PDB-5dc6: Crystal structure of D176N-Y306F HDAC8 in complex with a tetrapep...

ID or keywords:

Entry

Database: PDB / ID: 5dc6

Title

Crystal structure of D176N-Y306F HDAC8 in complex with a tetrapeptide substrate

Components

Fluor-de-Lys tetrapeptide assay substrate
Histone deacetylase 8

Keywords

HYDROLASE / histone deacetylase 8 / arginase fold / deacetylase / enzyme-substrate 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)
synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.553 Å

Authors

Decroos, C. / Lee, M.S. / Christianson, D.W.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM49758	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM40602	United States

Citation

Journal: Biochemistry / Year: 2016
Title: General Base-General Acid Catalysis in Human Histone Deacetylase 8.
Authors: Gantt, S.M. / Decroos, C. / Lee, M.S. / Gullett, L.E. / Bowman, C.M. / Christianson, D.W. / Fierke, C.A.

History

Deposition	Aug 23, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 3, 2016	Provider: repository / Type: Initial release
Revision 1.1	Feb 17, 2016	Group: Database references
Revision 1.2	Sep 13, 2017	Group: Author supporting evidence / Database references / Derived calculations Category: citation / pdbx_audit_support / pdbx_struct_oper_list Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3	Dec 25, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4	Sep 27, 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_conn_type 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.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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.5	Nov 15, 2023	Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5dc6.cif.gz	326.1 KB	Display	PDBx/mmCIF format
PDB format	pdb5dc6.ent.gz	264.3 KB	Display	PDB format
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Validation report

Summary document	5dc6_validation.pdf.gz	458.6 KB	Display	wwPDB validaton report
Full document	5dc6_full_validation.pdf.gz	460 KB	Display
Data in XML	5dc6_validation.xml.gz	33.6 KB	Display
Data in CIF	5dc6_validation.cif.gz	50.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dc/5dc6 ftp://data.pdbj.org/pub/pdb/validation_reports/dc/5dc6	HTTPS FTP

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Related structure data

Related structure data	5dc5C 5dc7C 5dc8C 3ewfS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5d1c-1 4qa7-d 3ewf-5 4qa6-1 4qa6-2 5d1c-2 5dc8-2 5dc7-2 5dc8-1 3ewf-2 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

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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) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

Deposited unit

A: Histone deacetylase 8

B: Histone deacetylase 8

C: Fluor-de-Lys tetrapeptide assay substrate

D: Fluor-de-Lys tetrapeptide assay substrate

hetero molecules

88.6 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Histone deacetylase 8

C: Fluor-de-Lys tetrapeptide assay substrate

hetero molecules

defined by author&software
44.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Histone deacetylase 8

D: Fluor-de-Lys tetrapeptide assay substrate

hetero molecules

defined by author&software
44.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	82.332, 98.206, 104.281
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

#1: Protein	Histone deacetylase 8 / HD8 Mass: 43215.008 Da / Num. of mol.: 2 / Mutation: D176N, Y306F 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
#2: Protein/peptide	Fluor-de-Lys tetrapeptide assay substrate Mass: 836.980 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

#1: Protein

Histone deacetylase 8 / HD8

Mass: 43215.008 Da / Num. of mol.: 2 / Mutation: D176N, Y306F
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

#2: Protein/peptide

Fluor-de-Lys tetrapeptide assay substrate

Mass: 836.980 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 598 molecules

#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.: 2 / Source method: obtained synthetically / Formula: K
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 591 / 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: 2.39 Å³/Da / Density % sol: 48.59 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 100 mM Tris (pH 8.0), 13% (w/v) PEG 8000, and 4 mM TCEP

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 20, 2015
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 1.55→49.103 Å / Num. obs: 122036 / % possible obs: 99.9 % / Redundancy: 7.1 % / R_merge(I) obs: 0.11 / Net I/σ(I): 15.6
Reflection shell	Resolution: 1.55→1.61 Å / Redundancy: 6.6 % / R_merge(I) obs: 1.039 / Mean I/σ(I) obs: 2 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
PHENIX	dev_1833	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3EWF

3ewf

Resolution: 1.553→49.103 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 16.69 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1663	6116	5.02 %
R_work	0.1467	-	-
obs	0.1477	121931	99.68 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.553→49.103 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5744	0	22	591	6357

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	6400
X-RAY DIFFRACTION	f_angle_d	1.246	8743
X-RAY DIFFRACTION	f_dihedral_angle_d	12.733	2339
X-RAY DIFFRACTION	f_chiral_restr	0.059	931
X-RAY DIFFRACTION	f_plane_restr	0.007	1153

