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- PDB-6xv6: Human Sirt6 3-318 in complex with ADP-ribose -

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Basic information

Entry
Database: PDB / ID: 6xv6
TitleHuman Sirt6 3-318 in complex with ADP-ribose
ComponentsNAD-dependent protein deacetylase sirtuin-6
KeywordsHYDROLASE / Deacylase / Activator / Allosteric / Isoform-selective
Function / homology
Function and homology information


histone H3K56 deacetylase activity, NAD-dependent / histone H3K18 deacetylase activity, NAD-dependent / ketone biosynthetic process / histone H3K9 deacetylase activity, hydrolytic mechanism / histone H3K9 deacetylase activity, NAD-dependent / protein delipidation / NAD+-protein-lysine ADP-ribosyltransferase activity / regulation of lipid catabolic process / chromosome, subtelomeric region / positive regulation of protein localization to chromatin ...histone H3K56 deacetylase activity, NAD-dependent / histone H3K18 deacetylase activity, NAD-dependent / ketone biosynthetic process / histone H3K9 deacetylase activity, hydrolytic mechanism / histone H3K9 deacetylase activity, NAD-dependent / protein delipidation / NAD+-protein-lysine ADP-ribosyltransferase activity / regulation of lipid catabolic process / chromosome, subtelomeric region / positive regulation of protein localization to chromatin / NAD+-protein-arginine ADP-ribosyltransferase activity / DNA damage sensor activity / NAD-dependent protein demyristoylase activity / NAD-dependent protein depalmitoylase activity / positive regulation of stem cell differentiation / negative regulation of D-glucose import / positive regulation of chondrocyte proliferation / transposable element silencing / NAD-dependent protein lysine deacetylase activity / cardiac muscle cell differentiation / protein acetyllysine N-acetyltransferase / pericentric heterochromatin formation / protein deacetylation / histone deacetylase activity, NAD-dependent / protein localization to site of double-strand break / positive regulation of blood vessel branching / negative regulation of glycolytic process / TORC2 complex binding / negative regulation of protein localization to chromatin / positive regulation of vascular endothelial cell proliferation / histone deacetylase regulator activity / negative regulation of protein import into nucleus / regulation of double-strand break repair via homologous recombination / regulation of protein secretion / positive regulation of double-strand break repair / DNA repair-dependent chromatin remodeling / positive regulation of stem cell proliferation / lncRNA binding / negative regulation of gene expression, epigenetic / NAD+-protein mono-ADP-ribosyltransferase activity / positive regulation of stem cell population maintenance / positive regulation of telomere maintenance / regulation of lipid metabolic process / site of DNA damage / negative regulation of cellular senescence / negative regulation of transcription elongation by RNA polymerase II / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+ poly-ADP-ribosyltransferase activity / NAD+ binding / negative regulation of gluconeogenesis / positive regulation of fat cell differentiation / subtelomeric heterochromatin formation / pericentric heterochromatin / response to UV / regulation of protein localization to plasma membrane / nucleosome binding / enzyme regulator activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / nucleotidyltransferase activity / positive regulation of protein export from nucleus / determination of adult lifespan / circadian regulation of gene expression / base-excision repair / regulation of circadian rhythm / positive regulation of insulin secretion / protein destabilization / chromatin DNA binding / Pre-NOTCH Transcription and Translation / positive regulation of fibroblast proliferation / protein import into nucleus / transcription corepressor activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / glucose homeostasis / double-strand break repair / site of double-strand break / positive regulation of cold-induced thermogenesis / Processing of DNA double-strand break ends / damaged DNA binding / chromatin remodeling / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / chromatin binding / chromatin / endoplasmic reticulum / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / DNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Sirtuin family / : / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / DHS-like NAD/FAD-binding domain superfamily
Similarity search - Domain/homology
Chem-AR6 / NICOTINAMIDE / NAD-dependent protein deacylase sirtuin-6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsYou, W. / Steegborn, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)STE1701/15 Germany
CitationJournal: Nat.Chem.Biol. / Year: 2021
Title: Binding site for activator MDL-801 on SIRT6.
Authors: You, W. / Steegborn, C.
History
DepositionJan 21, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2May 5, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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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-6
B: NAD-dependent protein deacetylase sirtuin-6
C: NAD-dependent protein deacetylase sirtuin-6
D: NAD-dependent protein deacetylase sirtuin-6
E: NAD-dependent protein deacetylase sirtuin-6
F: NAD-dependent protein deacetylase sirtuin-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,35054
Polymers210,0196
Non-polymers7,33148
Water9,080504
1
A: NAD-dependent protein deacetylase sirtuin-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1268
Polymers35,0031
Non-polymers1,1237
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NAD-dependent protein deacetylase sirtuin-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,60713
Polymers35,0031
Non-polymers1,60312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: NAD-dependent protein deacetylase sirtuin-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0387
Polymers35,0031
Non-polymers1,0356
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: NAD-dependent protein deacetylase sirtuin-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2269
Polymers35,0031
Non-polymers1,2238
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: NAD-dependent protein deacetylase sirtuin-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2269
Polymers35,0031
Non-polymers1,2238
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: NAD-dependent protein deacetylase sirtuin-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1268
Polymers35,0031
Non-polymers1,1237
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.689, 136.310, 90.096
Angle α, β, γ (deg.)90.000, 117.370, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

