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- PDB-2z32: Crystal structure of Keap1 complexed with Prothymosin alpha -

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Basic information

Entry
Database: PDB / ID: 2z32
TitleCrystal structure of Keap1 complexed with Prothymosin alpha
Components
  • Kelch-like ECH-associated protein 1
  • Prothymosin alpha
KeywordsTRANSCRIPTION / Kelch domain / b-propellor domain / Nrf2 regulation / Prothymosin-a interactor / Cytoplasm / Kelch repeat / Nucleus / Transcription regulation / Ubl conjugation / Acetylation / Phosphorylation / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


: / DNA-binding transcription factor binding => GO:0140297 / cellular response to carbohydrate stimulus / KEAP1-NFE2L2 pathway / regulation of epidermal cell differentiation / Neddylation / Antigen processing: Ubiquitination & Proteasome degradation / Ub-specific processing proteases / Cul3-RING ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity ...: / DNA-binding transcription factor binding => GO:0140297 / cellular response to carbohydrate stimulus / KEAP1-NFE2L2 pathway / regulation of epidermal cell differentiation / Neddylation / Antigen processing: Ubiquitination & Proteasome degradation / Ub-specific processing proteases / Cul3-RING ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / centriolar satellite / inclusion body / cellular response to interleukin-4 / regulation of autophagy / actin filament / adherens junction / disordered domain specific binding / cellular response to oxidative stress / midbody / histone binding / 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 / negative regulation of apoptotic process / endoplasmic reticulum / protein-containing complex / nucleoplasm / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Prothymosin/parathymosin / Prothymosin/parathymosin family / 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 ...Prothymosin/parathymosin / Prothymosin/parathymosin family / 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 / 6 Propeller / Neuraminidase / SKP1/BTB/POZ domain superfamily / Mainly Beta
Similarity search - Domain/homology
Prothymosin alpha / Kelch-like ECH-associated protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPadmanabhan, B. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2008
Title: Structural analysis of the complex of Keap1 with a prothymosin alpha peptide
Authors: Padmanabhan, B. / Nakamura, Y. / Yokoyama, S.
History
DepositionMay 31, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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: Prothymosin alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2777
Polymers36,7972
Non-polymers4805
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-63.7 kcal/mol
Surface area12080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.515, 103.515, 56.160
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Kelch-like ECH-associated protein 1 / Cytosolic inhibitor of Nrf2 / INrf2 / Keap1


Mass: 35006.277 Da / Num. of mol.: 1 / Fragment: Keap1-DC, UNP residues 309-607
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Keap1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CodonPlus (DE3)_RIL / References: UniProt: Q9Z2X8
#2: Protein/peptide Prothymosin alpha


Mass: 1790.664 Da / Num. of mol.: 1 / Fragment: Prothymosin-a peptide, UNP residues 39-54 / Source method: obtained synthetically
Details: synthetic peptide; This sequence occurs naturally in mouse.
References: UniProt: P26350
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Formula: H2O

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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: 2.36 Å3/Da / Density % sol: 47.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: Ammonium sulfate, Li2SO4, Na Citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 15, 2006 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 23352 / Num. obs: 21733 / % possible obs: 93.1 % / Observed criterion σ(I): -3 / Redundancy: 10.6 % / Rmerge(I) obs: 0.074
Reflection shellResolution: 2→2.07 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.228 / Num. unique all: 2299 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDN ENTRY 1X2J

1x2j


Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.64 / SU ML: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.175 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22317 1119 5.2 %RANDOM
Rwork0.16598 ---
obs0.16879 20530 92.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 33.266 Å2
Baniso -1Baniso -2Baniso -3
1--1.66 Å2-0.83 Å20 Å2
2---1.66 Å20 Å2
3---2.49 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2316 0 25 250 2591
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0212394
X-RAY DIFFRACTIONr_angle_refined_deg1.6191.9433265
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.415305
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.08823.07114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.22615351
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.7591521
X-RAY DIFFRACTIONr_chiral_restr0.1220.2342
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021885
X-RAY DIFFRACTIONr_nbd_refined0.2170.21091
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21613
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2242
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2180.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.250.220
X-RAY DIFFRACTIONr_mcbond_it1.2531.51532
X-RAY DIFFRACTIONr_mcangle_it2.02122395
X-RAY DIFFRACTIONr_scbond_it2.8153998
X-RAY DIFFRACTIONr_scangle_it4.2364.5870
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.216 88 -
Rwork0.176 1571 -
obs--99.64 %

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