PDB-5z94: Crystal Structure of SIRT3 in complex with H3K4bhb peptide

ID or keywords:

Entry

Database: PDB / ID: 5z94

Title

Crystal Structure of SIRT3 in complex with H3K4bhb peptide

Components

Gene for histone H3 (germline gene)
NAD-dependent protein deacetylase sirtuin-3, mitochondrial

Keywords

HYDROLASE / Rossmann fold

Function / homology

Function and homology information

positive regulation of catalase activity / positive regulation of ceramide biosynthetic process / peptidyl-lysine deacetylation / positive regulation of superoxide dismutase activity / NAD-dependent protein lysine deacetylase activity / protein acetyllysine N-acetyltransferase / protein deacetylation / NAD-dependent histone deacetylase activity / Regulation of FOXO transcriptional activity by acetylation / NAD+ binding ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.899 Å

Authors

Zhang, X. / Li, H.

Citation

Journal: To Be Published
Title: Crystal Structure of SIRT3 in complex with H3K4bhb peptide
Authors: Zhang, X. / Li, H.

History

Deposition	Feb 2, 2018	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Feb 6, 2019	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5z94.cif.gz	241.6 KB	Display	PDBx/mmCIF format
PDB format	pdb5z94.ent.gz	202.1 KB	Display	PDB format
PDBx/mmJSON format	5z94.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5z94_validation.pdf.gz	480.6 KB	Display	wwPDB validaton report
Full document	5z94_full_validation.pdf.gz	482.7 KB	Display
Data in XML	5z94_validation.xml.gz	27.8 KB	Display
Data in CIF	5z94_validation.cif.gz	41 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/z9/5z94 ftp://data.pdbj.org/pub/pdb/validation_reports/z9/5z94	HTTPS FTP

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Related structure data

Similar structure data	7kl4-d 1iep-1 4fz3-d 3glt-d 2j4z-2 1gx2-1 3lzb-1 4js8-d 4rs3-d 3jyn-d 3dae-2 1iz0-d 2h6d-d 4bvf-1 4apr-d 7chm-d 3pyy-1 3mn3-d 4o6l-1 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

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#213 - Sep 2017 Sirtuins similarity (8) #263 - Nov 2021 Acetohydroxyacid Synthase similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #194 - Feb 2016 Designer Insulins similarity (1) #233 - May 2019 S-Nitrosylated Hemoglobin similarity (1) #14 - Feb 2001 Insulin similarity (1) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (1) #149 - May 2012 Leptin similarity (1) #202 - Oct 2016 Dipeptidyl Peptidase 4 similarity (1) #222 - Jun 2018 Proteins and Nanoparticles similarity (1) #57 - Sep 2004 Catalase similarity (1) #94 - Oct 2007 Superoxide Dismutase similarity (1) #7 - Jul 2000 Nucleosome similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#213 - Sep 2017
Sirtuins
similarity (8)
#263 - Nov 2021
Acetohydroxyacid Synthase
similarity (1)
#122 - Feb 2010
Enhanceosome
similarity (1)
#194 - Feb 2016
Designer Insulins
similarity (1)
#233 - May 2019
S-Nitrosylated Hemoglobin
similarity (1)
#14 - Feb 2001
Insulin
similarity (1)
#258 - Jun 2021
Glucocorticoid Receptor and Dexamethasone
similarity (1)
#149 - May 2012
Leptin
similarity (1)
#202 - Oct 2016
Dipeptidyl Peptidase 4
similarity (1)
#222 - Jun 2018
Proteins and Nanoparticles
similarity (1)
#57 - Sep 2004
Catalase
similarity (1)
#94 - Oct 2007
Superoxide Dismutase
similarity (1)
#7 - Jul 2000
Nucleosome
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (1)

Deposited unit

A: NAD-dependent protein deacetylase sirtuin-3, mitochondrial

B: NAD-dependent protein deacetylase sirtuin-3, mitochondrial

C: Gene for histone H3 (germline gene)

D: Gene for histone H3 (germline gene)

hetero molecules

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

1

A: NAD-dependent protein deacetylase sirtuin-3, mitochondrial

C: Gene for histone H3 (germline gene)

hetero molecules

defined by author&software
Evidence: mass spectrometry
33.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: NAD-dependent protein deacetylase sirtuin-3, mitochondrial

D: Gene for histone H3 (germline gene)

hetero molecules

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

Unit cell

Length a, b, c (Å)	75.472, 76.260, 75.425
Angle α, β, γ (deg.)	90.00, 115.77, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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

#1: Protein	NAD-dependent protein deacetylase sirtuin-3, mitochondrial / hSIRT3 / Regulatory protein SIR2 homolog 3 / SIR2-like protein 3 Mass: 31427.162 Da / Num. of mol.: 2 / Fragment: UNP residues 117-399 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SIRT3, SIR2L3 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q9NTG7, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Protein/peptide	Gene for histone H3 (germline gene) Mass: 1650.879 Da / Num. of mol.: 2 / Fragment: UNP residues 2-16 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: V9H1G0

