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- PDB-3zgc: crystal structure of the KEAP1-NEH2 complex -

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Basic information

Entry
Database: PDB / ID: 3zgc
Titlecrystal structure of the KEAP1-NEH2 complex
Components
  • KELCH-LIKE ECH-ASSOCIATED PROTEIN 1
  • NUCLEAR FACTOR ERYTHROID 2-RELATED FACTOR 2
KeywordsTRANSCRIPTION / PROTEIN-PEPTIDE COMPLEX
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
ACETATE ION / 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: 2.2 Å
AuthorsHoerer, S. / Reinert, D. / Ostmann, K. / Hoevels, Y. / Nar, H.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2013
Title: Crystal-Contact Engineering to Obtain a Crystal Form of the Kelch Domain of Human Keap1 Suitable for Ligand-Soaking Experiments.
Authors: Horer, S. / Reinert, D. / Ostmann, K. / Hoevels, Y. / Nar, H.
History
DepositionDec 17, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_validate_close_contact / struct_conn / struct_conn_type
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: KELCH-LIKE ECH-ASSOCIATED PROTEIN 1
B: KELCH-LIKE ECH-ASSOCIATED PROTEIN 1
C: NUCLEAR FACTOR ERYTHROID 2-RELATED FACTOR 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,00813
Polymers68,4173
Non-polymers59010
Water9,908550
1
A: KELCH-LIKE ECH-ASSOCIATED PROTEIN 1
C: NUCLEAR FACTOR ERYTHROID 2-RELATED FACTOR 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8136
Polymers34,5772
Non-polymers2364
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-2.1 kcal/mol
Surface area11970 Å2
MethodPISA
2
B: KELCH-LIKE ECH-ASSOCIATED PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1957
Polymers33,8411
Non-polymers3546
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.103, 76.064, 207.541
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.001113, -0.8131, -0.5821), (-1, -0.003351, 0.002768), (-0.004201, 0.5821, -0.8131)
Vector: 15.5, -2.317, 40.87)

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Components

#1: Protein KELCH-LIKE ECH-ASSOCIATED PROTEIN 1 / CYTOSOLIC INHIBITOR OF NRF2 / INRF2 / KELCH-LIKE PROTEIN 19


Mass: 33840.848 Da / Num. of mol.: 2 / Fragment: KELCH DOMAIN OF HUMAN KEAP1, RESIDUES 321-609 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: Q14145
#2: Protein/peptide NUCLEAR FACTOR ERYTHROID 2-RELATED FACTOR 2 / NF-E2-RELATED FACTOR 2 / NFE2-RELATED FACTOR 2 / HEBP1 / NUCLEAR FACTOR / ERYTHROID DERIVED 2 / ...NF-E2-RELATED FACTOR 2 / NFE2-RELATED FACTOR 2 / HEBP1 / NUCLEAR FACTOR / ERYTHROID DERIVED 2 / LIKE 2 / NEH2-DERIVED PEPTIDE


Mass: 735.652 Da / Num. of mol.: 1 / Fragment: RESIDUES 76-82 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q16236
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 550 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsE540A E542A CHAIN C IS CYCLIZED VIA GLYCINE 76

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 4.4 Å3/Da / Density % sol: 72 % / Description: NONE
Crystal growpH: 5
Details: 4.0 M AMMONIUM ACETATE, 0.1 M SODIUM ACETATE TRIHYDRATE PH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.979
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 26, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→76.88 Å / Num. obs: 61950 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 44.6 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.1
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.9 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1U6D

1u6d


Resolution: 2.2→40 Å / Cor.coef. Fo:Fc: 0.9552 / Cor.coef. Fo:Fc free: 0.9489 / SU R Cruickshank DPI: 0.131 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.14 / SU Rfree Blow DPI: 0.122 / SU Rfree Cruickshank DPI: 0.118
RfactorNum. reflection% reflectionSelection details
Rfree0.1883 3097 5 %RANDOM
Rwork0.1724 ---
obs0.1732 61947 99.81 %-
Displacement parametersBiso mean: 40.64 Å2
Baniso -1Baniso -2Baniso -3
1--4.4114 Å20 Å20 Å2
2--3.6312 Å20 Å2
3---0.7802 Å2
Refine analyzeLuzzati coordinate error obs: 0.239 Å
Refinement stepCycle: LAST / Resolution: 2.2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4422 0 40 550 5012
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0084562HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.026202HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1498SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes102HARMONIC2
X-RAY DIFFRACTIONt_gen_planes702HARMONIC5
X-RAY DIFFRACTIONt_it4562HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.68
X-RAY DIFFRACTIONt_other_torsion16.16
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion564SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5310SEMIHARMONIC4
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2275 227 5 %
Rwork0.2211 4309 -
all0.2215 4536 -
obs--99.81 %

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