[English] 日本語
Yorodumi
- PDB-6n0m: CRYSTAL STRUCTURE OF SESTRIN2 IN COMPLEX WITH NV-0005138 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6n0m
TitleCRYSTAL STRUCTURE OF SESTRIN2 IN COMPLEX WITH NV-0005138
ComponentsSestrin-2
KeywordsSIGNALING PROTEIN / MTOR / LEUCINE / AMINO-ACID / SENSING
Function / homology
Function and homology information


regulation of response to reactive oxygen species / negative regulation of translation in response to endoplasmic reticulum stress / sulfiredoxin activity / L-leucine binding / Atg1/ULK1 kinase complex / oxidoreductase activity, acting on peroxide as acceptor / TORC2 complex / cellular response to leucine starvation / regulation of TORC1 signaling / PH domain binding ...regulation of response to reactive oxygen species / negative regulation of translation in response to endoplasmic reticulum stress / sulfiredoxin activity / L-leucine binding / Atg1/ULK1 kinase complex / oxidoreductase activity, acting on peroxide as acceptor / TORC2 complex / cellular response to leucine starvation / regulation of TORC1 signaling / PH domain binding / mitochondrial DNA metabolic process / nucleotide-activated protein kinase complex / cellular response to L-leucine / Amino acids regulate mTORC1 / triglyceride homeostasis / GDP-dissociation inhibitor activity / positive regulation of lipophagy / cellular oxidant detoxification / regulation of gluconeogenesis / fatty acid beta-oxidation / D-glucose import / positive regulation of macroautophagy / DNA damage response, signal transduction by p53 class mediator / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / response to glucose / cellular response to glucose starvation / negative regulation of TORC1 signaling / protein sequestering activity / positive regulation of TORC1 signaling / cellular response to amino acid starvation / reactive oxygen species metabolic process / cellular response to amino acid stimulus / TP53 Regulates Metabolic Genes / peroxidase activity / response to insulin / regulation of protein phosphorylation / negative regulation of cell growth / 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 / cytosol / cytoplasm
Similarity search - Function
Sestrin / PA26 p53-induced protein (sestrin) / AhpD-like
Similarity search - Domain/homology
4-(difluoromethyl)-L-leucine / Sestrin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsO'Neill, D.
CitationJournal: Sci Rep / Year: 2019
Title: Discovery of NV-5138, the first selective Brain mTORC1 activator.
Authors: Sengupta, S. / Giaime, E. / Narayan, S. / Hahm, S. / Howell, J. / O'Neill, D. / Vlasuk, G.P. / Saiah, E.
History
DepositionNov 7, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)238,20010
Polymers237,2945
Non-polymers9065
Water00
1
A: Sestrin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6402
Polymers47,4591
Non-polymers1811
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sestrin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6402
Polymers47,4591
Non-polymers1811
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Sestrin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6402
Polymers47,4591
Non-polymers1811
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Sestrin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6402
Polymers47,4591
Non-polymers1811
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Sestrin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6402
Polymers47,4591
Non-polymers1811
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)290.410, 290.410, 290.410
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23

-
Components

#1: Protein
Sestrin-2 / Hypoxia-induced gene


Mass: 47458.730 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SESN2, Hi95, SEST2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P58004, peroxiredoxin
#2: Chemical
ChemComp-K94 / 4-(difluoromethyl)-L-leucine


Mass: 181.180 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C7H13F2NO2 / Feature type: SUBJECT OF INVESTIGATION

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.38 Å3/Da / Density % sol: 71.9 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 1.35M Na malonate pH 6.5, 0.1M Mes pH 6.0 / PH range: 6-6.5

-
Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.98→48.4 Å / Num. obs: 82533 / % possible obs: 99.8 % / Redundancy: 23 % / Rmerge(I) obs: 0.53 / Net I/σ(I): 8.2
Reflection shellResolution: 2.98→3.06 Å / Mean I/σ(I) obs: 0.29 / CC1/2: 0.223 / Rrim(I) all: 0.543 / % possible all: 99.3

-
Processing

Software
NameVersionClassification
XDSdata reduction
REFMAC5.8.0103refinement
PDB_EXTRACT3.24data extraction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DJ4

5dj4


Resolution: 3.3→48.4 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.918 / SU B: 21.599 / SU ML: 0.337 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.425
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2502 3046 5 %RANDOM
Rwork0.1836 ---
obs0.1869 57875 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 218.53 Å2 / Biso mean: 107.251 Å2 / Biso min: 65.47 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 3.3→48.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14751 0 60 0 14811
Biso mean--100.86 --
Num. residues----1824
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01915191
X-RAY DIFFRACTIONr_bond_other_d0.0020.0214182
X-RAY DIFFRACTIONr_angle_refined_deg1.6071.95120589
X-RAY DIFFRACTIONr_angle_other_deg1.017332488
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.39451799
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.15822.814725
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.519152508
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.80815113
X-RAY DIFFRACTIONr_chiral_restr0.0840.22234
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216949
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023744
LS refinement shellResolution: 3.3→3.385 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 222 -
Rwork0.349 4222 -
all-4444 -
obs--99.93 %

+
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