[English] 日本語
Yorodumi
- PDB-5wfv: Kelch domain of human Keap1 bound to Nrf2 ETGE peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5wfv
TitleKelch domain of human Keap1 bound to Nrf2 ETGE peptide
Components
  • Kelch-like ECH-associated protein 1
  • Nrf2 ETGE peptide
KeywordsTRANSCRIPTION / Scaffold / Peptide-bound
Function / homology
Function and homology information


positive regulation of glutathione biosynthetic process / aflatoxin catabolic process / negative regulation of hematopoietic stem cell differentiation / integrated stress response signaling / Regulation of HMOX1 expression and activity / negative regulation of cellular response to hypoxia / NFE2L2 regulating TCA cycle genes / positive regulation of ERAD pathway / PERK-mediated unfolded protein response / regulation of removal of superoxide radicals ...positive regulation of glutathione biosynthetic process / aflatoxin catabolic process / negative regulation of hematopoietic stem cell differentiation / integrated stress response signaling / Regulation of HMOX1 expression and activity / negative regulation of cellular response to hypoxia / NFE2L2 regulating TCA cycle genes / positive regulation of ERAD pathway / PERK-mediated unfolded protein response / regulation of removal of superoxide radicals / regulation of cellular response to oxidative stress / cellular response to laminar fluid shear stress / regulation of epidermal cell differentiation / NFE2L2 regulating ER-stress associated genes / NFE2L2 regulating inflammation associated genes / mediator complex / cellular response to fluid shear stress / cellular response to methionine / NFE2L2 regulates pentose phosphate pathway genes / NFE2L2 regulating MDR associated enzymes / positive regulation of ubiquitin-dependent protein catabolic process / Regulation of NFE2L2 gene expression / Nuclear events mediated by NFE2L2 / negative regulation of response to oxidative stress / negative regulation of cardiac muscle cell apoptotic process / NFE2L2 regulating tumorigenic genes / NFE2L2 regulating anti-oxidant/detoxification enzymes / proteasomal ubiquitin-independent protein catabolic process / negative regulation of ferroptosis / regulation of innate immune response / Cul3-RING ubiquitin ligase complex / negative regulation of vascular associated smooth muscle cell migration / cellular response to angiotensin / regulation of embryonic development / positive regulation of blood coagulation / positive regulation of blood vessel endothelial cell migration / negative regulation of endothelial cell apoptotic process / ubiquitin-like ligase-substrate adaptor activity / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / endoplasmic reticulum unfolded protein response / transcription regulator inhibitor activity / cellular response to glucose starvation / inclusion body / cellular response to interleukin-4 / reactive oxygen species metabolic process / cell redox homeostasis / cellular response to copper ion / response to ischemia / transcription coregulator binding / positive regulation of D-glucose import across plasma membrane / actin filament / molecular condensate scaffold activity / Heme signaling / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / protein-DNA complex / positive regulation of neuron projection development / RNA polymerase II transcription regulator complex / centriolar satellite / cellular response to xenobiotic stimulus / cellular response to hydrogen peroxide / positive regulation of reactive oxygen species metabolic process / positive regulation of angiogenesis / disordered domain specific binding / cellular response to tumor necrosis factor / KEAP1-NFE2L2 pathway / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Neddylation / response to oxidative stress / cellular response to oxidative stress / DNA-binding transcription activator activity, RNA polymerase II-specific / midbody / ubiquitin-dependent protein catabolic process / cellular response to hypoxia / sequence-specific DNA binding / in utero embryonic development / Potential therapeutics for SARS / proteasome-mediated ubiquitin-dependent protein catabolic process / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / Ub-specific processing proteases / regulation of autophagy / protein ubiquitination / ciliary basal body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / inflammatory response / protein domain specific binding / ubiquitin protein ligase binding / centrosome / positive regulation of gene expression / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / endoplasmic reticulum / negative regulation of transcription by RNA polymerase II / Golgi apparatus / positive regulation of transcription by RNA polymerase II / DNA binding
Similarity search - Function
: / Basic leucine zipper domain, Maf-type / bZIP Maf transcription factor / Transcription factor, Skn-1-like, DNA-binding domain superfamily / Kelch-type beta propeller / Kelch-like ECH-associated protein 1 / : / KLHDC2/KLHL20/DRC7 Kelch-repeats domain / BTB-kelch protein / BTB/Kelch-associated ...: / Basic leucine zipper domain, Maf-type / bZIP Maf transcription factor / Transcription factor, Skn-1-like, DNA-binding domain superfamily / Kelch-type beta propeller / Kelch-like ECH-associated protein 1 / : / KLHDC2/KLHL20/DRC7 Kelch-repeats domain / BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Kelch motif / Kelch / Kelch repeat type 1 / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain / Basic-leucine zipper domain superfamily / Kelch-type beta propeller / BTB/POZ domain / BTB domain profile. / 6 Propeller / Neuraminidase / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / SKP1/BTB/POZ domain superfamily / Mainly Beta
Similarity search - Domain/homology
Kelch-like ECH-associated protein 1 / Nuclear factor erythroid 2-related factor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsCarolan, J.P. / Lynch, A.J. / Allen, K.N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM118078 United States
CitationJournal: Biochemistry / Year: 2020
Title: Interaction Energetics and Druggability of the Protein-Protein Interaction between Kelch-like ECH-Associated Protein 1 (KEAP1) and Nuclear Factor Erythroid 2 Like 2 (Nrf2).
Authors: Zhong, M. / Lynch, A. / Muellers, S.N. / Jehle, S. / Luo, L. / Hall, D.R. / Iwase, R. / Carolan, J.P. / Egbert, M. / Wakefield, A. / Streu, K. / Harvey, C.M. / Ortet, P.C. / Kozakov, D. / ...Authors: Zhong, M. / Lynch, A. / Muellers, S.N. / Jehle, S. / Luo, L. / Hall, D.R. / Iwase, R. / Carolan, J.P. / Egbert, M. / Wakefield, A. / Streu, K. / Harvey, C.M. / Ortet, P.C. / Kozakov, D. / Vajda, S. / Allen, K.N. / Whitty, A.
History
DepositionJul 12, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Apr 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 1.3Oct 4, 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: Kelch-like ECH-associated protein 1
B: Kelch-like ECH-associated protein 1
P: Nrf2 ETGE peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,9474
Polymers74,8503
Non-polymers961
Water2,072115
1
A: Kelch-like ECH-associated protein 1
P: Nrf2 ETGE peptide