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 (%)
1.553-1.5702	0.2677	166	0.2403	3611	X-RAY DIFFRACTION	93
1.5702-1.5887	0.2519	207	0.2337	3822	X-RAY DIFFRACTION	100
1.5887-1.6081	0.2138	210	0.2192	3817	X-RAY DIFFRACTION	100
1.6081-1.6284	0.2331	208	0.21	3799	X-RAY DIFFRACTION	100
1.6284-1.6499	0.2342	207	0.2006	3822	X-RAY DIFFRACTION	100
1.6499-1.6725	0.2361	225	0.1919	3793	X-RAY DIFFRACTION	100
1.6725-1.6964	0.2203	203	0.1916	3838	X-RAY DIFFRACTION	100
1.6964-1.7217	0.2307	174	0.1814	3883	X-RAY DIFFRACTION	100
1.7217-1.7486	0.2039	194	0.1736	3854	X-RAY DIFFRACTION	100
1.7486-1.7773	0.1852	204	0.1618	3826	X-RAY DIFFRACTION	100
1.7773-1.8079	0.1725	224	0.1534	3828	X-RAY DIFFRACTION	100
1.8079-1.8408	0.1621	184	0.1518	3826	X-RAY DIFFRACTION	100
1.8408-1.8762	0.1855	217	0.1442	3831	X-RAY DIFFRACTION	100
1.8762-1.9145	0.17	210	0.1402	3856	X-RAY DIFFRACTION	100
1.9145-1.9561	0.1654	186	0.144	3845	X-RAY DIFFRACTION	100
1.9561-2.0016	0.1824	203	0.1487	3860	X-RAY DIFFRACTION	100
2.0016-2.0517	0.1615	200	0.1445	3834	X-RAY DIFFRACTION	100
2.0517-2.1072	0.193	211	0.1437	3848	X-RAY DIFFRACTION	100
2.1072-2.1692	0.1577	195	0.1385	3874	X-RAY DIFFRACTION	100
2.1692-2.2392	0.1601	188	0.1376	3886	X-RAY DIFFRACTION	100
2.2392-2.3192	0.1745	204	0.1407	3859	X-RAY DIFFRACTION	100
2.3192-2.4121	0.1639	202	0.1425	3877	X-RAY DIFFRACTION	100
2.4121-2.5218	0.1837	218	0.1435	3868	X-RAY DIFFRACTION	100
2.5218-2.6548	0.1752	201	0.1473	3902	X-RAY DIFFRACTION	100
2.6548-2.8211	0.1533	219	0.1455	3872	X-RAY DIFFRACTION	100
2.8211-3.0389	0.1818	199	0.1472	3913	X-RAY DIFFRACTION	100
3.0389-3.3446	0.1739	229	0.1425	3887	X-RAY DIFFRACTION	100
3.3446-3.8284	0.1392	208	0.1338	3953	X-RAY DIFFRACTION	100
3.8284-4.8228	0.1193	203	0.1211	3986	X-RAY DIFFRACTION	100
4.8228-49.1276	0.1573	217	0.152	4145	X-RAY DIFFRACTION	100

