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

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Basic information

Entry
Database: PDB / ID: 5z94
TitleCrystal Structure of SIRT3 in complex with H3K4bhb peptide
Components
  • Gene for histone H3 (germline gene)
  • NAD-dependent protein deacetylase sirtuin-3, mitochondrial
KeywordsHYDROLASE / Rossmann fold
Function / homology
Function and homology information


positive regulation of superoxide dismutase activity / positive regulation of catalase activity / NAD-dependent protein lysine delactylase activity / positive regulation of ceramide biosynthetic process / peptidyl-lysine deacetylation / Maturation of TCA enzymes and regulation of TCA cycle / NAD-dependent protein lysine deacetylase activity / protein acetyllysine N-acetyltransferase / histone H3K14 deacetylase activity, NAD-dependent / histone H3K9 deacetylase activity, NAD-dependent ...positive regulation of superoxide dismutase activity / positive regulation of catalase activity / NAD-dependent protein lysine delactylase activity / positive regulation of ceramide biosynthetic process / peptidyl-lysine deacetylation / Maturation of TCA enzymes and regulation of TCA cycle / NAD-dependent protein lysine deacetylase activity / protein acetyllysine N-acetyltransferase / histone H3K14 deacetylase activity, NAD-dependent / histone H3K9 deacetylase activity, NAD-dependent / histone H4K16 deacetylase activity, NAD-dependent / histone H3K18 deacetylase activity, NAD-dependent / histone H3K56 deacetylase activity, NAD-dependent / histone H3K4 deacetylase activity, NAD-dependent / histone deacetylase activity, NAD-dependent / protein deacetylation / positive regulation of oxidative phosphorylation / Regulation of FOXO transcriptional activity by acetylation / protein lysine deacetylase activity / cellular response to stress / negative regulation of reactive oxygen species metabolic process / NAD+ binding / Mitochondrial unfolded protein response (UPRmt) / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / aerobic respiration / Transcriptional activation of mitochondrial biogenesis / negative regulation of ERK1 and ERK2 cascade / positive regulation of insulin secretion / structural constituent of chromatin / nucleosome / sequence-specific DNA binding / mitochondrial matrix / enzyme binding / protein-containing complex / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
SIR2/SIRT2 'Small Domain' / SIR2/SIRT2 'Small Domain' / Sirtuin, catalytic core small domain superfamily / Sirtuin family / : / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / TPP-binding domain / DHS-like NAD/FAD-binding domain superfamily ...SIR2/SIRT2 'Small Domain' / SIR2/SIRT2 'Small Domain' / Sirtuin, catalytic core small domain superfamily / Sirtuin family / : / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / TPP-binding domain / DHS-like NAD/FAD-binding domain superfamily / Histone H3 signature 1. / Histone H3/CENP-A / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / NAD-dependent protein deacetylase sirtuin-3, mitochondrial / Gene for histone H3 (germline gene)
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.899 Å
AuthorsZhang, X. / Li, H.
CitationJournal: To Be Published
Title: Crystal Structure of SIRT3 in complex with H3K4bhb peptide
Authors: Zhang, X. / Li, H.
History
DepositionFeb 2, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)67,23214
Polymers66,1564
Non-polymers1,07610
Water9,134507
1
A: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
C: Gene for histone H3 (germline gene)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6167
Polymers33,0782
Non-polymers5385
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-15 kcal/mol
Surface area13130 Å2
MethodPISA
2
B: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
D: Gene for histone H3 (germline gene)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6167
Polymers33,0782
Non-polymers5385
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-16 kcal/mol
Surface area12980 Å2
MethodPISA
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 number4
Space group name H-MP1211

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Components

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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

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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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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.95 Å3/Da / Density % sol: 58.37 %
Crystal growTemperature: 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

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 60593 / % possible obs: 99.8 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 26.4
Reflection shellResolution: 1.9→1.93 Å / Rmerge(I) obs: 0.542 / Num. unique obs: 3065 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod 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
RfactorNum. reflection% reflection
Rfree0.1911 2779 4.59 %
Rwork0.1607 --
obs0.1621 60593 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.899→37.636 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4406 0 62 507 4975
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064590
X-RAY DIFFRACTIONf_angle_d0.8516246
X-RAY DIFFRACTIONf_dihedral_angle_d16.2732750
X-RAY DIFFRACTIONf_chiral_restr0.054702
X-RAY DIFFRACTIONf_plane_restr0.006812
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.899-1.93170.28961050.23472733X-RAY DIFFRACTION94
1.9317-1.96690.24851250.2182876X-RAY DIFFRACTION100
1.9669-2.00470.23921860.19912884X-RAY DIFFRACTION100
2.0047-2.04560.20791580.17782849X-RAY DIFFRACTION100
2.0456-2.09010.19141330.15662888X-RAY DIFFRACTION100
2.0901-2.13870.19451450.16082864X-RAY DIFFRACTION100
2.1387-2.19220.18461300.15462912X-RAY DIFFRACTION100
2.1922-2.25140.1981520.15112858X-RAY DIFFRACTION100
2.2514-2.31770.17661270.1482916X-RAY DIFFRACTION100
2.3177-2.39250.17951150.15522935X-RAY DIFFRACTION100
2.3925-2.4780.23561190.16522906X-RAY DIFFRACTION100
2.478-2.57720.17561300.16362915X-RAY DIFFRACTION100
2.5772-2.69440.2321440.16982932X-RAY DIFFRACTION100
2.6944-2.83640.21291740.16432842X-RAY DIFFRACTION100
2.8364-3.01410.21641660.16372864X-RAY DIFFRACTION100
3.0141-3.24670.17341290.16562922X-RAY DIFFRACTION100
3.2467-3.57320.16321420.15472895X-RAY DIFFRACTION100
3.5732-4.08970.15851310.14432900X-RAY DIFFRACTION100
4.0897-5.15050.1511200.13682960X-RAY DIFFRACTION100
5.1505-37.64380.21071480.17582963X-RAY DIFFRACTION99
Refinement TLS params.