#1: Protein

NAD-dependent protein deacetylase sirtuin-3, mitochondrial / hSIRT3 / Regulatory protein SIR2 homolog 3 / SIR2-like protein 3

Mass: 31427.162 Da / Num. of mol.: 2 / Fragment: UNP residues 117-399
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: SIRT3, SIR2L3 / Production host:

Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9NTG7, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides

#2: Protein/peptide

Gene for histone H3 (germline gene)

Mass: 1650.879 Da / Num. of mol.: 2 / Fragment: UNP residues 2-16 / Source method: obtained synthetically / Source: (synth.)

Homo sapiens (human) / References: UniProt: V9H1G0

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Non-polymers , 5 types, 517 molecules

#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#6: Chemical	ChemComp-CIT / CITRIC ACID Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₈O₇
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 507 / 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: 2.95 Å³/Da / Density % sol: 58.37 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.2M Li2SO4, 0.1M sodium citrate, pH 6.0, 19% PEG 3,350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 25, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 1.9→50 Å / Num. obs: 60593 / % possible obs: 99.8 % / Redundancy: 3.7 % / R_merge(I) obs: 0.079 / Net I/σ(I): 26.4
Reflection shell	Resolution: 1.9→1.93 Å / R_merge(I) obs: 0.542 / Num. unique obs: 3065 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	(1.13_2998: ???)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.899→37.636 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.55 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1911	2779	4.59 %
R_work	0.1607	-	-
obs	0.1621	60593	99.5 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.899→37.636 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4406	0	62	507	4975

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	4590
X-RAY DIFFRACTION	f_angle_d	0.851	6246
X-RAY DIFFRACTION	f_dihedral_angle_d	16.273	2750
X-RAY DIFFRACTION	f_chiral_restr	0.054	702
X-RAY DIFFRACTION	f_plane_restr	0.006	812

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 (%)
1.899-1.9317	0.2896	105	0.2347	2733	X-RAY DIFFRACTION	94
1.9317-1.9669	0.2485	125	0.218	2876	X-RAY DIFFRACTION	100
1.9669-2.0047	0.2392	186	0.1991	2884	X-RAY DIFFRACTION	100
2.0047-2.0456	0.2079	158	0.1778	2849	X-RAY DIFFRACTION	100
2.0456-2.0901	0.1914	133	0.1566	2888	X-RAY DIFFRACTION	100
2.0901-2.1387	0.1945	145	0.1608	2864	X-RAY DIFFRACTION	100
2.1387-2.1922	0.1846	130	0.1546	2912	X-RAY DIFFRACTION	100
2.1922-2.2514	0.198	152	0.1511	2858	X-RAY DIFFRACTION	100
2.2514-2.3177	0.1766	127	0.148	2916	X-RAY DIFFRACTION	100
2.3177-2.3925	0.1795	115	0.1552	2935	X-RAY DIFFRACTION	100
2.3925-2.478	0.2356	119	0.1652	2906	X-RAY DIFFRACTION	100
2.478-2.5772	0.1756	130	0.1636	2915	X-RAY DIFFRACTION	100
2.5772-2.6944	0.232	144	0.1698	2932	X-RAY DIFFRACTION	100
2.6944-2.8364	0.2129	174	0.1643	2842	X-RAY DIFFRACTION	100
2.8364-3.0141	0.2164	166	0.1637	2864	X-RAY DIFFRACTION	100
3.0141-3.2467	0.1734	129	0.1656	2922	X-RAY DIFFRACTION	100
3.2467-3.5732	0.1632	142	0.1547	2895	X-RAY DIFFRACTION	100
3.5732-4.0897	0.1585	131	0.1443	2900	X-RAY DIFFRACTION	100
4.0897-5.1505	0.151	120	0.1368	2960	X-RAY DIFFRACTION	100
5.1505-37.6438	0.2107	148	0.1758	2963	X-RAY DIFFRACTION	99

