[English] 日本語
Yorodumi
- PDB-8in0: Structure of the Keap1 Kelch domain in complex with PGAM5-derived... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8in0
TitleStructure of the Keap1 Kelch domain in complex with PGAM5-derived peptide
Components
  • Kelch-like ECH-associated protein 1
  • PGAM5 12-mer peptide
KeywordsCYTOSOLIC PROTEIN / Kelch / PGAM5 derived peptide / Complex
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 / negative regulation of response to oxidative stress / Cul3-RING ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / centriolar satellite ...cellular response to carbohydrate stimulus / KEAP1-NFE2L2 pathway / regulation of epidermal cell differentiation / Neddylation / Antigen processing: Ubiquitination & Proteasome degradation / Ub-specific processing proteases / negative regulation of response to oxidative stress / Cul3-RING ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / centriolar satellite / cellular response to interleukin-4 / inclusion body / regulation of autophagy / actin filament / adherens junction / disordered domain specific binding / midbody / cellular response to oxidative stress / 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 / cytoplasm / cytosol
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
Kelch-like ECH-associated protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo (humans)
MethodX-RAY DIFFRACTION / AB INITIO PHASING / Resolution: 1.8 Å
AuthorsJiang, L. / Wang, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81874343 China
CitationJournal: To Be Published
Title: Structure of the Keap1 Kelch domain in complex with PGAM5-derived peptide
Authors: Jiang, L. / Wang, C.
History
DepositionMar 8, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Kelch-like ECH-associated protein 1
B: PGAM5 12-mer peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0906
Polymers39,7062
Non-polymers3844
Water3,963220
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.655, 103.655, 56.167
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

-
Components

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


Mass: 38301.953 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 PGAM5 12-mer peptide


Mass: 1403.565 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo (humans)
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 2.19 Å3/Da / Density % sol: 43.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: Ammonium sulfate, Lithium sulfate, Sodium citrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.8 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Nov 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.8 Å / Relative weight: 1
ReflectionResolution: 1.8→24.704 Å / Num. obs: 31965 / % possible obs: 99.91 % / Redundancy: 5.8 % / CC1/2: 0.957 / Net I/σ(I): 14.68
Reflection shellResolution: 1.8→1.864 Å / Num. unique obs: 3192 / CC1/2: 0.605

-
Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
CrysalisProdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.8→24.704 Å / Cor.coef. Fo:Fc: 0.877 / Cor.coef. Fo:Fc free: 0.864 / WRfactor Rfree: 0.233 / WRfactor Rwork: 0.202 / SU B: 4.457 / SU ML: 0.124 / Average fsc free: 0.8143 / Average fsc work: 0.8256 / Cross valid method: FREE R-VALUE / ESU R: 0.169 / ESU R Free: 0.154
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2847 1536 4.917 %
Rwork0.2533 29704 -
all0.255 --
obs-31240 97.485 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 17.466 Å2
Baniso -1Baniso -2Baniso -3
1-0.004 Å20.002 Å20 Å2
2--0.004 Å2-0 Å2
3----0.014 Å2
Refinement stepCycle: LAST / Resolution: 1.8→24.704 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2304 0 20 220 2544
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132374
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172081
X-RAY DIFFRACTIONr_angle_refined_deg1.6691.6393230
X-RAY DIFFRACTIONr_angle_other_deg1.351.5724801
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5065297
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.32220.515136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.24415355
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6351523
X-RAY DIFFRACTIONr_chiral_restr0.0720.2292
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022726
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02543
X-RAY DIFFRACTIONr_nbd_refined0.2090.2410
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2030.22118
X-RAY DIFFRACTIONr_nbtor_refined0.1640.21117
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.21109
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.2183
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0310.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2030.217
X-RAY DIFFRACTIONr_nbd_other0.1870.225
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1320.26
X-RAY DIFFRACTIONr_mcbond_it1.5941.6681194
X-RAY DIFFRACTIONr_mcbond_other1.5581.6671193
X-RAY DIFFRACTIONr_mcangle_it2.6132.4821489
X-RAY DIFFRACTIONr_mcangle_other2.6142.4841490
X-RAY DIFFRACTIONr_scbond_it2.1871.991180
X-RAY DIFFRACTIONr_scbond_other2.0991.9651162
X-RAY DIFFRACTIONr_scangle_it3.4052.8851741
X-RAY DIFFRACTIONr_scangle_other3.2882.8511717
X-RAY DIFFRACTIONr_lrange_it6.12720.1762655
X-RAY DIFFRACTIONr_lrange_other5.86219.8662601
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8470.3261340.2712226X-RAY DIFFRACTION99.873
1.847-1.8970.4841280.4311998X-RAY DIFFRACTION92.5958
1.897-1.9520.67990.671953X-RAY DIFFRACTION92.1419
1.952-2.0120.301890.2562074X-RAY DIFFRACTION99.6774
2.012-2.0780.288970.2252024X-RAY DIFFRACTION100
2.078-2.1510.2441000.2051913X-RAY DIFFRACTION100
2.151-2.2320.296650.2961715X-RAY DIFFRACTION90.8627
2.232-2.3230.529980.5291603X-RAY DIFFRACTION89.6679
2.323-2.4270.263830.21741X-RAY DIFFRACTION100
2.427-2.5450.219820.1791659X-RAY DIFFRACTION100
2.545-2.6830.278620.1871592X-RAY DIFFRACTION100
2.683-2.8450.256780.181482X-RAY DIFFRACTION100
2.845-3.0410.224970.1761374X-RAY DIFFRACTION100
3.041-3.2850.222580.1811319X-RAY DIFFRACTION100
3.285-3.5980.209760.1811178X-RAY DIFFRACTION98.6625
3.598-4.0220.23360.1881071X-RAY DIFFRACTION96.5126
4.022-4.6420.145570.124958X-RAY DIFFRACTION99.8033
4.642-5.6820.174430.151823X-RAY DIFFRACTION100
5.682-8.0190.175310.175652X-RAY DIFFRACTION100
8-100.152230.152349X-RAY DIFFRACTION95.6298

+
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