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- PDB-5wfl: Kelch domain of human Keap1 in open unliganded conformation -

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Basic information

Entry
Database: PDB / ID: 5wfl
TitleKelch domain of human Keap1 in open unliganded conformation
ComponentsKelch-like ECH-associated protein 1
KeywordsTRANSCRIPTION / Scaffold / Unliganded
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 / ubiquitin-like ligase-substrate adaptor activity / transcription regulator inhibitor activity / inclusion body / cellular response to interleukin-4 / actin filament / centriolar satellite ...regulation of epidermal cell differentiation / Nuclear events mediated by NFE2L2 / negative regulation of response to oxidative stress / Cul3-RING ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / transcription regulator inhibitor activity / inclusion body / cellular response to interleukin-4 / actin filament / centriolar satellite / 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 / Potential therapeutics for SARS / proteasome-mediated ubiquitin-dependent protein catabolic process / RNA polymerase II-specific DNA-binding transcription factor binding / Ub-specific processing proteases / protein ubiquitination / regulation of autophagy / endoplasmic reticulum / negative regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / cytosol / cytoplasm
Similarity search - Function
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-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 / 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
Kelch-like ECH-associated protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsCarolan, J.P. / Lynch, A.J. / Allen, K.N.
CitationJournal: Biochemistry / Year: 2020
Title: Interaction Energetics and Druggability of the Protein-Protein Interaction between Kelch-like ECH-Associated Protein 1 (KEAP1) and Nuclear Factor Erythroid 2 Like 2 (Nrf2).
Authors: Zhong, M. / Lynch, A. / Muellers, S.N. / Jehle, S. / Luo, L. / Hall, D.R. / Iwase, R. / Carolan, J.P. / Egbert, M. / Wakefield, A. / Streu, K. / Harvey, C.M. / Ortet, P.C. / Kozakov, D. / ...Authors: Zhong, M. / Lynch, A. / Muellers, S.N. / Jehle, S. / Luo, L. / Hall, D.R. / Iwase, R. / Carolan, J.P. / Egbert, M. / Wakefield, A. / Streu, K. / Harvey, C.M. / Ortet, P.C. / Kozakov, D. / Vajda, S. / Allen, K.N. / Whitty, A.
History
DepositionJul 12, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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
Revision 1.2Oct 4, 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
Revision 1.3Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,2797
Polymers73,7982
Non-polymers4805
Water2,756153
1
A: Kelch-like ECH-associated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1874
Polymers36,8991
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kelch-like ECH-associated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0913
Polymers36,8991
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)162.314, 68.730, 77.167
Angle α, β, γ (deg.)90.00, 117.73, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 36899.176 Da / Num. of mol.: 2 / Fragment: UNP residues 320-812 / Mutation: E540A, E542A
Source method: isolated from a genetically manipulated source
Details: ETE to ATA mutation to allow open crystal packing / Source: (gene. exp.) Homo sapiens (human) / Gene: KEAP1, INRF2, KIAA0132, KLHL19 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14145
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.58 Å3/Da / Density % sol: 52.35 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: 1.2 - 1.5 M ammonium sulfate, 0.1 M Bis-Tris pH = 6.0 - 6.5
PH range: 6.0 - 6.5

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Nitrogen stream
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97954 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 16, 2016
Details: Mirror: Rh coated flat bent M0, toroidal focusing post-monochromator M1
RadiationMonochromator: Si(111) and Si(220) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97954 Å / Relative weight: 1
ReflectionResolution: 1.93→35.92 Å / Num. obs: 55204 / % possible obs: 97 % / Redundancy: 3.5 % / CC1/2: 0.99 / Rmerge(I) obs: 0.09152 / Χ2: 1.062 / Net I/av σ(I): 18.9 / Net I/σ(I): 10.26
Reflection shellResolution: 1.93→1.999 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.2129 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 5414 / CC1/2: 0.966 / Χ2: 0.363 / % possible all: 96

