PDB-5d1c: Crystal structure of D233G-Y306F HDAC8 in complex with a tetrapep...

ID or keywords:

Entry

Database: PDB / ID: 5d1c

Title

Crystal structure of D233G-Y306F HDAC8 in complex with a tetrapeptide substrate

Components

HDAC8 Fluor de Lys tetrapeptide substrate
Histone deacetylase 8

Keywords

HYDROLASE / histone deacetylase / arginase/deacetylase fold / enzyme substrate complex

Function / homology

Function and homology information

histone decrotonylase activity / histone H4K16 deacetylase activity, hydrolytic mechanism / histone H4K5 deacetylase activity, hydrolytic mechanism / histone H4K8 deacetylase activity, hydrolytic mechanism / histone H3K4 deacetylase activity, hydrolytic mechanism / histone H3K14 deacetylase activity, hydrolytic mechanism / histone H4K12 deacetylase activity, hydrolytic mechanism / histone deacetylase / histone H3K9 deacetylase activity, hydrolytic mechanism / regulation of telomere maintenance ...
Similarity search - Function

Biological species

Homo sapiens (human)
unidentified (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.422 Å

Authors

Decroos, C. / Christianson, N.H. / Gullett, L.E. / Bowman, C.M. / Christianson, K.E. / Deardorff, M.A. / Christianson, D.W.

Funding support

United States, 2items

Citation

Journal: Biochemistry / Year: 2015
Title: Biochemical and Structural Characterization of HDAC8 Mutants Associated with Cornelia de Lange Syndrome Spectrum Disorders.
Authors: Decroos, C. / Christianson, N.H. / Gullett, L.E. / Bowman, C.M. / Christianson, K.E. / Deardorff, M.A. / Christianson, D.W.

History

Deposition	Aug 4, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 21, 2015	Provider: repository / Type: Initial release
Revision 1.1	Oct 28, 2015	Group: Database references
Revision 1.2	Nov 11, 2015	Group: Database references
Revision 1.3	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 1.4	Dec 25, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5	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 1.6	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
Revision 1.7	Oct 23, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5d1c.cif.gz	326.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5d1c.ent.gz	262.5 KB	Display	PDB format
PDBx/mmJSON format	5d1c.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5d1c_validation.pdf.gz	460.6 KB	Display	wwPDB validaton report
Full document	5d1c_full_validation.pdf.gz	463.7 KB	Display
Data in XML	5d1c_validation.xml.gz	36.2 KB	Display
Data in CIF	5d1c_validation.cif.gz	56.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/d1/5d1c ftp://data.pdbj.org/pub/pdb/validation_reports/d1/5d1c	HTTPS FTP

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Related structure data

Related structure data	5d1bC 5d1dC 3ewfS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5dc8-2 5dc6-1 5dc6-2 4qa6-2 6oda-1 4qa7-d 5dc7-2 5dc8-1 3ewf-5 6whz-3 4ly1-3 5ths-1 3mz6-d 7kbg-1 4rn0-1 1c3s-d 7kbh-3 4rn0-2 5tht-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

Related structure data

5d1bC

5d1dC

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

Deposited unit

A: Histone deacetylase 8

B: Histone deacetylase 8

C: HDAC8 Fluor de Lys tetrapeptide substrate

D: HDAC8 Fluor de Lys tetrapeptide substrate

hetero molecules

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

1

A: Histone deacetylase 8

C: HDAC8 Fluor de Lys tetrapeptide substrate

hetero molecules

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

2

B: Histone deacetylase 8

D: HDAC8 Fluor de Lys tetrapeptide substrate

hetero molecules

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

Unit cell

Length a, b, c (Å)	83.031, 97.936, 104.656
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: 43157.957 Da / Num. of mol.: 2 / Mutation: D233G, 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 / Strain (production host): BL21(DE3) / References: UniProt: Q9BY41, histone deacetylase
#2: Protein/peptide	HDAC8 Fluor de Lys tetrapeptide substrate Mass: 836.980 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) unidentified (others)

#1: Protein

Histone deacetylase 8 / HD8

Mass: 43157.957 Da / Num. of mol.: 2 / Mutation: D233G, 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 / Strain (production host): BL21(DE3) / References: UniProt: Q9BY41, histone deacetylase

#2: Protein/peptide

HDAC8 Fluor de Lys tetrapeptide substrate

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

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Non-polymers , 4 types, 818 molecules