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	0.4386	-0.5534	0.5531	0.7433	-0.5652	0.8073	0.0091	-0.1906	0.0698	0.2164	0.0192	-0.0359	-0.3405	-0.22	0	0.2138	0.0202	0.025	0.2738	-0.0216	0.1736	-15.9256	-1.3334	17.2126
2	-0.0016	-0.0105	-0.0276	0.0124	0.0365	0.0383	-0.0045	0.0776	-0.5802	0.4437	-0.0665	-0.7834	-0.1578	0.4172	-0.0002	0.359	-0.1109	-0.004	0.5229	0.0537	0.3969	7.7634	-0.2539	-3.4535
3	0.2268	0.0904	-0.127	0.4148	-0.0589	0.013	-0.1832	-0.0655	0.0523	0.1483	0.0585	-0.3664	0.0147	0.1926	-0	0.1932	0.0313	-0.037	0.158	0.0203	0.2006	2.3964	3.8922	-13.5171
4	0.508	0.5146	-0.1177	0.9812	0.1738	0.7314	-0.0115	0.0244	-0.0226	-0.1407	-0.0718	-0.0937	0.0858	-0.1693	0	0.1982	0.0062	0.0185	0.2179	0.0302	0.1805	-12.025	-8.4986	4.0738
5	0.5417	0.377	0.1201	-0.3075	-0.2512	1.25	-0.118	0.0346	-0.1001	0.0191	0.059	0.0589	0.1918	-0.1407	-0	0.2058	0.0067	0.0157	0.1217	0.0181	0.1639	-9.7754	-2.6446	-16.0439
6	0.1461	0.0132	-0.1666	0.5833	-0.3226	0.5577	0.0293	0.0182	0.1972	0.1019	0.0302	0.0525	-0.4362	-0.3155	-0.0001	0.2429	0.0734	0.0177	0.2855	-0.0061	0.2528	-17.8551	6.5097	5.0548
7	1.4271	0.3213	0.3532	0.9352	-0.7829	2.316	-0.0016	-0.4093	0.0263	0.2452	-0.085	-0.149	-0.2062	0.0086	-0.07	0.1447	0.0096	0.0122	0.1909	-0.0379	0.1414	-10.3997	-1.9289	15.8593
8	0.3507	-0.2792	0.3738	0.7463	-0.561	0.5581	0.0807	-0.1246	-0.2883	-0.1554	-0.0264	0.1803	0.1218	-0.2084	0.0044	0.1583	-0.0319	0.0023	0.2821	0.0146	0.2262	-43.7708	21.6633	-27.1156
9	0.1323	-0.2373	0.0729	0.911	-0.2456	0.0546	0.3974	0.5844	-0.3142	-0.8556	0.1559	0.2389	-0.3655	0.3277	0.0822	0.4071	0.0912	-0.0142	0.5918	-0.1138	0.3976	-14.756	20.6558	-39.4231
10	0.0921	-0.1598	-0.1188	0.4076	0.164	0.1351	0.0272	0.2114	0.1281	-0.3922	0.0557	-0.0048	0.1363	0.1002	0.0002	0.2405	0.001	-0.021	0.1715	0.0453	0.1744	-8.139	16.459	-30.2454
11	0.7194	-0.1487	0.0504	1.1007	0.528	0.473	0.0511	-0.2063	0.0793	-0.0062	-0.0991	-0.1362	-0.0096	-0.0229	-0	0.1627	0.0178	0.001	0.2066	0.0169	0.1891	-30.2331	28.8175	-24.9068
12	1.0284	-0.465	0.4859	-0.3508	0.1693	0.6485	-0.01	-0.1055	0.2057	0.0317	0.0536	0.0406	-0.0153	-0.0094	0.0013	0.1586	0.0105	-0.0115	0.1103	0.0108	0.202	-11.1351	22.9648	-18.1873
13	0.4732	-0.2686	0.237	0.5708	0.0305	0.2099	0.0637	-0.2857	-0.3381	0.0405	0.0391	0.1043	0.2722	-0.1889	0.0001	0.2243	-0.0281	0.018	0.2833	0.0638	0.2269	-33.3543	14.7602	-19.772
14	2.1216	-0.6255	0.4952	1.0899	-0.2832	1.6113	0.1383	0.1281	-0.2149	-0.2375	-0.0814	0.171	0.0931	-0.2874	0.0097	0.1342	-0.0408	0.0141	0.1728	-0.0043	0.1531	-39.7711	21.1926	-30.7575
15	0.2702	-0.0806	-0.235	0.0382	0.0736	0.1974	-0.135	-0.1573	0.4231	0.276	0.3218	0.3228	-0.6736	-0.229	0.016	0.4751	0.0888	-0.0031	0.1528	0.0021	0.3656	-11.1036	13.23	-5.1929
16	0.173	0.0208	0.0069	0.0259	0.0217	0.0495	0.1181	-0.0717	-0.3507	0.2808	0.1613	0.6362	0.4562	-0.0802	-0.003	0.3849	-0.0325	-0.0134	0.1529	0.0655	0.4015	-21.5219	7.0539	-21.6612

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 122 through 152 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 153 through 169 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 170 through 198 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 199 through 240 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 241 through 299 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 300 through 333 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 334 through 394 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 122 through 152 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 153 through 169 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 170 through 198 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 199 through 240 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 241 through 299 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 300 through 327 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 328 through 394 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 1 through 7 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 1 through 7 )

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