8B5B | pdb_00008b5b

Human BRD4 bromdomain 1 in complex with a H4 peptide containing acetyl lysine and ApmTri (H4K5acK8ApmTri)

• PDB DOI: https://doi.org/10.2210/pdb8B5B/pdb

• Classification: PEPTIDE BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-09-22 Released: 2023-01-11 
• Deposition Author(s): Braun, M.B., Bartlick, N., Stehle, T.
• Funding Organization(s): German Research Foundation (DFG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free: 
  0.246 (Depositor), 0.245 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

Synthesis, Biochemical Characterization, and Genetic Encoding of a 1,2,4-Triazole Amino Acid as an Acetyllysine Mimic for Bromodomains of the BET Family.

Kirchgassner, S., Braun, M.B., Bartlick, N., Koc, C., Reinkemeier, C.D., Lemke, E.A., Stehle, T., Schwarzer, D.

(2023) Angew Chem Int Ed Engl 62: e202215460-e202215460

• PubMed: 36585954 
• DOI: https://doi.org/10.1002/anie.202215460
• Primary Citation Related Structures: 
  8B5A, 8B5B, 8B5C


• PubMed Abstract: 
  

  Lysine acetylation is a charge-neutralizing post-translational modification of proteins bound by bromodomains (Brds). A 1,2,4-triazole amino acid (ApmTri) was established as acetyllysine (Kac) mimic recruiting Brds of the BET family in contrast to glutamine commonly used for simulating this modification. Optimization of triazole substituents and side chain spacing allowed BET Brd recruitment to ApmTri-containing peptides with affinities similar to native substrates. Crystal structures of ApmTri-containing peptides in complex with two BET Brds revealed the binding mode which mirrored that of Kac ligands. ApmTri was genetically encoded and recombinant ApmTri-containing proteins co-enriched BRD3(2) from cellular lysates. This interaction was blocked by BET inhibitor JQ1. With genetically encoded ApmTri, biochemistry is now provided with a stable Kac mimic reflecting charge neutralization and Brd recruitment, allowing new investigations into BET proteins in vitro and in vivo.

---

Organizational Affiliation: 
• Interfakultäres Institut für Biochemie, Universität Tübingen, Auf der Morgenstelle 34, 72076, Tübingen, Germany.
Current address: Department of Infection, Immunity & Cardiovascular Disease, University of Sheffield, The Medical School, Beech Hill Rd, Sheffield, S10 2RX, UK.
Biocenter, Johannes Gutenberg University Mainz, 55128, Mainz, Germany.
Institute of Molecular Biology Mainz, 55128, Mainz, Germany.
Current address: Department of Biosystems Science and Engineering Basel, ETH Zurich, Mattenstrasse 26, 4058, Basel, Switzerland.

Biological Assembly 1  

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

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

Biological Assembly Evidence: immunoprecipitation

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: immunoprecipitation

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 48.46 kDa 
• Atom Count: 3,458 
• Modeled Residue Count: 398 
• Deposited Residue Count: 413 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 4	A, B, C	129	Homo sapiens	Mutation(s): 0  Gene Names: BRD4, HUNK1
UniProt & NIH Common Fund Data Resources
Find proteins for O60885 (Homo sapiens) Explore O60885  Go to UniProtKB:  O60885
PHAROS:  O60885 GTEx:  ENSG00000141867

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
H4K5acK8ApmTri	D, E	13	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P62805 (Homo sapiens) Explore P62805  Go to UniProtKB:  P62805
PHAROS:  P62805 GTEx:  ENSG00000274618 ENSG00000197238 ENSG00000197837 ENSG00000158406 ENSG00000278705 ENSG00000197061 ENSG00000270882 ENSG00000270276 ENSG00000273542 ENSG00000277157 ENSG00000276966 ENSG00000276180 ENSG00000278637 ENSG00000275126

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	F [auth C]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free:  0.246 (Depositor), 0.245 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.508	α = 90
b = 51.78	β = 90
c = 170.739	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-01-11 
Deposition Author(s): Braun, M.B., Bartlick, N., Stehle, T.

---

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	SCHW 1163/9-1

Revision History  

• Version 1.0: 2023-01-11
  Type: Initial release
  
• Version 1.1: 2023-02-15
  Changes: Database references
• Version 1.2: 2023-03-15
  Changes: Database references
• Version 1.3: 2023-03-22
  Changes: Database references
• Version 2.0: 2023-05-24
  Changes: Non-polymer description
• Version 2.1: 2024-02-07
  Changes: Data collection, Derived calculations, Refinement description
• Version 2.2: 2024-10-23
  Changes: Structure summary