#3: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#4: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 811 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.42 Å³/Da / Density % sol: 49.13 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 100 mM Tris (pH 8.0), 10% (w/v) PEG 3350, 4 mM TCEP

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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
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: 1.42→44.4 Å / Num. obs: 159962 / % possible obs: 99.9 % / Redundancy: 12.5 % / R_merge(I) obs: 0.072 / Net I/σ(I): 28.5
Reflection shell	Resolution: 1.42→1.47 Å / Redundancy: 11.4 % / R_merge(I) obs: 1.112 / Mean I/σ(I) obs: 2.5 / % possible all: 100

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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: 1.422→44.353 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 15.66 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.167	8011	5.01 %	random
R_work	0.1464	-	-	-
obs	0.1474	159859	99.75 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.422→44.353 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5735	0	12	811	6558

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	6259
X-RAY DIFFRACTION	f_angle_d	1.272	8555
X-RAY DIFFRACTION	f_dihedral_angle_d	12.195	2300
X-RAY DIFFRACTION	f_chiral_restr	0.082	922
X-RAY DIFFRACTION	f_plane_restr	0.007	1117

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 (%)
1.4217-1.4379	0.268	241	0.2547	4781	X-RAY DIFFRACTION	95
1.4379-1.4548	0.271	266	0.2328	5009	X-RAY DIFFRACTION	100
1.4548-1.4725	0.2348	275	0.2064	4991	X-RAY DIFFRACTION	100
1.4725-1.4912	0.1993	278	0.1915	5041	X-RAY DIFFRACTION	100
1.4912-1.5108	0.2203	245	0.1881	5056	X-RAY DIFFRACTION	100
1.5108-1.5315	0.1767	264	0.1696	5010	X-RAY DIFFRACTION	100
1.5315-1.5534	0.1943	232	0.1641	5051	X-RAY DIFFRACTION	100
1.5534-1.5766	0.1924	277	0.1637	4998	X-RAY DIFFRACTION	100
1.5766-1.6012	0.191	244	0.1582	5045	X-RAY DIFFRACTION	100
1.6012-1.6275	0.1695	251	0.1546	5070	X-RAY DIFFRACTION	100
1.6275-1.6555	0.1858	293	0.1493	4978	X-RAY DIFFRACTION	100
1.6555-1.6856	0.1599	241	0.1431	5092	X-RAY DIFFRACTION	100
1.6856-1.7181	0.1745	280	0.146	5020	X-RAY DIFFRACTION	100
1.7181-1.7531	0.1788	271	0.1466	5034	X-RAY DIFFRACTION	100
1.7531-1.7912	0.1683	282	0.1434	5016	X-RAY DIFFRACTION	100
1.7912-1.8329	0.1618	277	0.1419	5075	X-RAY DIFFRACTION	100
1.8329-1.8788	0.1602	295	0.139	5010	X-RAY DIFFRACTION	100
1.8788-1.9296	0.1632	261	0.143	5077	X-RAY DIFFRACTION	100
1.9296-1.9863	0.1852	266	0.1488	5045	X-RAY DIFFRACTION	100
1.9863-2.0504	0.1757	241	0.1474	5100	X-RAY DIFFRACTION	100
2.0504-2.1237	0.1743	253	0.1479	5097	X-RAY DIFFRACTION	100
2.1237-2.2088	0.1562	241	0.1424	5091	X-RAY DIFFRACTION	100
2.2088-2.3093	0.1557	262	0.1428	5099	X-RAY DIFFRACTION	100
2.3093-2.431	0.161	296	0.1447	5066	X-RAY DIFFRACTION	100
2.431-2.5833	0.1615	253	0.151	5108	X-RAY DIFFRACTION	100
2.5833-2.7827	0.1608	295	0.1468	5092	X-RAY DIFFRACTION	100
2.7827-3.0627	0.1713	265	0.149	5156	X-RAY DIFFRACTION	100
3.0627-3.5057	0.1646	269	0.1408	5159	X-RAY DIFFRACTION	100
3.5057-4.4162	0.1377	298	0.1224	5173	X-RAY DIFFRACTION	100
