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- PDB-9gp5: Homodimer of BACH1 F9A mutant BTB domain -

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Basic information

Entry
Database: PDB / ID: 9gp5
TitleHomodimer of BACH1 F9A mutant BTB domain
ComponentsTranscription regulator protein BACH1
KeywordsDNA BINDING PROTEIN / BACH1 / back-to-back domain / BTB domain
Function / homology
Function and homology information


Regulation of HMOX1 expression and activity / ligand-modulated transcription factor activity / regulation of metabolic process / NFE2L2 regulating anti-oxidant/detoxification enzymes / Regulation of BACH1 activity / Heme signaling / DNA-binding transcription repressor activity, RNA polymerase II-specific / RNA polymerase II transcription regulator complex / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific ...Regulation of HMOX1 expression and activity / ligand-modulated transcription factor activity / regulation of metabolic process / NFE2L2 regulating anti-oxidant/detoxification enzymes / Regulation of BACH1 activity / Heme signaling / DNA-binding transcription repressor activity, RNA polymerase II-specific / RNA polymerase II transcription regulator complex / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / DNA repair / heme binding / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
BACH, basic leucine zipper (bZIP) domain / Basic leucine zipper domain, Maf-type / bZIP Maf transcription factor / Transcription factor, Skn-1-like, DNA-binding domain superfamily / : / 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 ...BACH, basic leucine zipper (bZIP) domain / Basic leucine zipper domain, Maf-type / bZIP Maf transcription factor / Transcription factor, Skn-1-like, DNA-binding domain superfamily / : / 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 / 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
Transcription regulator protein BACH1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSchroeder, M. / Goretzki, B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell / Year: 2024
Title: Dual BACH1 regulation by complementary SCF-type E3 ligases.
Authors: Benedikt Goretzki / Maryam Khoshouei / Martin Schröder / Patrick Penner / Luca Egger / Christine Stephan / Dayana Argoti / Nele Dierlamm / Jimena Maria Rada / Sandra Kapps / Catrin Swantje ...Authors: Benedikt Goretzki / Maryam Khoshouei / Martin Schröder / Patrick Penner / Luca Egger / Christine Stephan / Dayana Argoti / Nele Dierlamm / Jimena Maria Rada / Sandra Kapps / Catrin Swantje Müller / Zacharias Thiel / Merve Mutlu / Claude Tschopp / David Furkert / Felix Freuler / Simon Haenni / Laurent Tenaillon / Britta Knapp / Alexandra Hinniger / Philipp Hoppe / Enrico Schmidt / Sascha Gutmann / Mario Iurlaro / Grigory Ryzhakov / César Fernández /
Abstract: Broad-complex, tramtrack, and bric-à-brac domain (BTB) and CNC homolog 1 (BACH1) is a key regulator of the cellular oxidative stress response and an oncogene that undergoes tight post-translational ...Broad-complex, tramtrack, and bric-à-brac domain (BTB) and CNC homolog 1 (BACH1) is a key regulator of the cellular oxidative stress response and an oncogene that undergoes tight post-translational control by two distinct F-box ubiquitin ligases, SCF and SCF. However, how both ligases recognize BACH1 under oxidative stress is unclear. In our study, we elucidate the mechanism by which FBXO22 recognizes a quaternary degron in a domain-swapped β-sheet of the BACH1 BTB dimer. Cancer-associated mutations and cysteine modifications destabilize the degron and impair FBXO22 binding but simultaneously expose an otherwise shielded degron in the dimer interface, allowing FBXL17 to recognize BACH1 as a monomer. These findings shed light on a ligase switch mechanism that enables post-translational regulation of BACH1 by complementary ligases depending on the stability of its BTB domain. Our results provide mechanistic insights into the oxidative stress response and may spur therapeutic approaches for targeting oxidative stress-related disorders and cancer.
History
DepositionSep 6, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Transcription regulator protein BACH1
D: Transcription regulator protein BACH1


Theoretical massNumber of molelcules
Total (without water)27,9642
Polymers27,9642
Non-polymers00
Water2,450136
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-25 kcal/mol
Surface area11650 Å2
Unit cell
Length a, b, c (Å)31.084, 70.334, 65.246
Angle α, β, γ (deg.)90.00, 93.44, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Transcription regulator protein BACH1 / BTB and CNC homolog 1 / HA2303


Mass: 13981.938 Da / Num. of mol.: 2 / Mutation: F9A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BACH1 / Production host: Escherichia coli (E. coli) / References: UniProt: O14867
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.55 Å3/Da / Density % sol: 51.69 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.02 M HEPES, 0.15 M NaCl, 5% (w/v) glycerol, 0.001 M TCEP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 30, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.9→70.33 Å / Num. obs: 22172 / % possible obs: 99.9 % / Redundancy: 5.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.039 / Rrim(I) all: 0.092 / Χ2: 1.01 / Net I/σ(I): 11.4 / Num. measured all: 115094
Reflection shellResolution: 1.9→1.94 Å / % possible obs: 99.9 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.63 / Num. measured all: 7737 / Num. unique obs: 1433 / CC1/2: 0.79 / Rpim(I) all: 0.292 / Rrim(I) all: 0.697 / Χ2: 1.05 / Net I/σ(I) obs: 2.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
Aimlessdata scaling
autoPROCdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→47.8 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.937 / SU B: 6.573 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22555 1128 5.1 %RANDOM
Rwork0.19459 ---
obs0.19624 21023 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.237 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å2-0 Å20.14 Å2
2--0.38 Å2-0 Å2
3----0.07 Å2
Refinement stepCycle: 1 / Resolution: 1.9→47.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1755 0 0 136 1891
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0121818
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161723
X-RAY DIFFRACTIONr_angle_refined_deg1.6951.6332470
X-RAY DIFFRACTIONr_angle_other_deg0.5581.573960
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4955235
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.182510
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.62310311
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0840.2296
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022143
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02417
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3912.029931
X-RAY DIFFRACTIONr_mcbond_other2.3692.029931
X-RAY DIFFRACTIONr_mcangle_it3.4163.6221169
X-RAY DIFFRACTIONr_mcangle_other3.4153.6251170
X-RAY DIFFRACTIONr_scbond_it3.8372.444887
X-RAY DIFFRACTIONr_scbond_other3.8352.445888
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8144.2911302
X-RAY DIFFRACTIONr_long_range_B_refined7.7922.162077
X-RAY DIFFRACTIONr_long_range_B_other7.78722.032056
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 72 -
Rwork0.246 1577 -
obs--99.88 %
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)
11.61611.5565-0.35454.0249-0.8191.2654-0.04-0.073-0.1275-0.0670.00670.07830.1598-0.18210.03330.0324-0.01160.00320.04830.00110.0288-3.9501-4.164417.8539
21.49531.27420.42063.49110.51021.2093-0.0848-0.09030.1186-0.02890.0298-0.1233-0.1790.11420.0550.0395-0.0012-0.01160.0378-0.00820.03334.010514.684917.892
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1C5 - 118
2X-RAY DIFFRACTION2D6 - 118

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