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- PDB-6iso: Human SIRT3 Recognizing H3K4cr -

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Basic information

Entry
Database: PDB / ID: 6iso
TitleHuman SIRT3 Recognizing H3K4cr
Components
  • ARG-THR-LYS-GLN-THR-ALA-ARG
  • NAD-dependent protein deacetylase sirtuin-3, mitochondrial
KeywordsHYDROLASE / Posttranslational modification / Sirtuins / Histones / Complex.
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 / protein deacetylation / histone 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 / protein deacetylation / histone deacetylase activity, NAD-dependent / 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 / positive regulation of insulin secretion / negative regulation of ERK1 and ERK2 cascade / sequence-specific DNA binding / mitochondrial matrix / enzyme binding / protein-containing complex / mitochondrion / 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 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
(2E)-BUT-2-ENAL / NAD-dependent protein deacetylase sirtuin-3, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsWang, Y. / Hao, Q.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
GRF766510 Hong Kong
CitationJournal: Elife / Year: 2014
Title: Identification of 'erasers' for lysine crotonylated histone marks using a chemical proteomics approach.
Authors: Bao, X. / Wang, Y. / Li, X. / Li, X.M. / Liu, Z. / Yang, T. / Wong, C.F. / Zhang, J. / Hao, Q. / Li, X.D.
History
DepositionNov 17, 2018Deposition site: PDBJ / Processing site: PDBJ
SupersessionJan 23, 2019ID: 4V1C
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type / struct_ncs_dom_lim
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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_type.id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
C: ARG-THR-LYS-GLN-THR-ALA-ARG
B: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
D: ARG-THR-LYS-GLN-THR-ALA-ARG
E: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
F: ARG-THR-LYS-GLN-THR-ALA-ARG
H: ARG-THR-LYS-GLN-THR-ALA-ARG
G: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
L: ARG-THR-LYS-GLN-THR-ALA-ARG
I: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
J: ARG-THR-LYS-GLN-THR-ALA-ARG
K: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,69227
Polymers188,57612
Non-polymers1,11615
Water3,261181
1
A: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
C: ARG-THR-LYS-GLN-THR-ALA-ARG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5654
Polymers31,4292
Non-polymers1352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-5 kcal/mol
Surface area12530 Å2
MethodPISA
2
B: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
D: ARG-THR-LYS-GLN-THR-ALA-ARG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6575
Polymers31,4292
Non-polymers2283
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-4 kcal/mol
Surface area12710 Å2
MethodPISA
3
E: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
F: ARG-THR-LYS-GLN-THR-ALA-ARG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6575
Polymers31,4292
Non-polymers2283
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-5 kcal/mol
Surface area12620 Å2
MethodPISA
4
H: ARG-THR-LYS-GLN-THR-ALA-ARG
G: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6575
Polymers31,4292
Non-polymers2283
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-5 kcal/mol
Surface area12370 Å2
MethodPISA
5
L: ARG-THR-LYS-GLN-THR-ALA-ARG
K: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5914
Polymers31,4292
Non-polymers1622
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-2 kcal/mol
Surface area9770 Å2
MethodPISA
6
I: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
J: ARG-THR-LYS-GLN-THR-ALA-ARG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5654
Polymers31,4292
Non-polymers1352
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area780 Å2
ΔGint-4 kcal/mol
Surface area12520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.085, 138.085, 225.342
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22E
13A
23G
14A
24I
15B
25E
16B
26G
17B
27I
18E
28G
19E
29I
110G
210I

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSLEULEUAA122 - 3942 - 274
21LYSLYSLEULEUBC122 - 3942 - 274
12LYSLYSLEULEUAA122 - 3942 - 274
22LYSLYSLEULEUEE122 - 3942 - 274
13GLYGLYLEULEUAA121 - 3941 - 274
23GLYGLYLEULEUGH121 - 3941 - 274
14LYSLYSLYSLYSAA122 - 3932 - 273
24LYSLYSLYSLYSIJ122 - 3932 - 273
15LYSLYSLEULEUBC122 - 3942 - 274
25LYSLYSLEULEUEE122 - 3942 - 274
16LYSLYSLEULEUBC122 - 3942 - 274
26LYSLYSLEULEUGH122 - 3942 - 274
17LYSLYSLYSLYSBC122 - 3932 - 273
27LYSLYSLYSLYSIJ122 - 3932 - 273
18LYSLYSLEULEUEE122 - 3942 - 274
28LYSLYSLEULEUGH122 - 3942 - 274
19LYSLYSLYSLYSEE122 - 3932 - 273
29LYSLYSLYSLYSIJ122 - 3932 - 273
110LYSLYSLYSLYSGH122 - 3932 - 273
210LYSLYSLYSLYSIJ122 - 3932 - 273

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10

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Components

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Protein / Protein/peptide , 2 types, 12 molecules ABEGIKCDFHLJ

#1: Protein
NAD-dependent protein deacetylase sirtuin-3, mitochondrial / hSIRT3 / Regulatory protein SIR2 homolog 3 / SIR2-like protein 3


Mass: 30566.305 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SIRT3, SIR2L3
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: Q9NTG7, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Protein/peptide
ARG-THR-LYS-GLN-THR-ALA-ARG


Mass: 862.997 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 196 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-CRD / (2E)-BUT-2-ENAL / CROTONALDEHYDE


Mass: 70.090 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H6O
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 2.85 Å3/Da / Density % sol: 60.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 12% PEG4K, 0.1 M sodium malonate, pH 6.5, 5% isopropanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. obs: 51122 / % possible obs: 99.5 % / Redundancy: 7.1 % / Net I/σ(I): 19.96
Reflection shellResolution: 2.96→3.02 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GLR

3glr


Resolution: 2.95→39.25 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.853 / SU B: 17.22 / SU ML: 0.319 / Cross valid method: THROUGHOUT / ESU R Free: 0.442 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27519 2319 5.1 %RANDOM
Rwork0.22144 ---
obs0.22414 43339 97.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.693 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: 1 / Resolution: 2.95→39.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12006 0 49 181 12236
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01312314
X-RAY DIFFRACTIONr_bond_other_d0.0010.01711853
X-RAY DIFFRACTIONr_angle_refined_deg1.5021.64816711
X-RAY DIFFRACTIONr_angle_other_deg1.3581.57327355
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.37251513
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.89520.425635
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.014152018
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.16615112
X-RAY DIFFRACTIONr_chiral_restr0.0710.21572
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213575
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022645
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.6534.9536117
X-RAY DIFFRACTIONr_mcbond_other4.6544.9526116
X-RAY DIFFRACTIONr_mcangle_it7.1887.4137607
X-RAY DIFFRACTIONr_mcangle_other7.1877.4147608
X-RAY DIFFRACTIONr_scbond_it4.6395.3886197
X-RAY DIFFRACTIONr_scbond_other4.6395.3896198
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.2597.9339105
X-RAY DIFFRACTIONr_long_range_B_refined12.23993.47449293
X-RAY DIFFRACTIONr_long_range_B_other12.23793.48549277
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A80790.11
12B80790.11
21A80540.12
22E80540.12
31A77420.12
32G77420.12
41A73290.14
42I73290.14
51B78220.12
52E78220.12
61B76890.13
62G76890.13
71B72560.14
72I72560.14
81E75640.13
82G75640.13
91E72700.13
92I72700.13
101G72090.15
102I72090.15
LS refinement shellResolution: 2.95→3.026 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 142 -
Rwork0.267 2802 -
obs--87.67 %

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