[English] 日本語
Yorodumi
- PDB-6iso: Human SIRT3 Recognizing H3K4cr -

+
Open data


ID or keywords:

Loading...

-
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 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 / NAD-dependent histone deacetylase activity / protein deacetylation / 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 / NAD-dependent histone deacetylase activity / protein deacetylation / Regulation of FOXO transcriptional activity by acetylation / NAD+ binding / 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 / negative regulation of ERK1 and ERK2 cascade / positive regulation of insulin secretion / transferase activity / 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 / Rossmann fold ...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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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: 0 / Refine code: 0

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

-
Components

-
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)

-
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 / 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 / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
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

-
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

-
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 %

+
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://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