PDB-4rn0: Crystal structure of S39D HDAC8 in complex with a largazole analogue.

ID or keywords:

Entry

Database: PDB / ID: 4rn0

Title

Crystal structure of S39D HDAC8 in complex with a largazole analogue.

Components

Histone deacetylase 8

Keywords

HYDROLASE/HYDROLASE INHIBITOR /

metalloenzyme /

hydrolase /

histone deacetylase /

enzyme inhibitor complex / largazole analogue / thiol inhibitor / arginase/deacetylase fold / HYDROLASE-HYDROLASE INHIBITOR complex

Function / homology

Function and homology information

histone decrotonylase activity /

histone deacetylase / protein lysine deacetylase activity /

regulation of telomere maintenance /

Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / mitotic sister chromatid cohesion /

histone deacetylase activity / nuclear chromosome / Notch-HLH transcription pathway /

histone deacetylase complex ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.761 Å

Authors

Decroos, C. / Christianson, D.W.

Citation

Journal: Biochemistry / Year: 2015
Title: Variable Active Site Loop Conformations Accommodate the Binding of Macrocyclic Largazole Analogues to HDAC8.
Authors: Decroos, C. / Clausen, D.J. / Haines, B.E. / Wiest, O. / Williams, R.M. / Christianson, D.W.

History

Deposition	Oct 22, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 8, 2015	Provider: repository / Type: Initial release
Revision 1.1	Apr 22, 2015	Group: Database references
Revision 1.2	Sep 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4rn0.cif.gz	311.7 KB	Display	PDBx/mmCIF format
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PDBx/mmJSON format	4rn0.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/rn/4rn0 ftp://data.pdbj.org/pub/pdb/validation_reports/rn/4rn0	HTTPS FTP

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Related structure data

Related structure data	4rn1C 4rn2C 3ewfS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4qa3-2 3ezp-2 4qa2-2 6hsk-2 7jvv-1 4qa5-1 5fcw-1 5ths-2 5d1d-2 2v5w-2 5tht-2 5d1c-1 4qa4-d 4rn1-1 3mz3-1 5dc5-1 4rn2-1 6odc-3 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

4rn1C

4rn2C

3ewfS

C: citing same article (ref.)

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#122 - Feb 2010 Enhanceosome similarity (1) #205 - Jan 2017 Nuclear Pore Complex similarity (1) #134 - Feb 2011 Integrin similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #194 - Feb 2016 Designer Insulins similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1) #259 - Jul 2021 Designed Proteins and Citizen Science similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#122 - Feb 2010
Enhanceosome
similarity (1)
#205 - Jan 2017
Nuclear Pore Complex
similarity (1)
#134 - Feb 2011
Integrin
similarity (1)
#172 - Apr 2014
RecA and Rad51
similarity (1)
#194 - Feb 2016
Designer Insulins
similarity (1)
#234 - Jun 2019
MDM2 and Cancer
similarity (1)
#259 - Jul 2021
Designed Proteins and Citizen Science
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (1)

Deposited unit

A: Histone deacetylase 8

B: Histone deacetylase 8

hetero molecules

88 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Histone deacetylase 8

hetero molecules

defined by author
44.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Histone deacetylase 8

hetero molecules

defined by author
43.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	53.921, 85.006, 94.665
Angle α, β, γ (deg.)	90.00, 100.33, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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Protein , 1 types, 2 molecules AB

#1: Protein	Histone deacetylase 8 / / HD8 Mass: 43260.000 Da / Num. of mol.: 2 / Fragment: S39D HDAC8 / Mutation: S39D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HDAC8, HDACL1, CDA07 / Plasmid: pHD2-Xa-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9BY41, histone deacetylase

#1: Protein

Histone deacetylase 8 /

/ HD8

Mass: 43260.000 Da / Num. of mol.: 2 / Fragment: S39D HDAC8 / Mutation: S39D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: HDAC8, HDACL1, CDA07 / Plasmid: pHD2-Xa-His / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9BY41,

histone deacetylase

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Non-polymers , 6 types, 750 molecules

