[English] 日本語
Yorodumi
- PDB-2dyh: Crystal structure of the Keap1 protein in complexed with the N-te... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2dyh
TitleCrystal structure of the Keap1 protein in complexed with the N-terminal region of the Nrf2 transcription factor
Components
  • Kelch-like ECH-associated protein 1
  • Nrf2/Neh2 peptide from Nuclear factor erythroid 2-related factor 2
KeywordsTRANSCRIPTION / bet-propeller / Kelch motif / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
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-type beta propeller / Kelch-like ECH-associated protein 1 / : / BTB-kelch protein / BTB/Kelch-associated / 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-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 / 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 / 6 Propeller / Neuraminidase / SKP1/BTB/POZ domain superfamily / Mainly Beta
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: 1.9 Å
AuthorsPadmanabhan, B. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Mol.Cell.Biol. / Year: 2007
Title: Different electrostatic potentials define ETGE and DLG motifs as hinge and latch in oxidative stress response
Authors: Tong, K.I. / Padmanabhan, B. / Kobayashi, A. / Shang, C. / Hirotsu, Y. / Yokoyama, S. / Yamamoto, M.
History
DepositionSep 14, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Kelch-like ECH-associated protein 1
B: Nrf2/Neh2 peptide from Nuclear factor erythroid 2-related factor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4809
Polymers36,8072
Non-polymers6727
Water5,531307
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.131, 103.131, 56.141
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

-
Components

#1: Protein Kelch-like ECH-associated protein 1 / Keap1 / Cytosolic inhibitor of Nrf2


Mass: 35006.277 Da / Num. of mol.: 1 / Fragment: Keap1-DC
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CodonPlus (DE3)_RIL / References: UniProt: Q9Z2X8
#2: Protein/peptide Nrf2/Neh2 peptide from Nuclear factor erythroid 2-related factor 2 / NF-E2-related factor 2 / NFE2-related factor 2 / Nuclear factor / erythroid derived 2 / like 2


Mass: 1801.053 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Nrf2 peptide, synthetic peptide / References: UniProt: Q60795
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / 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: 2.34 Å3/Da / Density % sol: 47.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: Ammonium sulfate, Lithium Sulfate, Sodium Citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 16, 2005 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 27043 / Num. obs: 26542 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 8.6 % / Rmerge(I) obs: 0.086
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.398 / Num. unique all: 2359 / % possible all: 88

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DNAdata collection
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1X2J

1x2j


Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.172 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.144 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21102 1335 5 %RANDOM
Rwork0.17237 ---
obs0.17432 25143 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.302 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å2-0.4 Å20 Å2
2---0.8 Å20 Å2
3---1.19 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2321 0 35 307 2663
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0212405
X-RAY DIFFRACTIONr_angle_refined_deg1.551.953275
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0185300
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.52422.895114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.5315357
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8111522
X-RAY DIFFRACTIONr_chiral_restr0.1180.2344
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021874
X-RAY DIFFRACTIONr_nbd_refined0.2210.21078
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21616
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2235
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2180.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1710.227
X-RAY DIFFRACTIONr_mcbond_it1.1421.51532
X-RAY DIFFRACTIONr_mcangle_it1.80822388
X-RAY DIFFRACTIONr_scbond_it2.69131014
X-RAY DIFFRACTIONr_scangle_it3.814.5887
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 92 -
Rwork0.219 1621 -
obs--86.43 %

+
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