Theoretical massNumber of molelcules
Total (without water)37,9512
Polymers37,9512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint1 kcal/mol
Surface area11920 Å2
MethodPISA
2
B: Kelch-like ECH-associated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9952
Polymers36,8991
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-12 kcal/mol
Surface area11810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.919, 69.253, 79.228
Angle α, β, γ (deg.)90.00, 118.50, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Kelch-like ECH-associated protein 1 / Cytosolic inhibitor of Nrf2 / INrf2 / Kelch-like protein 19


Mass: 36899.176 Da / Num. of mol.: 2 / Fragment: UNP residues 320-612 / Mutation: E540A, E542A
Source method: isolated from a genetically manipulated source
Details: Histidine-tagged variant of human Keap1 Kelch domain, including mutations for altered crystallographic packing
Source: (gene. exp.) Homo sapiens (human) / Gene: KEAP1, INRF2, KIAA0132, KLHL19 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14145
#2: Protein/peptide Nrf2 ETGE peptide


Mass: 1052.089 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: Q16236*PLUS
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53.12 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: 1.2 - 1.5 M Ammonium Sulfate, 0.1 M Bis-Tris pH = 6.0 - 6.5
PH range: 6.0 - 6.5

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Nitrogen stream
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 29, 2016
RadiationMonochromator: Cryo-Cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.69→52.14 Å / Num. obs: 58943 / % possible obs: 93 % / Redundancy: 3.5 % / CC1/2: 0.994 / Rmerge(I) obs: 0.06899 / Net I/σ(I): 15.18
Reflection shellResolution: 1.91→1.978 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.3304 / Mean I/σ(I) obs: 3.74 / Num. unique obs: 5843 / CC1/2: 0.886 / % possible all: 97

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WLF

5wlf


Resolution: 1.91→52.14 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.13
RfactorNum. reflection% reflectionSelection details
Rfree0.2274 1353 2.42 %Random selection
Rwork0.1995 ---
obs0.2002 55914 92.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 37.12 Å2
Refinement stepCycle: LAST / Resolution: 1.91→52.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4470 0 5 115 4590
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074600
X-RAY DIFFRACTIONf_angle_d0.96267
X-RAY DIFFRACTIONf_dihedral_angle_d13.2272669
X-RAY DIFFRACTIONf_chiral_restr0.061670
X-RAY DIFFRACTIONf_plane_restr0.005827
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.91-1.97830.28241330.25425239X-RAY DIFFRACTION89
1.9783-2.05750.28411300.23515310X-RAY DIFFRACTION91
2.0575-2.15120.26871370.2285398X-RAY DIFFRACTION92
2.1512-2.26460.22461350.22395350X-RAY DIFFRACTION92
2.2646-2.40650.26051420.21465554X-RAY DIFFRACTION95
2.4065-2.59230.28521410.23555583X-RAY DIFFRACTION95
2.5923-2.85320.31330.22635533X-RAY DIFFRACTION94
2.8532-3.2660.24921320.21835549X-RAY DIFFRACTION94
3.266-4.11480.18951310.18075422X-RAY DIFFRACTION92
4.1148-69.06020.17291390.15785623X-RAY DIFFRACTION93
Refinement TLS params.Method: refined / Origin x: -37.8434 Å / Origin y: -14.2627 Å / Origin z: 27.9836 Å
111213212223313233
T0.2061 Å2-0.0523 Å2-0.0083 Å2-0.2576 Å20.0383 Å2--0.2937 Å2
L-0.1689 °2-0.1315 °2-0.1649 °2--0.1071 °20.0104 °2--1.5889 °2
S0.0008 Å °-0.0527 Å °-0.0424 Å °0.0363 Å °-0.0251 Å °0.025 Å °0.0001 Å °-0.1049 Å °0.0288 Å °
Refinement TLS groupSelection details: all

+
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