[English] 日本語
Yorodumi
- PDB-7k2n: Kelch domain of human KEAP1 bound to Nrf2-based cyclic peptide, c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7k2n
TitleKelch domain of human KEAP1 bound to Nrf2-based cyclic peptide, c[BAL-DEETGE]
Components
  • (BAL)DPETGE
  • Kelch-like ECH-associated protein 1
KeywordsPROTEIN BINDING/Inhibitor / Peptide inhibitor / Inhibitor complex / Loop-mimic / PROTEIN BINDING / cyclic peptide / PROTEIN BINDING-Inhibitor complex
Function / homology
Function and homology information


regulation of epidermal cell differentiation / Nuclear events mediated by NFE2L2 / negative regulation of response to oxidative stress / Cul3-RING ubiquitin ligase complex / centriolar satellite / ubiquitin-like ligase-substrate adaptor activity / cellular response to interleukin-4 / inclusion body / regulation of autophagy / actin filament ...regulation of epidermal cell differentiation / Nuclear events mediated by NFE2L2 / negative regulation of response to oxidative stress / Cul3-RING ubiquitin ligase complex / centriolar satellite / ubiquitin-like ligase-substrate adaptor activity / cellular response to interleukin-4 / inclusion body / regulation of autophagy / actin filament / negative regulation of DNA-binding transcription factor activity / disordered domain specific binding / KEAP1-NFE2L2 pathway / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Neddylation / cellular response to oxidative stress / midbody / ubiquitin-dependent protein catabolic process / in utero embryonic development / RNA polymerase II-specific DNA-binding transcription factor binding / Potential therapeutics for SARS / Ub-specific processing proteases / protein ubiquitination / endoplasmic reticulum / 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
Kelch-like ECH-associated protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsMuellers, S.N. / Allen, K.N.
CitationJournal: J.Am.Chem.Soc. / Year: 2021
Title: Recapitulating the Binding Affinity of Nrf2 for KEAP1 in a Cyclic Heptapeptide, Guided by NMR, X-ray Crystallography, and Machine Learning.
Authors: Ortet, P.C. / Muellers, S.N. / Viarengo-Baker, L.A. / Streu, K. / Szymczyna, B.R. / Beeler, A.B. / Allen, K.N. / Whitty, A.
History
DepositionSep 8, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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: (BAL)DPETGE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,1545
Polymers66,9623
Non-polymers1922
Water1,58588
1
A: Kelch-like ECH-associated protein 1
P: (BAL)DPETGE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0324
Polymers33,8402
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-27 kcal/mol
Surface area11610 Å2
MethodPISA
2
B: Kelch-like ECH-associated protein 1


Theoretical massNumber of molelcules
Total (without water)33,1221
Polymers33,1221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.079, 68.739, 77.014
Angle α, β, γ (deg.)90.000, 117.658, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

-
Components

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


Mass: 33122.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KEAP1, INRF2, KIAA0132, KLHL19 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14145
#2: Protein/peptide (BAL)DPETGE


Mass: 717.679 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 3 Å3/Da / Density % sol: 58.96 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 1.2 - 1.5 M Ammonium Sulfate, 0.5-0.7% PEG-MME-550, 0.1 M Bis-Tris pH = 6.0 - 6.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 2.218→29.52 Å / Num. obs: 37146 / % possible obs: 99.3 % / Redundancy: 2 % / Biso Wilson estimate: 40.14 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.04734 / Rpim(I) all: 0.04734 / Rrim(I) all: 0.06694 / Net I/σ(I): 9.85
Reflection shellResolution: 2.218→2.297 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.3502 / Mean I/σ(I) obs: 1.74 / Num. unique obs: 3602 / CC1/2: 0.836 / CC star: 0.954 / Rpim(I) all: 0.3502 / Rrim(I) all: 4952 / % possible all: 96.85

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WFL

5wfl


Resolution: 2.22→29.52 Å / SU ML: 0.3564 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 31.5109
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.29 2000 5.39 %
Rwork0.2472 35117 -
obs0.2495 37117 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.48 Å2
Refinement stepCycle: LAST / Resolution: 2.22→29.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4445 0 10 88 4543
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00864564
X-RAY DIFFRACTIONf_angle_d1.14796217
X-RAY DIFFRACTIONf_chiral_restr0.06663
X-RAY DIFFRACTIONf_plane_restr0.0057820
X-RAY DIFFRACTIONf_dihedral_angle_d16.1189660
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.22-2.270.3881340.35122416X-RAY DIFFRACTION95.79
2.27-2.330.39921510.32952485X-RAY DIFFRACTION99.66
2.33-2.40.31881410.29992495X-RAY DIFFRACTION99.62
2.4-2.480.32641390.29912508X-RAY DIFFRACTION99.62
2.48-2.570.331430.29482486X-RAY DIFFRACTION99.58
2.57-2.670.36741420.29122492X-RAY DIFFRACTION99.32
2.67-2.790.31411400.29462510X-RAY DIFFRACTION99.4
2.79-2.940.29761390.26482506X-RAY DIFFRACTION99.66
2.94-3.120.28341460.27192540X-RAY DIFFRACTION99.89
3.12-3.370.3221390.25412499X-RAY DIFFRACTION99.85
3.37-3.70.27371460.23922516X-RAY DIFFRACTION99.74
3.7-4.240.25351450.20982547X-RAY DIFFRACTION99.85
4.24-5.330.2371450.19972519X-RAY DIFFRACTION99.55
5.34-29.520.29871500.22942598X-RAY DIFFRACTION99.49

+
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