1T64

Crystal Structure of human HDAC8 complexed with Trichostatin A

• PDB DOI: https://doi.org/10.2210/pdb1T64/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2004-05-05 Released: 2004-07-27 
• Deposition Author(s): Somoza, J.R., Skene, R.J., Katz, B.A., Mol, C., Ho, J.D., Jennings, A.J., Luong, C., Arvai, A., Buggy, J.J., Chi, E., Tang, J., Sang, B.-C., Verner, E., Wynands, R., Leahy, E.M., Dougan, D.R., Snell, G., Navre, M., Knuth, M.W., Swanson, R.V., McRee, D.E., Tari, L.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.221 
• R-Value Work: 0.172 
• R-Value Observed: 0.172 

Starting Model: experimental

Literature

Structural Snapshots of Human HDAC8 Provide Insights into the Class I Histone Deacetylases

Somoza, J.R., Skene, R.J., Katz, B.A., Mol, C., Ho, J.D., Jennings, A.J., Luong, C., Arvai, A., Buggy, J.J., Chi, E., Tang, J., Sang, B.-C., Verner, E., Wynands, R., Leahy, E.M., Dougan, D.R., Snell, G., Navre, M., Knuth, M.W., Swanson, R.V., McRee, D.E., Tari, L.W.

(2004) Structure 12: 1325-1334

• PubMed: 15242608 
• DOI: https://doi.org/10.1016/j.str.2004.04.012
• Primary Citation of Related Structures:  
  1T64, 1T67, 1T69, 1VKG


• PubMed Abstract: 
  

  Modulation of the acetylation state of histones plays a pivotal role in the regulation of gene expression. Histone deacetylases (HDACs) catalyze the removal of acetyl groups from lysines near the N termini of histones. This reaction promotes the condensation of chromatin, leading to repression of transcription. HDAC deregulation has been linked to several types of cancer, suggesting a potential use for HDAC inhibitors in oncology. Here we describe the first crystal structures of a human HDAC: the structures of human HDAC8 complexed with four structurally diverse hydroxamate inhibitors. This work sheds light on the catalytic mechanism of the HDACs, and on differences in substrate specificity across the HDAC family. The structure also suggests how phosphorylation of Ser39 affects HDAC8 activity.

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Organizational Affiliation: 

Celera, 180 Kimball Way, South San Francisco, CA 94080 USA. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 85.2 kDa 
• Atom Count: 6,410 
• Modelled Residue Count: 728 
• Deposited Residue Count: 754 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone deacetylase 8	A, B	377	Homo sapiens	Mutation(s): 0  EC: 3.5.1 (UniProt), 3.5.1.98 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BY41 (Homo sapiens) Explore Q9BY41  Go to UniProtKB:  Q9BY41
PHAROS:  Q9BY41 GTEx:  ENSG00000147099

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TSN	H [auth A], I [auth A], O [auth B], P [auth B]	TRICHOSTATIN A C17 H22 N2 O3 RTKIYFITIVXBLE-QEQCGCAPSA-N
ZN	C [auth A], J [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	D [auth A], E [auth A], K [auth B], L [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA	F [auth A], G [auth A], M [auth B], N [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
TSN	BindingDB:  1T64	Ki: min: 45, max: 504 (nM) from 5 assay(s)
		Kd: min: 390, max: 490 (nM) from 2 assay(s)
		IC50: min: 1.38, max: 4550 (nM) from 56 assay(s)
		-TΔS: min: 0.08, max: 1.13 (kJ/mol) from 3 assay(s)
		ΔH: min: -4.90e+1, max: -3.69e+1 (kJ/mol) from 3 assay(s)
		ΔG: -3.60e+1 (kJ/mol) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.221 
• R-Value Work: 0.172 
• R-Value Observed: 0.172 
• Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.014	α = 90
b = 81.014	β = 90
c = 114.178	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-07-27 
Deposition Author(s): Somoza, J.R., Skene, R.J., Katz, B.A., Mol, C., Ho, J.D., Jennings, A.J., Luong, C., Arvai, A., Buggy, J.J., Chi, E., Tang, J., Sang, B.-C., Verner, E., Wynands, R., Leahy, E.M., Dougan, D.R., Snell, G., Navre, M., Knuth, M.W., Swanson, R.V., McRee, D.E., Tari, L.W.

Revision History  

• Version 1.0: 2004-07-27
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description