[English] 日本語
Yorodumi
- PDB-5cuf: X-ray crystal structure of SeMet human Sestrin2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5cuf
TitleX-ray crystal structure of SeMet human Sestrin2
ComponentsSestrin-2
KeywordsOXIDOREDUCTASE / alkylhydroperoxidase
Function / homology
Function and homology information


regulation of response to reactive oxygen species / sulfiredoxin activity / negative regulation of translation in response to endoplasmic reticulum stress / L-leucine binding / Atg1/ULK1 kinase complex / TORC2 complex / regulation of TORC1 signaling / oxidoreductase activity, acting on peroxide as acceptor / PH domain binding / cellular response to leucine starvation ...regulation of response to reactive oxygen species / sulfiredoxin activity / negative regulation of translation in response to endoplasmic reticulum stress / L-leucine binding / Atg1/ULK1 kinase complex / TORC2 complex / regulation of TORC1 signaling / oxidoreductase activity, acting on peroxide as acceptor / PH domain binding / cellular response to leucine starvation / mitochondrial DNA metabolic process / nucleotide-activated protein kinase complex / cellular response to L-leucine / Amino acids regulate mTORC1 / positive regulation of lipophagy / triglyceride homeostasis / GDP-dissociation inhibitor activity / regulation of gluconeogenesis / cellular oxidant detoxification / fatty acid beta-oxidation / regulation of cAMP/PKA signal transduction / D-glucose import / regulation of protein phosphorylation / positive regulation of macroautophagy / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / response to glucose / cellular response to glucose starvation / negative regulation of TORC1 signaling / positive regulation of TORC1 signaling / reactive oxygen species metabolic process / protein sequestering activity / cellular response to amino acid starvation / TP53 Regulates Metabolic Genes / DNA damage response, signal transduction by p53 class mediator / cellular response to amino acid stimulus / peroxidase activity / negative regulation of cell growth / response to insulin / positive regulation of protein localization to nucleus / KEAP1-NFE2L2 pathway / glucose homeostasis / cellular response to oxidative stress / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / lysosomal membrane / protein-containing complex binding / mitochondrion / nucleus / cytoplasm / cytosol
Similarity search - Function
Sestrin / PA26 p53-induced protein (sestrin) / AhpD-like
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.5 Å
AuthorsKim, H. / An, S. / Ro, S.-H. / Lee, J.H. / Cho, U.-S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)2P30-DK020572 United States
Ellison Medical FoundationAG-NS-0932-12 United States
CitationJournal: Nat Commun / Year: 2015
Title: Janus-faced Sestrin2 controls ROS and mTOR signalling through two separate functional domains.
Authors: Kim, H. / An, S. / Ro, S.H. / Teixeira, F. / Jin Park, G. / Kim, C. / Cho, C.S. / Kim, J.S. / Jakob, U. / Hee Lee, J. / Cho, U.S.
History
DepositionJul 24, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_entry_details / pdbx_modification_feature / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sestrin-2
B: Sestrin-2
C: Sestrin-2
D: Sestrin-2
E: Sestrin-2


Theoretical massNumber of molelcules
Total (without water)277,2125
Polymers277,2125
Non-polymers00
Water00
1
A: Sestrin-2


Theoretical massNumber of molelcules
Total (without water)55,4421
Polymers55,4421
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sestrin-2


Theoretical massNumber of molelcules
Total (without water)55,4421
Polymers55,4421
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Sestrin-2


Theoretical massNumber of molelcules
Total (without water)55,4421
Polymers55,4421
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Sestrin-2


Theoretical massNumber of molelcules
Total (without water)55,4421
Polymers55,4421
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Sestrin-2


Theoretical massNumber of molelcules
Total (without water)55,4421
Polymers55,4421
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)292.680, 292.680, 292.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15B
25C
16B
26D
17B
27E
18C
28D
19C
29E
110D
210E

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: _ / Auth seq-ID: 66 - 478 / Label seq-ID: 69 - 481

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14AA
24EE
15BB
25CC
16BB
26DD
17BB
27EE
18CC
28DD
19CC
29EE
110DD
210EE

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

-
Components

#1: Protein
Sestrin-2 / Hi95


Mass: 55442.457 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SESN2, SEST2 / Production host: Escherichia coli (E. coli) / References: UniProt: P58004
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.79 Å3/Da / Density % sol: 67.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M MES 1.15 M sodium malonate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97879 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 6, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97879 Å / Relative weight: 1
ReflectionResolution: 3.5→44.12 Å / Num. obs: 52390 / % possible obs: 99.9 % / Redundancy: 88.6 % / Rmerge(I) obs: 0.305 / Net I/σ(I): 28.5
Reflection shellResolution: 3.5→3.59 Å / Redundancy: 3.7 % / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.5→44.12 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.885 / SU B: 23.627 / SU ML: 0.358 / Cross valid method: THROUGHOUT / ESU R Free: 0.532
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27194 2592 4.9 %RANDOM
Rwork0.23538 ---
obs0.23715 49798 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 103.032 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3.5→44.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15032 0 0 0 15032
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.01915432
X-RAY DIFFRACTIONr_bond_other_d0.0150.0214393
X-RAY DIFFRACTIONr_angle_refined_deg1.8241.95920907
X-RAY DIFFRACTIONr_angle_other_deg1.888333038
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.75151815
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.16522.895760
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.301152407
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.07515120
X-RAY DIFFRACTIONr_chiral_restr0.0950.22240
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02117210
X-RAY DIFFRACTIONr_gen_planes_other0.0110.023800
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_it13.32110.8727350
X-RAY DIFFRACTIONr_mcbond_other13.32110.8737349
X-RAY DIFFRACTIONr_mcangle_it16.6416.4539135
X-RAY DIFFRACTIONr_mcangle_other16.6416.4529136
X-RAY DIFFRACTIONr_scbond_it10.84310.1648082
X-RAY DIFFRACTIONr_scbond_other10.84310.1648083
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other15.34415.44811773
X-RAY DIFFRACTIONr_long_range_B_refined20.02260884
X-RAY DIFFRACTIONr_long_range_B_other20.02260885
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)
11A456840.08
12B456840.08
21A456900.08
22C456900.08
31A455240.08
32D455240.08
41A455760.08
42E455760.08
51B459220.06
52C459220.06
61B459500.06
62D459500.06
71B459700.06
72E459700.06
81C461080.05
82D461080.05
91C460340.05
92E460340.05
101D462500.04
102E462500.04
LS refinement shellResolution: 3.5→3.591 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 204 -
Rwork0.302 3633 -
obs--99.97 %

+
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