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XTG

1xtg


Resolution: 1.93→35.918 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 25.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2219 1650 2.99 %Random selection
Rwork0.197 ---
obs0.1978 55165 97.34 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.93→35.918 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4397 0 25 153 4575
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0144529
X-RAY DIFFRACTIONf_angle_d1.3896172
X-RAY DIFFRACTIONf_dihedral_angle_d9.4633093
X-RAY DIFFRACTIONf_chiral_restr0.092657
X-RAY DIFFRACTIONf_plane_restr0.01811
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.98680.28931330.24144371X-RAY DIFFRACTION96
1.9868-2.05090.25721370.21674451X-RAY DIFFRACTION98
2.0509-2.12420.2461370.20124416X-RAY DIFFRACTION98
2.1242-2.20920.26231400.2124484X-RAY DIFFRACTION98
2.2092-2.30980.24761350.2094412X-RAY DIFFRACTION97
2.3098-2.43150.22481350.2064342X-RAY DIFFRACTION95
2.4315-2.58380.24031400.22064498X-RAY DIFFRACTION98
2.5838-2.78330.27941380.21144475X-RAY DIFFRACTION98
2.7833-3.06320.24531350.20674417X-RAY DIFFRACTION96
3.0632-3.50610.20371380.20174541X-RAY DIFFRACTION99
3.5061-4.41610.19481410.16964514X-RAY DIFFRACTION98
4.4161-35.92460.2021410.1914594X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.76050.08320.04361.3849-1.03991.59020.47162.32130.8750.50540.30981.1813-0.5751-1.63730.0365-0.03450.2386-0.13531.96180.47250.6878-53.799923.436946.6629
20.1031-0.31480.28090.9882-1.02781.7051-0.40122.2836-0.1907-0.24580.32990.2452-0.082-0.734-0.30440.3701-0.2443-0.05821.7182-0.07510.4907-55.009314.312550.4906
30.8296-0.02071.44140.920.98833.4561-0.92351.7487-0.7832-0.41060.15250.33441.015-0.85660.23260.3878-0.49060.02681.2394-0.47470.5517-43.02699.610445.7917
40.6054-0.11490.11040.7947-0.22530.094-0.89381.5466-1.2662-0.46970.10510.06570.8881-1.3370.43420.6-0.31030.15031.0023-0.3140.6403-37.97328.796246.064
54.8740.5059-1.20213.2286-0.08546.5311-0.30971.1646-0.2227-0.43120.0548-0.08610.1255-0.80270.2220.2612-0.0310.01720.5219-0.02510.3648-29.678517.604445.3209
62.3394-0.4173-0.43120.1862-0.06580.32810.9641.28951.4808-0.22520.21360.1564-1.4695-1.4931-0.17470.55170.25480.15810.81160.38330.7787-34.097129.993645.4813
7-0.01040.0152-0.15840.6634-1.2182.16440.88471.27971.6702-0.0809-0.14680.2642-0.9638-1.3832-0.32610.58380.46060.25411.12470.68111.0661-44.166633.684347.1989
82.64621.4772-0.45933.8668-1.28721.8805-0.03280.45150.0366-0.13640.12410.26260.0798-0.2875-0.09190.2541-0.0214-0.07340.4293-0.05140.336-40.463714.2296-1.8552
96.95072.8853-3.00794.8988-1.39344.636-0.40620.811-0.0014-0.49070.2697-0.21420.1904-0.262-0.02780.24720.0295-0.07730.40260.01950.2958-35.776524.8640.0332
101.59440.61140.12322.29810.00061.1167-0.09980.01880.1313-0.06040.03150.2744-0.0924-0.48240.07750.21480.0559-0.03880.39750.01250.3108-39.537826.58076.8324
111.8724-1.11311.39252.9524-1.33653.0296-0.2433-0.41890.1510.36890.17840.1199-0.358-0.22310.08920.24510.0491-0.06140.2837-0.02950.2636-30.038628.815313.6173
123.3917-1.0095-1.83183.8807-0.0197.017-0.1304-0.2360.07540.41770.05650.0151-0.5613-0.53190.08320.31040.036-0.10980.356-0.00440.3139-21.996225.062118.417
131.8596-0.05061.36532.61630.13885.2516-0.0053-0.2618-0.00280.28840.0195-0.01360.0959-0.2489-0.00080.2641-0.016-0.05980.28280.00360.2898-22.544810.598615.4954
144.1094-1.9116-0.34462.2902-0.5045.05980.13390.2356-0.31180.2111-0.14840.04130.3361-0.35350.06470.2838-0.0757-0.06250.2945-0.04670.3221-31.30566.01478.1752
150.90910.3391-0.20212.2152-0.04922.63550.03240.0923-0.2261-0.0129-0.02120.09390.2038-0.2833-0.00680.2394-0.0795-0.05070.3128-0.03470.3167-34.58746.46153.5013
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 327 through 377 )
2X-RAY DIFFRACTION2chain 'A' and (resid 378 through 405 )
3X-RAY DIFFRACTION3chain 'A' and (resid 406 through 428 )
4X-RAY DIFFRACTION4chain 'A' and (resid 429 through 475 )
5X-RAY DIFFRACTION5chain 'A' and (resid 476 through 522 )
6X-RAY DIFFRACTION6chain 'A' and (resid 523 through 569 )
7X-RAY DIFFRACTION7chain 'A' and (resid 570 through 609 )
8X-RAY DIFFRACTION8chain 'B' and (resid 325 through 365 )
9X-RAY DIFFRACTION9chain 'B' and (resid 366 through 389 )
10X-RAY DIFFRACTION10chain 'B' and (resid 390 through 428 )
11X-RAY DIFFRACTION11chain 'B' and (resid 429 through 475 )
12X-RAY DIFFRACTION12chain 'B' and (resid 476 through 500 )
13X-RAY DIFFRACTION13chain 'B' and (resid 501 through 547 )
14X-RAY DIFFRACTION14chain 'B' and (resid 548 through 569 )
15X-RAY DIFFRACTION15chain 'B' and (resid 570 through 614 )

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