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- PDB-8bbk: Crystal structure of human Sirt3 in complex with a fragment of th... -

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Basic information

Entry
Database: PDB / ID: 8bbk
TitleCrystal structure of human Sirt3 in complex with a fragment of the human AROS protein
Components
  • Active regulator of SIRT1
  • NAD-dependent protein deacetylase sirtuin-3, mitochondrial
KeywordsHYDROLASE / Sirtuin 3 / peptide complex / AROS / inhibitor
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 / Maturation of TCA enzymes and regulation of TCA cycle / peptidyl-lysine deacetylation / 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 / Maturation of TCA enzymes and regulation of TCA cycle / peptidyl-lysine deacetylation / 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 / Regulation of HSF1-mediated heat shock response / 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 / small-subunit processome / Transcriptional activation of mitochondrial biogenesis / positive regulation of insulin secretion / negative regulation of ERK1 and ERK2 cascade / ribosomal small subunit biogenesis / sequence-specific DNA binding / mitochondrial matrix / nucleolus / enzyme binding / protein-containing complex / mitochondrion / RNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Active regulator of SIRT1 / Active regulator of SIRT1, or 40S ribosomal protein S19-binding 1 / Sirtuin, catalytic core small domain superfamily / Sirtuin family / : / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / DHS-like NAD/FAD-binding domain superfamily
Similarity search - Domain/homology
Active regulator of SIRT1 / NAD-dependent protein deacetylase sirtuin-3, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.27 Å
AuthorsSteegborn, C. / Weiss, S.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)STE1701/15 Germany
CitationJournal: Int J Mol Sci / Year: 2022
Title: Molecular Mechanism of Sirtuin 1 Modulation by the AROS Protein.
Authors: Weiss, S. / Adolph, R.S. / Schweimer, K. / DiFonzo, A. / Meleshin, M. / Schutkowski, M. / Steegborn, C.
History
DepositionOct 13, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
G: Active regulator of SIRT1
B: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
H: Active regulator of SIRT1
C: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
I: Active regulator of SIRT1
D: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
J: Active regulator of SIRT1
E: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
K: Active regulator of SIRT1
F: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
L: Active regulator of SIRT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)354,97418
Polymers354,58212
Non-polymers3926
Water00
1
A: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
G: Active regulator of SIRT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1623
Polymers59,0972
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
H: Active regulator of SIRT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1623
Polymers59,0972
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
I: Active regulator of SIRT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1623
Polymers59,0972
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
J: Active regulator of SIRT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1623
Polymers59,0972
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
K: Active regulator of SIRT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1623
Polymers59,0972
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
L: Active regulator of SIRT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1623
Polymers59,0972
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)110.215, 110.215, 344.362
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 121 or resid 123 through 183...
21(chain B and (resid 121 or resid 123 through 183...
31(chain C and (resid 121 or resid 123 through 183...
41(chain D and (resid 121 or resid 123 through 183...
51(chain E and (resid 121 or resid 123 through 183...
61(chain F and (resid 121 or resid 123 through 183...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYGLYGLY(chain A and (resid 121 or resid 123 through 183...AA121121
12LEULEUPROPRO(chain A and (resid 121 or resid 123 through 183...AA123 - 183123 - 183
13PHEPHEPROPRO(chain A and (resid 121 or resid 123 through 183...AA185 - 189185 - 189
14PROPROPHEPHE(chain A and (resid 121 or resid 123 through 183...AA191 - 294191 - 294
15GLUGLUMETMET(chain A and (resid 121 or resid 123 through 183...AA296 - 383296 - 383
16ASPASPLEULEU(chain A and (resid 121 or resid 123 through 183...AA385 - 394385 - 394
17ZNZNZNZN(chain A and (resid 121 or resid 123 through 183...AM401
21GLYGLYGLYGLY(chain B and (resid 121 or resid 123 through 183...BC121121
22LEULEUPROPRO(chain B and (resid 121 or resid 123 through 183...BC123 - 183123 - 183
23PHEPHEPROPRO(chain B and (resid 121 or resid 123 through 183...BC185 - 189185 - 189
24PROPROPHEPHE(chain B and (resid 121 or resid 123 through 183...BC191 - 294191 - 294
25GLUGLUMETMET(chain B and (resid 121 or resid 123 through 183...BC296 - 383296 - 383
26ASPASPLEULEU(chain B and (resid 121 or resid 123 through 183...BC385 - 394385 - 394
27ZNZNZNZN(chain B and (resid 121 or resid 123 through 183...BN401
31GLYGLYGLYGLY(chain C and (resid 121 or resid 123 through 183...CE121121
32LEULEUPROPRO(chain C and (resid 121 or resid 123 through 183...CE123 - 183123 - 183
33PHEPHEPROPRO(chain C and (resid 121 or resid 123 through 183...CE185 - 189185 - 189
34PROPROPHEPHE(chain C and (resid 121 or resid 123 through 183...CE191 - 294191 - 294
35GLUGLUMETMET(chain C and (resid 121 or resid 123 through 183...CE296 - 383296 - 383
36ASPASPLEULEU(chain C and (resid 121 or resid 123 through 183...CE385 - 394385 - 394
37ZNZNZNZN(chain C and (resid 121 or resid 123 through 183...CO401
41GLYGLYGLYGLY(chain D and (resid 121 or resid 123 through 183...DG121121
42LEULEUPROPRO(chain D and (resid 121 or resid 123 through 183...DG123 - 183123 - 183
43PHEPHEPROPRO(chain D and (resid 121 or resid 123 through 183...DG185 - 189185 - 189
44PROPROPHEPHE(chain D and (resid 121 or resid 123 through 183...DG191 - 294191 - 294
45GLUGLUMETMET(chain D and (resid 121 or resid 123 through 183...DG296 - 383296 - 383
46ASPASPLEULEU(chain D and (resid 121 or resid 123 through 183...DG385 - 394385 - 394
47ZNZNZNZN(chain D and (resid 121 or resid 123 through 183...DP401
51GLYGLYGLYGLY(chain E and (resid 121 or resid 123 through 183...EI121121
52LEULEUPROPRO(chain E and (resid 121 or resid 123 through 183...EI123 - 183123 - 183
53PHEPHEPROPRO(chain E and (resid 121 or resid 123 through 183...EI185 - 189185 - 189
54PROPROPHEPHE(chain E and (resid 121 or resid 123 through 183...EI191 - 294191 - 294
55GLUGLUMETMET(chain E and (resid 121 or resid 123 through 183...EI296 - 383296 - 383
56ASPASPLEULEU(chain E and (resid 121 or resid 123 through 183...EI385 - 394385 - 394
57ZNZNZNZN(chain E and (resid 121 or resid 123 through 183...EQ401
61GLYGLYGLYGLY(chain F and (resid 121 or resid 123 through 183...FK121121
62LEULEUPROPRO(chain F and (resid 121 or resid 123 through 183...FK123 - 183123 - 183
63PHEPHEPROPRO(chain F and (resid 121 or resid 123 through 183...FK185 - 189185 - 189
64PROPROMETMET(chain F and (resid 121 or resid 123 through 183...FK191 - 383191 - 383
65ASPASPLEULEU(chain F and (resid 121 or resid 123 through 183...FK385 - 394385 - 394
66ZNZNZNZN(chain F and (resid 121 or resid 123 through 183...FR401