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	1.1274	0.0591	-0.2525	2.073	0.4641	1.0674	0.0505	0.2089	0.0741	-0.2752	-0.0213	-0.2125	-0.1482	0.0858	-0.0327	0.2361	-0.0088	0.0413	0.2235	0.0311	0.1979	-1.1845	-2.1915	-9.0896
2	1.8292	-0.3781	-0.5881	1.4538	0.471	1.7399	0.0201	0.2544	-0.1402	-0.1308	-0.1156	0.0998	0.0497	-0.1975	0.0983	0.1576	0.0112	0.0042	0.1599	-0.0252	0.141	-13.728	-15.6511	-7.0142
3	1.2758	-0.8547	-0.1369	1.385	0.393	1.2981	-0.0578	-0.0775	-0.1386	0.1127	0.0636	0.0036	0.1731	0.0507	-0.0117	0.1574	0.0067	-0.001	0.1448	0.0074	0.1754	-5.7489	-19.3301	9.2334
4	0.6742	-0.1889	-0.0131	1.4343	-0.045	0.7885	-0.0339	-0.0835	0.0647	0.1181	0.0309	-0.2015	-0.0708	0.134	0.0101	0.145	-0.0092	-0.0212	0.1784	-0.0081	0.1838	-0.7693	-2.8888	9.5266
5	0.998	-0.141	-0.2376	1.8829	-0.6784	1.7058	-0.0304	-0.2433	0.0938	0.3987	0.1134	-0.0044	-0.0886	0.0442	-0.075	0.221	-0.0114	-0.0351	0.2125	-0.0258	0.1542	-6.7985	-1.0564	17.6555
6	1.4638	-0.2683	0.2084	2.3669	-0.0098	1.5799	-0.0033	0.1736	-0.1031	-0.2456	0.0115	0.1742	0.1076	0.086	-0.0084	0.2189	0.0085	-0.0329	0.2229	-0.0168	0.1911	-38.911	0.8384	-6.5714
7	1.1662	0.9434	-0.4257	1.0848	-0.0712	0.6938	-0.0164	0.1522	-0.0309	-0.1995	0.0764	0.3759	0.0458	-0.1822	-0.063	0.1951	-0.0048	-0.0582	0.2384	-0.0097	0.2576	-46.1072	-2.2093	-3.2999
8	2.2073	0.1849	-0.2487	2.7796	0.2422	2.0065	0.012	0.548	0.1021	-0.4789	-0.0876	0.054	-0.2525	-0.1189	0.023	0.3142	0.011	-0.0193	0.2808	0.0465	0.2126	-30.2987	18.38	-12.3955
9	2.2075	-0.1723	0.6901	1.3669	-0.3247	1.4991	-0.0009	0.3656	-0.0111	-0.199	-0.0461	-0.0416	-0.0715	0.1549	0.0448	0.2504	0.008	-0.0217	0.1877	0.0036	0.1593	-30.0022	11.8235	-8.2006
10	1.2903	-0.2213	-0.1066	1.5338	-0.127	1.2775	-0.0381	0.058	0.0825	0.0113	0.0035	0.1206	-0.1462	-0.1004	0.0359	0.1888	0.0309	-0.0186	0.1582	0.0028	0.1707	-36.8936	11.4875	-0.1226
11	1.2545	-0.3802	0.2811	1.7217	-0.4108	2.3915	-0.0981	0.033	0.1383	-0.0483	0.0068	0.2072	-0.3438	-0.1553	0.0341	0.2337	0.054	-0.0193	0.1709	0.0044	0.2422	-44.4971	20.0134	3.4499
12	0.9366	-1.0555	0.2398	2.6254	-0.4084	1.0408	-0.1575	-0.0036	0.0865	0.0912	0.0827	0.0149	-0.2437	-0.0419	0.0541	0.1962	0.0241	-0.0141	0.1584	-0.0072	0.1812	-33.7006	17.6267	10.4444
13	1.4947	-0.969	-0.0384	1.8555	0.1349	1.3261	-0.1056	-0.1393	0.2985	0.0801	0.1096	-0.1286	-0.3798	0.0304	0.0485	0.2664	0.0001	-0.0308	0.174	-0.0145	0.1866	-28.6871	20.4766	15.0984
14	1.0532	-0.8787	0.2613	2.5357	-0.4269	1.2009	-0.0826	-0.1372	-0.032	0.3253	0.0591	0.2063	-0.1178	-0.1241	0.0262	0.2682	0.0534	0.0416	0.2283	-0.0128	0.1769	-38.2667	10.5418	21.583
15	0.9909	-0.3632	-0.0012	1.1896	0.0495	1.0512	-0.0698	-0.1291	0.009	0.1318	0.0646	0.1749	-0.0407	-0.135	0.0311	0.1703	0.0157	0.0303	0.184	0.0063	0.2039	-40.4848	4.9602	12.2256
16	1.3209	-0.2116	0.3062	2.5206	0.5333	1.6191	-0.039	-0.0441	-0.0779	0.0716	0.0017	0.3734	0.164	-0.2255	0.0223	0.1678	-0.0196	0.0101	0.1885	0.0032	0.2141	-43.5414	-8.3925	6.201
17	0.7805	0.1418	0.3108	2.0516	0.7753	1.7931	-0.0407	-0.1483	-0.0067	0.2682	0.1035	-0.0596	-0.0783	-0.0068	-0.0425	0.191	0.0134	0.0199	0.2117	0.0147	0.1513	-32.42	3.082	21.1073

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 156 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 157 through 225 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 226 through 336 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 337 through 376 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 14 through 36 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 37 through 63 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 64 through 85 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 86 through 127 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 128 through 156 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 157 through 176 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 177 through 202 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 203 through 225 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 226 through 255 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 256 through 307 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 308 through 336 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 337 through 377 )

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

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Non-polymers , 4 types, 598 molecules

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-Protein / Protein/peptide , 2 types, 4 molecules ABCD

-Non-polymers , 4 types, 598 molecules

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

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-Feb 9, 2022. New format data for meta-information of EMDB entries

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+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

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Open data

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Basic information

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Download

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Validation report

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Related structure data

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Links

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Assembly

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

-
Non-polymers , 4 types, 598 molecules

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

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About Yorodumi

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News

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Aug 12, 2020. Covid-19 info

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi