• R-Value Work: 0.184 
• R-Value Observed: 0.187 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.665	α = 90
b = 85.725	β = 90
c = 117.723	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
ADSC	data collection
DENZO	data reduction
HKL-2000	data scaling
PHASES	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-06-10 
Deposition Author(s): Murzina, N.V., Pei, X.-Y., Pratap, J.V., Sparkes, M., Vicente-Garcia, J., Ben-Shahar, T.R., Verreault, A., Luisi, B.F., Laue, E.D.

Revision History  

• Version 1.0: 2008-06-10
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2018-01-24
  Changes: Structure summary