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Components

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


Mass: 43628.023 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 (E. coli)
References: UniProt: Q9NTG7, protein acetyllysine N-acetyltransferase
#2: Protein
Active regulator of SIRT1 / 40S ribosomal protein S19-binding protein 1 / RPS19-binding protein 1 / S19BP


Mass: 15468.907 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPS19BP1, AROS / Production host: Escherichia coli (E. coli) / References: UniProt: Q86WX3
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN

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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: 1.7 Å3/Da / Density % sol: 27.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 12 % PEG 8.000, 0.1 M HEPES pH 7.5 and 0.2 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 3.27→49.19 Å / Num. obs: 38569 / % possible obs: 99.7 % / Redundancy: 10.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.316 / Net I/σ(I): 7.9
Reflection shellResolution: 3.27→3.38 Å / Num. unique obs: 3207 / CC1/2: 0.339

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GLS

3gls


Resolution: 3.27→49.19 Å / SU ML: 0.54 / Cross valid method: THROUGHOUT / Phase error: 30.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2614 1928 5 %
Rwork0.202 36629 -
obs0.205 38557 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 164.72 Å2 / Biso mean: 95.5454 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 3.27→49.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13074 0 6 0 13080
Biso mean--94.73 --
Num. residues----1662
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4842X-RAY DIFFRACTION4.498TORSIONAL
12B4842X-RAY DIFFRACTION4.498TORSIONAL
13C4842X-RAY DIFFRACTION4.498TORSIONAL
14D4842X-RAY DIFFRACTION4.498TORSIONAL
15E4842X-RAY DIFFRACTION4.498TORSIONAL
16F4842X-RAY DIFFRACTION4.498TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.27-3.350.40331350.34792566270198
3.35-3.440.40451350.346725662701100
3.44-3.540.4351350.336625692704100
3.54-3.650.39071350.302625652700100
3.65-3.780.33871370.27926082745100
3.78-3.940.2991370.249825932730100
3.94-4.120.32121350.227425642699100
4.12-4.330.2671360.209825962732100
4.33-4.60.25951380.177826162754100
4.6-4.960.24081380.161826132751100
4.96-5.460.24171380.169526332771100
5.46-6.240.22671390.161626362775100
6.25-7.860.20231420.175127042846100
7.86-49.190.19111480.1562800294899

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