[English] 日本語
Yorodumi
- PDB-7weu: Crystal structure of Peroxiredoxin I in complex with compound 19-048 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7weu
TitleCrystal structure of Peroxiredoxin I in complex with compound 19-048
ComponentsPeroxiredoxin-1
KeywordsOXIDOREDUCTASE / Inhibitor / Complex / Peroxiredoxin
Function / homology
Function and homology information


leukocyte activation / regulation of non-canonical NF-kappaB signal transduction / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / natural killer cell activation / NFE2L2 regulating anti-oxidant/detoxification enzymes / erythrocyte homeostasis / regulation of stress-activated MAPK cascade / natural killer cell mediated cytotoxicity / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models ...leukocyte activation / regulation of non-canonical NF-kappaB signal transduction / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / natural killer cell activation / NFE2L2 regulating anti-oxidant/detoxification enzymes / erythrocyte homeostasis / regulation of stress-activated MAPK cascade / natural killer cell mediated cytotoxicity / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / Detoxification of Reactive Oxygen Species / canonical NF-kappaB signal transduction / removal of superoxide radicals / cell redox homeostasis / skeletal system development / TP53 Regulates Metabolic Genes / hydrogen peroxide catabolic process / peroxidase activity / melanosome / response to oxidative stress / fibroblast proliferation / cell population proliferation / cadherin binding / extracellular space / RNA binding / extracellular exosome / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Peroxiredoxin, AhpC-type / : / Peroxiredoxin, C-terminal / C-terminal domain of 1-Cys peroxiredoxin / Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin ...Peroxiredoxin, AhpC-type / : / Peroxiredoxin, C-terminal / C-terminal domain of 1-Cys peroxiredoxin / Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Unknown ligand / Peroxiredoxin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsZhang, H. / Luo, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81903538 China
CitationJournal: Signal Transduct Target Ther / Year: 2023
Title: Celastrol suppresses colorectal cancer via covalent targeting peroxiredoxin 1.
Authors: Xu, H. / Zhao, H. / Ding, C. / Jiang, D. / Zhao, Z. / Li, Y. / Ding, X. / Gao, J. / Zhou, H. / Luo, C. / Chen, G. / Zhang, A. / Xu, Y. / Zhang, H.
History
DepositionDec 24, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2023Group: 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 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Peroxiredoxin-1
B: Peroxiredoxin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7773
Polymers38,6742
Non-polymers1031
Water8,035446
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-9 kcal/mol
Surface area14760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.925, 77.820, 81.152
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein Peroxiredoxin-1 / Natural killer cell-enhancing factor A / NKEF-A / Proliferation-associated gene protein / PAG / ...Natural killer cell-enhancing factor A / NKEF-A / Proliferation-associated gene protein / PAG / Thioredoxin peroxidase 2 / Thioredoxin-dependent peroxide reductase 2 / Thioredoxin-dependent peroxiredoxin 1


Mass: 19337.066 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRDX1, PAGA, PAGB, TDPX2
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q06830, thioredoxin-dependent peroxiredoxin
#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Mass: 103.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 446 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.87 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: Tacsimate pH 8.0 (v/v) and 20% PEG3350 (v/v)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.81→35.98 Å / Num. obs: 37334 / % possible obs: 99.94 % / Redundancy: 13.3 % / Biso Wilson estimate: 17.88 Å2 / CC1/2: 0.999 / Net I/σ(I): 33.54
Reflection shellResolution: 1.814→1.879 Å / Num. unique obs: 3669 / CC1/2: 0.991

-
Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XCS

4xcs


Resolution: 1.81→35.98 Å / SU ML: 0.133 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.178
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1955 1854 4.97 %
Rwork0.1556 35457 -
obs0.1575 37311 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.83 Å2
Refinement stepCycle: LAST / Resolution: 1.81→35.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2616 0 40 446 3102
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00612726
X-RAY DIFFRACTIONf_angle_d0.90693703
X-RAY DIFFRACTIONf_chiral_restr0.0631404
X-RAY DIFFRACTIONf_plane_restr0.0068476
X-RAY DIFFRACTIONf_dihedral_angle_d3.16221607
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.81-1.860.20921490.16482651X-RAY DIFFRACTION100
1.86-1.920.20641440.162701X-RAY DIFFRACTION100
1.92-1.980.19191430.15582694X-RAY DIFFRACTION100
1.98-2.050.19751530.1522693X-RAY DIFFRACTION100
2.05-2.130.20351350.15392684X-RAY DIFFRACTION99.96
2.13-2.230.20911320.15472709X-RAY DIFFRACTION100
2.23-2.350.19061240.16112729X-RAY DIFFRACTION100
2.35-2.490.19881530.1692691X-RAY DIFFRACTION99.96
2.49-2.690.18871670.16512710X-RAY DIFFRACTION100
2.69-2.960.19321370.16922747X-RAY DIFFRACTION100
2.96-3.380.22741360.16062755X-RAY DIFFRACTION100
3.38-4.260.18831120.13892818X-RAY DIFFRACTION100
4.26-35.980.17551690.14852875X-RAY DIFFRACTION99.61

+
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