4.4162-44.3747	0.1682	299	0.1413	5308	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	5.8076	-0.0151	0.0561	2.2594	0.0688	2.8828	-0.0117	0.3276	-0.0729	-0.2761	0.028	-0.1145	-0.1676	-0.0883	-0.0039	0.1716	0.0074	0.0441	0.1239	0.006	0.1252	-1.4761	-0.6762	-6.1788
2	0.7695	-0.3963	-0.1786	1.5722	0.2202	0.7071	0.0008	0.1565	0.0328	-0.221	0.0494	-0.3809	-0.0763	0.1702	-0.0756	0.1286	-0.0156	0.0637	0.1665	-0.0074	0.1805	4.8296	2.3395	-3.1655
3	4.3755	-1.6503	1.6453	2.2723	-0.0317	1.7179	0.1824	0.6692	-0.207	-0.4261	-0.1964	-0.0753	0.3589	0.2498	0.025	0.2498	0.0216	0.0156	0.2313	-0.0762	0.183	-10.5223	-18.9319	-11.9948
4	2.282	-0.0538	-0.2852	1.4587	0.2663	1.5225	-0.0449	0.3977	-0.1386	-0.1911	-0.0202	0.0767	0.1014	-0.1564	0.0577	0.1741	-0.0081	0.0199	0.1467	-0.0257	0.1222	-11.4703	-11.8817	-8.216
5	0.8579	-0.4548	0.0927	1.1559	0.0584	1.039	-0.0389	-0.0058	-0.1401	0.0076	0.0164	-0.0722	0.2174	0.0388	0.0195	0.1358	0.0238	0.0147	0.0865	0.0026	0.13	-5.4192	-16.5427	7.0857
6	0.5418	-0.2655	0.0797	1.5289	-0.0856	0.8467	-0.0581	-0.1008	-0.0261	0.1612	0.0473	-0.1863	0.0264	0.1147	0.0233	0.0972	0.0231	-0.0239	0.1223	0.0033	0.1108	-0.6622	-3.0245	13.3958
7	0.5132	-0.1341	-0.0379	2.0453	-0.9012	1.3144	-0.0785	-0.1606	-0.0441	0.2371	0.1761	0.1116	0.1024	-0.0421	-0.1121	0.1753	0.0282	0.0066	0.1666	0.0134	0.1073	-8.6113	-2.2391	20.592
8	1.3025	0.3152	0.1998	2.3613	-0.5589	1.0314	0.0163	0.2172	-0.1273	-0.3361	0.011	0.2218	0.1839	-0.0824	-0.0216	0.1818	-0.0137	-0.0328	0.1577	-0.0345	0.1406	-40.2613	1.8056	-8.9931
9	2.6766	-0.4153	0.3948	2.6517	0.1915	2.1528	0.1666	0.4904	0.216	-0.3146	-0.3007	-0.0989	-0.3355	0.1753	-0.0204	0.156	0.01	0.002	0.2071	0.0663	0.1207	-25.8448	21.239	-11.022
10	1.6692	-0.2234	0.1691	1.5814	-0.2912	1.5106	0.0028	0.2005	0.0658	-0.1277	-0.0674	-0.0601	0.0046	0.1459	0.0232	0.0969	0.0099	-0.0023	0.0978	0.0187	0.0617	-28.3289	13.8305	-5.6322
11	1.2656	-0.8278	-0.2031	1.5094	-0.1922	1.1049	-0.0759	-0.0978	0.1087	0.1417	0.0914	0.0172	-0.1388	-0.0333	-0.0112	0.0831	0.0144	0.005	0.0793	-0.0013	0.0822	-35.8815	18.9054	9.2173
12	0.8214	-0.1693	-0.0274	1.3905	-0.0464	0.7541	-0.0596	-0.0985	-0.1176	0.1348	0.0665	0.2148	0.0812	-0.1286	0.0128	0.0944	-0.0014	0.0307	0.118	0.0228	0.1296	-40.9586	2.9688	9.717
13	0.8601	-0.2726	0.0291	2.2884	0.8821	1.4436	-0.0414	-0.2779	-0.1186	0.379	0.1273	0.0208	0.0533	-0.0927	-0.0749	0.2061	0.0142	0.0334	0.1974	0.0327	0.1301	-35.1256	1.8721	17.9476

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 14 through 36 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 37 through 63 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 64 through 85 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 86 through 127 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 128 through 225 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 226 through 336 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 337 through 377 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 14 through 63 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 64 through 85 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 86 through 156 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 157 through 225 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 226 through 336 )
13	X-RAY DIFFRACTION	13	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, 818 molecules

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