[English] 日本語
Yorodumi
- PDB-8q1r: mouse Keap1 in complex with stapled peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8q1r
Titlemouse Keap1 in complex with stapled peptide
Components
  • Kelch-like ECH-associated protein 1
  • Stapled peptide
KeywordsLIGASE / Keap1 / cyclic peptide / E3 ligase adaptor / antioxidant response
Function / homology
Function and homology information


cellular response to carbohydrate stimulus / KEAP1-NFE2L2 pathway / regulation of epidermal cell differentiation / Neddylation / Antigen processing: Ubiquitination & Proteasome degradation / Ub-specific processing proteases / Cul3-RING ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / centriolar satellite / inclusion body ...cellular response to carbohydrate stimulus / KEAP1-NFE2L2 pathway / regulation of epidermal cell differentiation / Neddylation / Antigen processing: Ubiquitination & Proteasome degradation / Ub-specific processing proteases / Cul3-RING ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / centriolar satellite / inclusion body / cellular response to interleukin-4 / regulation of autophagy / actin filament / adherens junction / disordered domain specific binding / cellular response to oxidative stress / midbody / ubiquitin-dependent protein catabolic process / in utero embryonic development / RNA polymerase II-specific DNA-binding transcription factor binding / protein ubiquitination / negative regulation of gene expression / focal adhesion / regulation of DNA-templated transcription / endoplasmic reticulum / protein-containing complex / nucleoplasm / identical protein binding / cytosol / cytoplasm
Similarity search - Function
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 / Kelch-type beta propeller ...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 / 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
Chem-IZS / Kelch-like ECH-associated protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å
AuthorsKack, H. / Wissler, L.
Funding support Sweden, United Kingdom, Czech Republic, 5items
OrganizationGrant numberCountry
Swedish Research Council2018-07152 Sweden
UK Research and Innovation (UKRI) United Kingdom
Other government2019-02496 Sweden
Other government22-07138O Czech Republic
Other private22.39 United Kingdom
CitationJournal: Chem Sci / Year: 2023
Title: A cell-active cyclic peptide targeting the Nrf2/Keap1 protein-protein interaction.
Authors: Iegre, J. / Krajcovicova, S. / Gunnarsson, A. / Wissler, L. / Kack, H. / Luchniak, A. / Tangefjord, S. / Narjes, F. / Spring, D.R.
History
DepositionAug 1, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Kelch-like ECH-associated protein 1
E: Stapled peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6665
Polymers34,2952
Non-polymers3703
Water4,990277
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-12 kcal/mol
Surface area12040 Å2
Unit cell
Length a, b, c (Å)103.039, 103.039, 55.727
Angle α, β, γ (deg.)90, 90, 120
Int Tables number169
Space group name H-MP61

-
Components

-
Protein / Protein/peptide , 2 types, 2 molecules AE

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


Mass: 33305.250 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 Stapled peptide /


Mass: 990.090 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 4 types, 280 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#5: Chemical ChemComp-IZS / ethyl 2-[(4,6-diethylpyrimidin-2-yl)-methyl-amino]ethanoate


Mass: 251.325 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H21N3O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 277 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.9
Details: 0.7-0.9M Lithium Sulfate, 0.5-0.7M Ammonium sulfate and 0.1M Sodium Citrate pH5.9

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.976254 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 29, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976254 Å / Relative weight: 1
ReflectionResolution: 1.33→89.234 Å / Num. obs: 523089 / % possible obs: 88.3 % / Redundancy: 9.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.082 / Net I/σ(I): 12.3
Reflection shellResolution: 1.33→1.43 Å / Rmerge(I) obs: 0.762 / Num. unique obs: 2656 / CC1/2: 0.571

-
Processing

Software
NameVersionClassification
BUSTER2.11.8 (8-JUN-2022)refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.33→19.22 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.962 / SU R Cruickshank DPI: 0.057 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.059 / SU Rfree Blow DPI: 0.063 / SU Rfree Cruickshank DPI: 0.061
RfactorNum. reflection% reflectionSelection details
Rfree0.2287 3400 -RANDOM
Rwork0.1958 ---
obs0.1973 69409 88.7 %-
Displacement parametersBiso mean: 31.78 Å2
Baniso -1Baniso -2Baniso -3
1-0.3438 Å20 Å20 Å2
2--0.3438 Å20 Å2
3----0.6876 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 1.33→19.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2213 0 92 277 2582
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0122389HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.213259HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d821SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes428HARMONIC5
X-RAY DIFFRACTIONt_it2389HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion292SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2354SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion5.59
X-RAY DIFFRACTIONt_other_torsion14
LS refinement shellResolution: 1.33→1.34 Å
RfactorNum. reflection% reflection
Rfree0.6777 77 -
Rwork0.5929 --
obs--55.06 %
Refinement TLS params.Origin x: -90.1115 Å / Origin y: 100.689 Å / Origin z: -3.084 Å
111213212223313233
T-0.0719 Å2-0.005 Å20.0003 Å2--0.0907 Å20.0217 Å2--0.2663 Å2
L1.0438 °20.4446 °2-0.179 °2-1.4581 °20.1626 °2--0.414 °2
S0.0646 Å °-0.0014 Å °-0.004 Å °-0.0014 Å °-0.0369 Å °0.0002 Å °-0.004 Å °0.0002 Å °-0.0277 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A325 - 612
2X-RAY DIFFRACTION1{ A|* }A1103 - 1379
3X-RAY DIFFRACTION1{ A|* }A1380

+
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