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
11ASPASPLEULEUAA14 - 29712 - 295
21ASPASPLEULEUBB14 - 29712 - 295
12ALAALALYSLYSAA7 - 2965 - 294
22ALAALALYSLYSCC7 - 2965 - 294
13TYRTYRLEULEUAA12 - 29710 - 295
23TYRTYRLEULEUDD12 - 29710 - 295
14ALAALALEULEUAA13 - 29711 - 295
24ALAALALEULEUEE13 - 29711 - 295
15ASNASNLEULEUAA4 - 2972 - 295
25ASNASNLEULEUFF4 - 2972 - 295
16ASPASPLYSLYSBB14 - 29612 - 294
26ASPASPLYSLYSCC14 - 29612 - 294
17ASPASPLEULEUBB14 - 29712 - 295
27ASPASPLEULEUDD14 - 29712 - 295
18ASPASPGLUGLUBB14 - 29812 - 296
28ASPASPGLUGLUEE14 - 29812 - 296
19ASPASPLEULEUBB14 - 29712 - 295
29ASPASPLEULEUFF14 - 29712 - 295
110TYRTYRLYSLYSCC12 - 29610 - 294
210TYRTYRLYSLYSDD12 - 29610 - 294
111ALAALALYSLYSCC13 - 29611 - 294
211ALAALALYSLYSEE13 - 29611 - 294
112ALAALALYSLYSCC7 - 2965 - 294
212ALAALALYSLYSFF7 - 2965 - 294
113ALAALALEULEUDD13 - 29711 - 295
213ALAALALEULEUEE13 - 29711 - 295
114TYRTYRLEULEUDD12 - 29710 - 295
214TYRTYRLEULEUFF12 - 29710 - 295
115ALAALALEULEUEE13 - 29711 - 295
215ALAALALEULEUFF13 - 29711 - 295

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
NAD-dependent protein deacetylase sirtuin-6 / Regulatory protein SIR2 homolog 6 / SIR2-like protein 6


Mass: 35003.105 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SIRT6, SIR2L6 / Plasmid: pET28a-SUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): codon+
References: UniProt: Q8N6T7, protein acetyllysine N-acetyltransferase

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Non-polymers , 6 types, 552 molecules

#2: Chemical
ChemComp-AR6 / [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE / Adenosine-5-Diphosphoribose


Mass: 559.316 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C15H23N5O14P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-NCA / NICOTINAMIDE


Mass: 122.125 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H6N2O
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 504 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.4 Å3/Da / Density % sol: 48.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 85 mM HEPES pH 7.5, 85 mM sodium chloride, 1.36 M (NH4)2SO4, 15% glycerol
PH range: 7.0-7.7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.75→46.72 Å / Num. obs: 191591 / % possible obs: 99 % / Redundancy: 3.9 % / CC1/2: 0.994 / Rrim(I) all: 0.14 / Net I/σ(I): 6.3
Reflection shellResolution: 1.75→1.86 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 30474 / CC1/2: 0.342 / Rrim(I) all: 1.59 / % possible all: 97.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3K35

3k35


Resolution: 1.75→46.72 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.95 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2246 2099 1.1 %RANDOM
Rwork0.2003 ---
obs0.2006 189464 99.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 171.59 Å2 / Biso mean: 31.337 Å2 / Biso min: 16.19 Å2
Baniso -1Baniso -2Baniso -3
1--1.11 Å20 Å2-0.21 Å2
2--1.12 Å20 Å2
3---0.13 Å2
Refinement stepCycle: final / Resolution: 1.75→46.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13200 0 434 504 14138
Biso mean--38.51 29.54 -
Num. residues----1702
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01313906
X-RAY DIFFRACTIONr_bond_other_d0.0340.01712980
X-RAY DIFFRACTIONr_angle_refined_deg1.5251.65818917
X-RAY DIFFRACTIONr_angle_other_deg2.2541.58230021
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.33751689
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.10120.041729
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.966152264
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.59215144
X-RAY DIFFRACTIONr_chiral_restr0.0740.21789
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215258
X-RAY DIFFRACTIONr_gen_planes_other0.0120.022946
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A83560.08
12B83560.08
21A84950.09
22C84950.09
31A84420.08
32D84420.08
41A84300.08
42E84300.08
51A86790.08
52F86790.08
61B83520.09
62C83520.09
71B84410.08
72D84410.08
81B85030.08
82E85030.08
91B83980.07
92F83980.07
101C83610.09
102D83610.09
111C83510.08
112E83510.08
121C84490.08
122F84490.08
131D85070.07
132E85070.07
141D84610.08
142F84610.08
151E84090.08
152F84090.08
LS refinement shellResolution: 1.75→1.795 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.367 151 -
Rwork0.355 13702 -
obs--96.87 %

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