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- PDB-5nlb: Crystal structure of human CUL3 N-terminal domain bound to KEAP1 ... -

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Basic information

Entry
Database: PDB / ID: 5nlb
TitleCrystal structure of human CUL3 N-terminal domain bound to KEAP1 BTB and 3-box
Components
  • Cullin-3
  • Kelch-like ECH-associated protein 1
KeywordsLIGASE / E3 ubiquitin ligase
Function / homology
Function and homology information


liver morphogenesis / positive regulation of mitotic cell cycle phase transition / trophectodermal cellular morphogenesis / POZ domain binding / nuclear protein quality control by the ubiquitin-proteasome system / regulation protein catabolic process at postsynapse / polar microtubule / negative regulation of response to oxidative stress / anaphase-promoting complex-dependent catabolic process / COPII vesicle coating ...liver morphogenesis / positive regulation of mitotic cell cycle phase transition / trophectodermal cellular morphogenesis / POZ domain binding / nuclear protein quality control by the ubiquitin-proteasome system / regulation protein catabolic process at postsynapse / polar microtubule / negative regulation of response to oxidative stress / anaphase-promoting complex-dependent catabolic process / COPII vesicle coating / stem cell division / regulation of epidermal cell differentiation / RHOBTB3 ATPase cycle / embryonic cleavage / cell projection organization / positive regulation of mitotic metaphase/anaphase transition / Notch binding / RHOBTB1 GTPase cycle / Nuclear events mediated by NFE2L2 / fibroblast apoptotic process / negative regulation of Rho protein signal transduction / negative regulation of type I interferon production / ubiquitin ligase complex scaffold activity / mitotic metaphase chromosome alignment / Cul3-RING ubiquitin ligase complex / stress fiber assembly / positive regulation of cytokinesis / protein monoubiquitination / centriolar satellite / ubiquitin-like ligase-substrate adaptor activity / sperm flagellum / cellular response to interleukin-4 / protein autoubiquitination / protein K48-linked ubiquitination / RHOBTB2 GTPase cycle / endoplasmic reticulum to Golgi vesicle-mediated transport / gastrulation / inclusion body / positive regulation of TORC1 signaling / cyclin binding / intrinsic apoptotic signaling pathway / positive regulation of protein ubiquitination / regulation of autophagy / integrin-mediated signaling pathway / Degradation of DVL / actin filament / cellular response to amino acid stimulus / Hedgehog 'on' state / protein destabilization / G1/S transition of mitotic cell cycle / negative regulation of DNA-binding transcription factor activity / mitotic spindle / Wnt signaling pathway / spindle pole / Regulation of RAS by GAPs / protein polyubiquitination / KEAP1-NFE2L2 pathway / ubiquitin protein ligase activity / disordered domain specific binding / cell migration / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / cellular response to oxidative stress / gene expression / midbody / ubiquitin-dependent protein catabolic process / postsynapse / proteasome-mediated ubiquitin-dependent protein catabolic process / in utero embryonic development / RNA polymerase II-specific DNA-binding transcription factor binding / Potential therapeutics for SARS / protein ubiquitination / Ub-specific processing proteases / inflammatory response / centrosome / glutamatergic synapse / ubiquitin protein ligase binding / positive regulation of cell population proliferation / Golgi apparatus / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / extracellular exosome / nucleoplasm / membrane / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Cullin Repeats / 5 helical Cullin repeat like / Kelch-like ECH-associated protein 1 / : / BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Cullin protein neddylation domain / Cullin, conserved site ...Cullin Repeats / 5 helical Cullin repeat like / Kelch-like ECH-associated protein 1 / : / BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Cullin protein neddylation domain / Cullin, conserved site / Cullin family signature. / Cullin / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin protein neddylation domain / Kelch / Kelch repeat type 1 / Kelch motif / Cullin / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin family / Cullin family profile. / 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 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Cullin-3 / Kelch-like ECH-associated protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.45 Å
AuthorsAdamson, R. / Krojer, T. / Pinkas, D.M. / Bartual, S.G. / Burgess-Brown, N.A. / Borkowska, O. / Chalk, R. / Newman, J.A. / Kopec, J. / Dixon-Clarke, S.E. ...Adamson, R. / Krojer, T. / Pinkas, D.M. / Bartual, S.G. / Burgess-Brown, N.A. / Borkowska, O. / Chalk, R. / Newman, J.A. / Kopec, J. / Dixon-Clarke, S.E. / Mathea, S. / Sethi, R. / Velupillai, S. / Mackinnon, S. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bullock, A.
CitationJournal: Free Radic Biol Med / Year: 2023
Title: Structural and biochemical characterization establishes a detailed understanding of KEAP1-CUL3 complex assembly.
Authors: Adamson, R.J. / Payne, N.C. / Bartual, S.G. / Mazitschek, R. / Bullock, A.N.
History
DepositionApr 4, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3Nov 8, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Jan 17, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kelch-like ECH-associated protein 1
B: Cullin-3


Theoretical massNumber of molelcules
Total (without water)58,8952
Polymers58,8952
Non-polymers00
Water0
1
A: Kelch-like ECH-associated protein 1
B: Cullin-3

A: Kelch-like ECH-associated protein 1
B: Cullin-3


Theoretical massNumber of molelcules
Total (without water)117,7914
Polymers117,7914
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_557x,-y,-z+21
Buried area6900 Å2
ΔGint-59 kcal/mol
Surface area50470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.000, 233.380, 164.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 17147.742 Da / Num. of mol.: 1 / Fragment: UNP residues 51-204
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 Cullin-3 / / CUL-3


Mass: 41747.715 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CUL3, KIAA0617 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13618

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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: 3.34 Å3/Da / Density % sol: 63.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 15% PEG3350, 10% ethylene glycol, 0.2M potassium citrate tribasic

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3.45→40.382 Å / Num. obs: 10899 / % possible obs: 99.86 % / Redundancy: 6.42 % / Net I/σ(I): 12.94

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4AP2

4ap2


Resolution: 3.45→40.382 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 38.05
RfactorNum. reflection% reflection
Rfree0.2878 520 4.77 %
Rwork0.2382 --
obs0.2406 10899 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.45→40.382 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3882 0 0 0 3882
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113936
X-RAY DIFFRACTIONf_angle_d1.4385294
X-RAY DIFFRACTIONf_dihedral_angle_d14.5892412
X-RAY DIFFRACTIONf_chiral_restr0.072597
X-RAY DIFFRACTIONf_plane_restr0.011688
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.45-3.7970.39431270.32452521X-RAY DIFFRACTION99
3.797-4.34580.35021230.27872555X-RAY DIFFRACTION100
4.3458-5.47310.27571360.27462574X-RAY DIFFRACTION100
5.4731-40.38430.25931340.1992729X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -24.2994 Å / Origin y: 30.7683 Å / Origin z: 166.8826 Å
111213212223313233
T0.9714 Å20.0341 Å20.1823 Å2-1.4063 Å2-0.2905 Å2--1.1361 Å2
L0.7208 °2-0.7499 °20.4155 °2-4.9521 °2-1.3646 °2--2.1668 °2
S-0.1615 Å °-0.0386 Å °0.0103 Å °0.451 Å °0.2486 Å °-0.3087 Å °-0.1782 Å °-0.2383 Å °-0.0816 Å °
Refinement TLS groupSelection details: all

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