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

IDL11 (°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)
10.4386-0.55340.55310.7433-0.56520.80730.0091-0.19060.06980.21640.0192-0.0359-0.3405-0.2200.21380.02020.0250.2738-0.02160.1736-15.9256-1.333417.2126
2-0.0016-0.0105-0.02760.01240.03650.0383-0.00450.0776-0.58020.4437-0.0665-0.7834-0.15780.4172-0.00020.359-0.1109-0.0040.52290.05370.39697.7634-0.2539-3.4535
30.22680.0904-0.1270.4148-0.05890.013-0.1832-0.06550.05230.14830.0585-0.36640.01470.1926-00.19320.0313-0.0370.1580.02030.20062.39643.8922-13.5171
40.5080.5146-0.11770.98120.17380.7314-0.01150.0244-0.0226-0.1407-0.0718-0.09370.0858-0.169300.19820.00620.01850.21790.03020.1805-12.025-8.49864.0738
50.54170.3770.1201-0.3075-0.25121.25-0.1180.0346-0.10010.01910.0590.05890.1918-0.1407-00.20580.00670.01570.12170.01810.1639-9.7754-2.6446-16.0439
60.14610.0132-0.16660.5833-0.32260.55770.02930.01820.19720.10190.03020.0525-0.4362-0.3155-0.00010.24290.07340.01770.2855-0.00610.2528-17.85516.50975.0548
71.42710.32130.35320.9352-0.78292.316-0.0016-0.40930.02630.2452-0.085-0.149-0.20620.0086-0.070.14470.00960.01220.1909-0.03790.1414-10.3997-1.928915.8593
80.3507-0.27920.37380.7463-0.5610.55810.0807-0.1246-0.2883-0.1554-0.02640.18030.1218-0.20840.00440.1583-0.03190.00230.28210.01460.2262-43.770821.6633-27.1156
90.1323-0.23730.07290.911-0.24560.05460.39740.5844-0.3142-0.85560.15590.2389-0.36550.32770.08220.40710.0912-0.01420.5918-0.11380.3976-14.75620.6558-39.4231
100.0921-0.1598-0.11880.40760.1640.13510.02720.21140.1281-0.39220.0557-0.00480.13630.10020.00020.24050.001-0.0210.17150.04530.1744-8.13916.459-30.2454
110.7194-0.14870.05041.10070.5280.4730.0511-0.20630.0793-0.0062-0.0991-0.1362-0.0096-0.0229-00.16270.01780.0010.20660.01690.1891-30.233128.8175-24.9068
121.0284-0.4650.4859-0.35080.16930.6485-0.01-0.10550.20570.03170.05360.0406-0.0153-0.00940.00130.15860.0105-0.01150.11030.01080.202-11.135122.9648-18.1873
130.4732-0.26860.2370.57080.03050.20990.0637-0.2857-0.33810.04050.03910.10430.2722-0.18890.00010.2243-0.02810.0180.28330.06380.2269-33.354314.7602-19.772
142.1216-0.62550.49521.0899-0.28321.61130.13830.1281-0.2149-0.2375-0.08140.1710.0931-0.28740.00970.1342-0.04080.01410.1728-0.00430.1531-39.771121.1926-30.7575
150.2702-0.0806-0.2350.03820.07360.1974-0.135-0.15730.42310.2760.32180.3228-0.6736-0.2290.0160.47510.0888-0.00310.15280.00210.3656-11.103613.23-5.1929
160.1730.02080.00690.02590.02170.04950.1181-0.0717-0.35070.28080.16130.63620.4562-0.0802-0.0030.3849-0.0325-0.01340.15290.06550.4015-21.52197.0539-21.6612
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 122 through 152 )
2X-RAY DIFFRACTION2chain 'A' and (resid 153 through 169 )
3X-RAY DIFFRACTION3chain 'A' and (resid 170 through 198 )
4X-RAY DIFFRACTION4chain 'A' and (resid 199 through 240 )
5X-RAY DIFFRACTION5chain 'A' and (resid 241 through 299 )
6X-RAY DIFFRACTION6chain 'A' and (resid 300 through 333 )
7X-RAY DIFFRACTION7chain 'A' and (resid 334 through 394 )
8X-RAY DIFFRACTION8chain 'B' and (resid 122 through 152 )
9X-RAY DIFFRACTION9chain 'B' and (resid 153 through 169 )
10X-RAY DIFFRACTION10chain 'B' and (resid 170 through 198 )
11X-RAY DIFFRACTION11chain 'B' and (resid 199 through 240 )
12X-RAY DIFFRACTION12chain 'B' and (resid 241 through 299 )
13X-RAY DIFFRACTION13chain 'B' and (resid 300 through 327 )
14X-RAY DIFFRACTION14chain 'B' and (resid 328 through 394 )
15X-RAY DIFFRACTION15chain 'C' and (resid 1 through 7 )
16X-RAY DIFFRACTION16chain 'D' and (resid 1 through 7 )

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