#2: Chemical	ChemComp-L6G / (5R,8S,11S)-5-methyl-8-(propan-2-yl)-11-[(1E)-4-sulfanylbut-1-en-1-yl]-3,17-dithia-7,10,14,19,20-pentaazatricyclo[14.2.1.1~2,5~]icosa-1(18),2(20),16(19)-triene-6,9,13-trione Mass: 495.682 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₂₉N₅O₃S₃
#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#5: Chemical	ChemComp-IMD / IMIDAZOLE / Imidazole Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₅N₂
#6: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#7: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 740 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.47 Å³/Da / Density % sol: 50.14 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.3 Details: 0.1 M Imidazole (pH=7.0), 4 mM tris(2-carboxyethyl)phosphine (TCEP), 8% PEG 8000, pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 23, 2014 / Details: mirrors
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.075 Å / Relative weight: 1
Reflection	Resolution: 1.76→50 Å / Num. all: 83014 / Num. obs: 82963 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.5 % / R_merge(I) obs: 0.073 / Net I/σ(I): 21.3
Reflection shell	Resolution: 1.76→1.82 Å / Redundancy: 7.3 % / R_merge(I) obs: 0.317 / Mean I/σ(I) obs: 7.6 / Num. unique all: 8280 / % possible all: 100

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Processing

Software

Name	Version	Classification
CBASS		data collection
PHASER		phasing
PHENIX	(phenix.refine: dev_1833)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EWF

3ewf

Resolution: 1.761→42.906 Å / SU ML: 0.15 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 15.29 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1621	4145	5 %	random
R_work	0.1367	-	-	-
obs	0.138	82932	99.81 %	-
all	-	83147	-	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 22.4 Å²

Refinement step

Cycle: LAST / Resolution: 1.761→42.906 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5563	0	81	740	6384

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	5963
X-RAY DIFFRACTION	f_angle_d	1.327	8143
X-RAY DIFFRACTION	f_dihedral_angle_d	14.859	2201
X-RAY DIFFRACTION	f_chiral_restr	0.06	901
X-RAY DIFFRACTION	f_plane_restr	0.007	1045

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.7614-1.7814	0.1962	141	0.1629	2522	X-RAY DIFFRACTION	96
1.7814-1.8024	0.1893	122	0.1526	2662	X-RAY DIFFRACTION	100
1.8024-1.8244	0.2275	121	0.1441	2623	X-RAY DIFFRACTION	100
1.8244-1.8475	0.1835	141	0.1403	2628	X-RAY DIFFRACTION	100
1.8475-1.8718	0.1833	150	0.1384	2597	X-RAY DIFFRACTION	100
1.8718-1.8974	0.1994	131	0.1376	2622	X-RAY DIFFRACTION	100
1.8974-1.9245	0.1908	132	0.1401	2643	X-RAY DIFFRACTION	100
1.9245-1.9533	0.1944	125	0.1384	2593	X-RAY DIFFRACTION	100
1.9533-1.9838	0.188	134	0.1397	2639	X-RAY DIFFRACTION	100
1.9838-2.0163	0.1585	139	0.1387	2663	X-RAY DIFFRACTION	100
2.0163-2.0511	0.1761	120	0.1405	2611	X-RAY DIFFRACTION	100
2.0511-2.0884	0.1682	138	0.1424	2614	X-RAY DIFFRACTION	100
2.0884-2.1285	0.1572	138	0.1298	2619	X-RAY DIFFRACTION	100
2.1285-2.172	0.1668	130	0.131	2624	X-RAY DIFFRACTION	100
2.172-2.2192	0.1485	115	0.133	2635	X-RAY DIFFRACTION	100
2.2192-2.2708	0.1594	133	0.1309	2626	X-RAY DIFFRACTION	100
2.2708-2.3276	0.1609	131	0.1302	2652	X-RAY DIFFRACTION	100
2.3276-2.3905	0.1835	142	0.1361	2619	X-RAY DIFFRACTION	100
2.3905-2.4609	0.1777	139	0.1345	2650	X-RAY DIFFRACTION	100
2.4609-2.5403	0.1553	161	0.1387	2594	X-RAY DIFFRACTION	100
2.5403-2.6311	0.1659	148	0.1345	2620	X-RAY DIFFRACTION	100
2.6311-2.7364	0.1606	134	0.1371	2624	X-RAY DIFFRACTION	100
2.7364-2.8609	0.1583	137	0.1408	2661	X-RAY DIFFRACTION	100
2.8609-3.0117	0.1553	150	0.1458	2608	X-RAY DIFFRACTION	100
3.0117-3.2003	0.1681	145	0.1492	2612	X-RAY DIFFRACTION	100
3.2003-3.4474	0.1601	142	0.1411	2655	X-RAY DIFFRACTION	100
3.4474-3.7941	0.1456	163	0.1337	2612	X-RAY DIFFRACTION	100
3.7941-4.3426	0.1529	140	0.1159	2654	X-RAY DIFFRACTION	100
4.3426-5.4695	0.1329	153	0.1258	2651	X-RAY DIFFRACTION	100
5.4695-42.9187	0.1636	150	0.1525	2654	X-RAY DIFFRACTION	98

