[English] 日本語
Yorodumi
- PDB-7eca: Crystal structure of the Keap1 complex with a peptide base on ETG... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7eca
TitleCrystal structure of the Keap1 complex with a peptide base on ETGE motif.
Components
  • Kelch-like ECH-associated protein 1
  • LEU-ASP-GLU-GLU-THR-GLY-GLU-PHE-LEU-PRO
KeywordsCYTOSOLIC PROTEIN / Nrf2 / Oxidative stress / cancer
Function / homology
Function and homology information


positive regulation of glutathione biosynthetic process / aflatoxin catabolic process / negative regulation of hematopoietic stem cell differentiation / Nuclear events mediated by NFE2L2 / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / negative regulation of cellular response to hypoxia / PERK-mediated unfolded protein response / cellular response to carbohydrate stimulus / negative regulation of vascular associated smooth muscle cell migration / regulation of removal of superoxide radicals ...positive regulation of glutathione biosynthetic process / aflatoxin catabolic process / negative regulation of hematopoietic stem cell differentiation / Nuclear events mediated by NFE2L2 / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / negative regulation of cellular response to hypoxia / PERK-mediated unfolded protein response / cellular response to carbohydrate stimulus / negative regulation of vascular associated smooth muscle cell migration / regulation of removal of superoxide radicals / KEAP1-NFE2L2 pathway / regulation of epidermal cell differentiation / Neddylation / cellular response to laminar fluid shear stress / Antigen processing: Ubiquitination & Proteasome degradation / Ub-specific processing proteases / cellular response to fluid shear stress / cellular response to angiotensin / negative regulation of response to oxidative stress / negative regulation of cardiac muscle cell apoptotic process / Cul3-RING ubiquitin ligase complex / proteasomal ubiquitin-independent protein catabolic process / regulation of innate immune response / regulation of embryonic development / transcription factor binding / ubiquitin-like ligase-substrate adaptor activity / centriolar satellite / positive regulation of blood vessel endothelial cell migration / positive regulation of blood coagulation / cellular response to interleukin-4 / cellular response to glucose starvation / negative regulation of endothelial cell apoptotic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / endoplasmic reticulum unfolded protein response / inclusion body / cellular response to copper ion / response to endoplasmic reticulum stress / : / molecular condensate scaffold activity / cell redox homeostasis / regulation of autophagy / transcription coregulator binding / response to ischemia / positive regulation of glucose import / actin filament / protein-DNA complex / adherens junction / positive regulation of neuron projection development / cellular response to hydrogen peroxide / RNA polymerase II transcription regulator complex / positive regulation of angiogenesis / positive regulation of reactive oxygen species metabolic process / disordered domain specific binding / cellular response to xenobiotic stimulus / cellular response to tumor necrosis factor / cellular response to oxidative stress / midbody / cellular response to hypoxia / ubiquitin-dependent protein catabolic process / DNA-binding transcription activator activity, RNA polymerase II-specific / proteasome-mediated ubiquitin-dependent protein catabolic process / in utero embryonic development / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / protein ubiquitination / inflammatory response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / negative regulation of gene expression / focal adhesion / centrosome / ubiquitin protein ligase binding / positive regulation of gene expression / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / Golgi apparatus / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
: / Basic leucine zipper domain, Maf-type / bZIP Maf transcription factor / Transcription factor, Skn-1-like, DNA-binding domain superfamily / Kelch-like ECH-associated protein 1 / : / BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch ...: / Basic leucine zipper domain, Maf-type / bZIP Maf transcription factor / Transcription factor, Skn-1-like, DNA-binding domain superfamily / Kelch-like ECH-associated protein 1 / : / BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Kelch / Kelch repeat type 1 / Kelch motif / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain superfamily / Basic-leucine zipper domain / Kelch-type beta propeller / BTB/POZ domain / BTB domain profile. / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / SKP1/BTB/POZ domain superfamily
Similarity search - Domain/homology
Nuclear factor erythroid 2-related factor 2 / Kelch-like ECH-associated protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.00006351943 Å
AuthorsCheng, L. / Wang, C.
CitationJournal: Life Sci / Year: 2021
Title: New insights into the mechanism of Keap1-Nrf2 interaction based on cancer-associated mutations.
Authors: Cheng, L. / Wang, H. / Li, S. / Liu, Z. / Wang, C.
History
DepositionMar 11, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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: Kelch-like ECH-associated protein 1
B: LEU-ASP-GLU-GLU-THR-GLY-GLU-PHE-LEU-PRO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,82113
Polymers39,7642
Non-polymers1,05711
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-148 kcal/mol
Surface area12000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.814, 102.814, 54.812
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

-
Components

#1: Protein Kelch-like ECH-associated protein 1 / Cytosolic inhibitor of Nrf2 / INrf2


Mass: 36850.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Keap1, Inrf2, Kiaa0132 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Z2X8
#2: Protein/peptide LEU-ASP-GLU-GLU-THR-GLY-GLU-PHE-LEU-PRO


Mass: 2914.154 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q60795
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: Lithium Sulfate,Ammonium Sulfate,sodium citrate 5.1

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54184 Å
DetectorType: OXFORD ONYX CCD / Detector: CCD / Date: Jul 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 2→20.135 Å / Num. obs: 22476 / % possible obs: 99.83 % / Redundancy: 8.4 % / Biso Wilson estimate: 20.3899710197 Å2 / CC1/2: 0.996 / Net I/σ(I): 1.96
Reflection shellResolution: 2→2.11 Å / Num. unique obs: 164132 / CC1/2: 0.994

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
CrysalisPro1.171.40.54adata reduction
CCP47.0.053data scaling
CCP47.0.053phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1x2r

1x2r


Resolution: 2.00006351943→20.1349848749 Å / SU ML: 0.237795283374 / Cross valid method: FREE R-VALUE / σ(F): 1.35299871149 / Phase error: 25.3838261616
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.235456817831 1147 5.10526550051 %
Rwork0.196822366979 21320 -
obs0.198818141711 22467 99.9466168424 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.6687614344 Å2
Refinement stepCycle: LAST / Resolution: 2.00006351943→20.1349848749 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2300 0 55 160 2515
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002379120852572400
X-RAY DIFFRACTIONf_angle_d0.5773137651913273
X-RAY DIFFRACTIONf_chiral_restr0.0473419261539342
X-RAY DIFFRACTIONf_plane_restr0.00395850771617424
X-RAY DIFFRACTIONf_dihedral_angle_d5.825473150271364
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.0910.30547494461450.273893598772657X-RAY DIFFRACTION99.8218738867
2.091-2.20110.2892402960421430.2274109854362643X-RAY DIFFRACTION99.9641191245
2.2011-2.33880.3022365909061240.2410544941092653X-RAY DIFFRACTION99.9280316661
2.3388-2.51910.2946799726781310.2229791234442674X-RAY DIFFRACTION99.9643620813
2.5191-2.7720.2716085925911570.2153108903282644X-RAY DIFFRACTION100
2.772-3.17180.2441185882031460.1968067796262647X-RAY DIFFRACTION100
3.1718-3.9910.1945233823761510.161425567062674X-RAY DIFFRACTION100
3.991-6.640.1808859169741500.1671297174922728X-RAY DIFFRACTION99.9305555556

+
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