2RNW | pdb_00002rnw

The Structural Basis for Site-Specific Lysine-Acetylated Histone Recognition by the Bromodomains of the Human Transcriptional Co-Activators PCAf and CBP

• PDB DOI: https://doi.org/10.2210/pdb2RNW/pdb

• Classification: TRANSFERASE/NUCLEAR PROTEIN
• Organism(s): Homo sapiens, Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-02-03 Released: 2008-05-06 
• Deposition Author(s): Zeng, L., Zhang, Q., Gerona-Navarro, G., Zhou, M.M.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

Structural Basis of Site-Specific Histone Recognition by the Bromodomains of Human Coactivators PCAF and CBP/p300

Zeng, L., Zhang, Q., Gerona-Navarro, G., Moshkina, N., Zhou, M.M.

(2008) Structure 16: 643-652

• PubMed: 18400184 
• DOI: https://doi.org/10.1016/j.str.2008.01.010
• Primary Citation Related Structures: 
  2RNW, 2RNX, 2RNY


• PubMed Abstract: 
  

  Histone lysine acetylation is central to epigenetic control of gene transcription. Bromodomains of chromosomal proteins function as acetyl-lysine (Kac) binding domains. However, how bromodomains recognize site-specific histones remains unanswered. Here, we report three three-dimensional solution structures of the bromodomains of the human transcriptional coactivators CREB-binding protein (CBP) and p300/CBP-associated factor (PCAF) bound to peptides derived from histone acetylation sites at lysines 36 and 9 in H3, and lysine 20 in H4. From structural and biochemical binding analyses, we determine consensus histone recognition by the bromodomains of PCAF and CBP, which represent two different subgroups of the bromodomain family. Through bromodomain residues in the ZA and BC loops, PCAF prefers acetylation sites with a hydrophobic residue at (Kac+2) position and a positively charged or aromatic residue at (Kac+3), whereas CBP favors bulky hydrophobic residues at (Kac+1) and (Kac+2), a positively charged residue at (Kac-1), and an aromatic residue at (Kac-2).

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Organizational Affiliation: 
• Department of Structural and Chemical Biology, Mount Sinai School of Medicine, New York University, New York, NY 10029, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 15.66 kDa 
• Atom Count: 1,099 
• Modeled Residue Count: 133 
• Deposited Residue Count: 133 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone acetyltransferase PCAF	A	118	Homo sapiens	Mutation(s): 0  EC: 2.3.1.48 (PDB Primary Data), 2.3.1.57 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q92831 (Homo sapiens) Explore Q92831  Go to UniProtKB:  Q92831
PHAROS:  Q92831 GTEx:  ENSG00000114166

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3	B	15	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P61830 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P61830  Go to UniProtKB:  P61830

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ALY	B	L-PEPTIDE LINKING	C8 H16 N2 O3		LYS

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-05-06 
Deposition Author(s): Zeng, L., Zhang, Q., Gerona-Navarro, G., Zhou, M.M.

Revision History  

• Version 1.0: 2008-05-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2022-03-16
  Changes: Data collection, Database references, Derived calculations
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection
• Version 2.1: 2024-10-16
  Changes: Structure summary