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	0.0945	0.0397	0.0642	0.1166	0.0338	0.2728	-0.0109	0.0702	0.1561	-0.0974	0.0099	-0.1447	-0.1029	0.2178	0.0128	0.1692	-0.0436	0.0163	0.1396	0.0106	0.1583	7.2307	27.841	-23.9615
2	0.0502	-0.0098	-0.0386	0.146	-0.0083	0.0317	0.1519	-0.6	0.0498	0.0938	-0.0306	-0.3018	-0.0713	0.1541	0.0041	0.1651	-0.0331	-0.0364	0.3064	-0.0036	0.169	13.0813	15.1172	-3.7288
3	0.3127	0.1978	0.1128	0.1186	0.0119	0.356	0.0246	-0.0571	-0.0331	-0.0272	-0.0264	-0.078	0.017	0.132	-0.0034	0.1159	-0.0218	-0.004	0.1383	-0.0078	0.1191	5.5951	18.4019	-12.3404
4	0.2502	-0.08	-0.0601	0.1236	-0.0401	0.1724	0.009	-0.1572	0.0071	0.0125	-0.0524	0.0202	-0.0201	-0.0615	-0.0128	0.1076	-0.0103	0.0014	0.1335	-0.0302	0.0953	-9.7879	18.1932	-7.2214
5	0.5126	0.1245	-0.0034	0.3107	-0.0335	0.7249	-0.0447	0.0648	0.1054	-0.1075	-0.0135	0.079	-0.0661	-0.146	-0.0652	0.1174	0.0116	-0.0139	0.1091	-0.0048	0.1113	-10.7759	22.0451	-25.5616
6	0.0774	0.0329	0.0047	0.0147	0.0092	0.2014	0.0304	-0.0624	0.0747	-0.0098	0.0095	0.1238	-0.0959	-0.1205	0.0144	0.0848	-0.0086	-0.0013	0.2488	-0.053	0.169	-26.0425	16.8875	-9.7531
7	0.3597	-0.1257	0.1344	0.2216	-0.0231	0.1719	-0.0256	-0.0327	-0.0087	0.0315	0.0018	-0.1722	0.0168	0.1424	0.0119	0.1324	0.0085	0.0016	0.1159	0.0145	0.172	13.9259	-12.875	-26.8781
8	0.1031	0.0017	-0.0838	0.0591	-0.0924	0.1959	-0.0017	0.0185	0.0577	0.01	-0.0677	-0.118	-0.067	0.2171	0	0.1696	-0.0157	-0.0049	0.162	0.0008	0.2092	15.6193	-6.303	-32.5432
9	0.3803	0.2266	-0.0885	0.2311	0.0265	0.3123	-0.0078	0.1682	-0.0053	-0.1271	-0.0245	0.0067	-0.0224	-0.0348	-0.0495	0.1286	0.0074	-0.0084	0.1109	-0.0284	0.1056	2.7447	-10.7859	-38.4044
10	0.0894	-0.1392	0.0479	0.7321	0.0554	0.7339	0.1205	0.2556	-0.19	-0.2415	-0.1224	0.5471	-0.0173	-0.3143	0.0947	0.1707	0.0139	-0.1086	0.2023	-0.0756	0.1922	-11.4575	-12.8948	-40.0493
11	0.5474	-0.0512	0.0411	0.5471	-0.1153	0.2367	-0.014	-0.0629	-0.1781	0.0625	0.0039	0.1462	0.051	-0.0838	0.009	0.1235	-0.0116	0.0063	0.1119	0.0033	0.1582	-4.4954	-15.3641	-21.7417
12	0.0771	-0.0359	-0.0106	0.0881	-0.0117	-0.0026	-0.0653	0.1444	0.0168	-0.2592	-0.1166	0.1909	0.0293	-0.1031	-0.2606	0.1285	0.0126	-0.2793	0.3369	-0.1676	0.3794	-15.2744	-13.9819	-45.8822

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 14 through 63 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 64 through 85 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 86 through 156 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 157 through 225 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 226 through 358 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 359 through 378 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 14 through 83 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 84 through 127 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 128 through 212 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 213 through 255 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 256 through 358 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 359 through 382 )

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Protein , 1 types, 2 molecules AB

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Non-polymers , 6 types, 750 molecules

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