[English] 日本語
Yorodumi
- PDB-8bbk: Crystal structure of human Sirt3 in complex with a fragment of th... -

+
Open data


ID or keywords:

Loading...

-
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 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 ...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 / Regulation of HSF1-mediated heat shock response / negative regulation of reactive oxygen species metabolic process / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / aerobic respiration / Transcriptional activation of mitochondrial biogenesis / positive regulation of insulin secretion / negative regulation of ERK1 and ERK2 cascade / transferase activity / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
Phasing

PhasingMethod: molecular replacement

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more