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- PDB-9gra: Homodimer of BACH1 BTB domain in complex with 2-Methyl-2,4-pentanediol -

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Basic information

Entry
Database: PDB / ID: 9gra
TitleHomodimer of BACH1 BTB domain in complex with 2-Methyl-2,4-pentanediol
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 DNA-templated transcription / regulation of transcription by RNA polymerase II / 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: 1.47 Å
AuthorsGutmann, S. / Hinniger, A. / 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 11, 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
A: Transcription regulator protein BACH1
B: Transcription regulator protein BACH1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2343
Polymers28,1162
Non-polymers1181
Water6,593366
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-33 kcal/mol
Surface area12970 Å2
Unit cell
Length a, b, c (Å)31.129, 69.459, 64.867
Angle α, β, γ (deg.)90.00, 91.86, 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: 14058.035 Da / Num. of mol.: 2
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: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 366 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.49 Å3/Da / Density % sol: 50.66 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.16 M Ammonium sulfate, 0.08 M Tris-HCl, 14.4 % (w/v) PEG3350, 6 % (v/v) MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9999415 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Mar 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999415 Å / Relative weight: 1
ReflectionResolution: 1.47→64.83 Å / Num. obs: 47040 / % possible obs: 99.9 % / Redundancy: 5.1 % / CC1/2: 0.993 / Net I/σ(I): 5
Reflection shellResolution: 1.47→1.49 Å / Redundancy: 5 % / Num. unique obs: 2340 / CC1/2: 0.333 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.21.1_5286: ???)refinement
Aimlessdata scaling
autoPROCdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.47→64.83 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2344 2413 5.13 %
Rwork0.1951 --
obs0.197 47014 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.47→64.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1932 0 8 366 2306
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013
X-RAY DIFFRACTIONf_angle_d1.299
X-RAY DIFFRACTIONf_dihedral_angle_d12.599719
X-RAY DIFFRACTIONf_chiral_restr0.104317
X-RAY DIFFRACTIONf_plane_restr0.012349
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.47-1.50.31321330.2792629X-RAY DIFFRACTION100
1.5-1.530.31451660.27012580X-RAY DIFFRACTION100
1.53-1.570.27231870.2552553X-RAY DIFFRACTION100
1.57-1.610.27991540.24222592X-RAY DIFFRACTION100
1.61-1.650.25071370.22842654X-RAY DIFFRACTION100
1.65-1.70.25631530.22182608X-RAY DIFFRACTION100
1.7-1.750.26631380.22252606X-RAY DIFFRACTION100
1.75-1.820.23261230.20712643X-RAY DIFFRACTION100
1.82-1.890.29931470.20112573X-RAY DIFFRACTION100
1.89-1.970.20761570.1882651X-RAY DIFFRACTION100
1.97-2.080.26551420.19032625X-RAY DIFFRACTION100
2.08-2.210.24061000.18412666X-RAY DIFFRACTION100
2.21-2.380.24141170.18222643X-RAY DIFFRACTION100
2.38-2.620.19651420.1882626X-RAY DIFFRACTION100
2.62-30.25161200.18752629X-RAY DIFFRACTION100
3-3.780.2131530.18292636X-RAY DIFFRACTION100
3.78-64.830.19311440.17352687X-RAY DIFFRACTION100
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)
10.7154-0.30760.14860.80780.02670.6796-0.0219-0.03920.06580.0891-0.0015-0.0049-0.0956-0.03860.00990.0786-0.0066-0.00150.0794-0.00450.07978.22940.716516.1294
20.6135-0.324-0.13360.7282-0.02750.6150.00390.0076-0.08250.0903-0.04-0.02940.07110.05220.01880.0926-0.0061-0.01060.09330.00560.097318.7745-20.851815.9802
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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