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- PDB-9ofu: Dimer of HIF-1a-ARNT Heterodimers Complexed on 52-bp HRE/HAS -

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Basic information

Entry
Database: PDB / ID: 9ofu
TitleDimer of HIF-1a-ARNT Heterodimers Complexed on 52-bp HRE/HAS
Components
  • 52-nt Hypoxia Response Element (Forward)
  • 52-nt Hypoxia Response Element (Reverse)
  • Aryl hydrocarbon receptor nuclear translocator
  • Hypoxia-inducible factor 1-alpha
KeywordsDNA BINDING PROTEIN / Complex / Hypoxia / Transcription / Cancer / Dimer / Higher-ordered
Function / homology
Function and homology information


epithelial cell differentiation involved in mammary gland alveolus development / neural fold elevation formation / iris morphogenesis / intestinal epithelial cell maturation / : / hypoxia-inducible factor-1alpha signaling pathway / positive regulation of chemokine-mediated signaling pathway / elastin metabolic process / regulation of transforming growth factor beta2 production / glandular epithelial cell maturation ...epithelial cell differentiation involved in mammary gland alveolus development / neural fold elevation formation / iris morphogenesis / intestinal epithelial cell maturation / : / hypoxia-inducible factor-1alpha signaling pathway / positive regulation of chemokine-mediated signaling pathway / elastin metabolic process / regulation of transforming growth factor beta2 production / glandular epithelial cell maturation / nuclear aryl hydrocarbon receptor complex / hemoglobin biosynthetic process / negative regulation of mesenchymal cell apoptotic process / cardiac ventricle morphogenesis / connective tissue replacement involved in inflammatory response wound healing / positive regulation of hormone biosynthetic process / negative regulation of growth / Aryl hydrocarbon receptor signalling / aryl hydrocarbon receptor complex / Cellular response to hypoxia / retina vasculature development in camera-type eye / mesenchymal cell apoptotic process / PTK6 Expression / negative regulation of bone mineralization / intracellular oxygen homeostasis / regulation of protein neddylation / B-1 B cell homeostasis / collagen metabolic process / vascular endothelial growth factor production / positive regulation of protein sumoylation / dopaminergic neuron differentiation / Xenobiotics / transcription regulator activator activity / STAT3 nuclear events downstream of ALK signaling / negative regulation of thymocyte apoptotic process / lactate metabolic process / Phase I - Functionalization of compounds / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / positive regulation of cytokine production involved in inflammatory response / negative regulation of TOR signaling / insulin secretion involved in cellular response to glucose stimulus / positive regulation of vascular endothelial growth factor receptor signaling pathway / response to iron ion / Regulation of gene expression by Hypoxia-inducible Factor / neural crest cell migration / embryonic hemopoiesis / regulation of glycolytic process / DNA-binding transcription repressor activity / motile cilium / PTK6 promotes HIF1A stabilization / DNA-binding transcription activator activity / muscle cell cellular homeostasis / positive regulation of neuroblast proliferation / digestive tract morphogenesis / axonal transport of mitochondrion / response to muscle activity / heart looping / bone mineralization / intracellular glucose homeostasis / E-box binding / aryl hydrocarbon receptor binding / outflow tract morphogenesis / TOR signaling / positive regulation of vascular endothelial growth factor production / positive regulation of epithelial cell migration / positive regulation of macroautophagy / epithelial to mesenchymal transition / neuroblast proliferation / cellular response to interleukin-1 / positive regulation of blood vessel endothelial cell migration / chondrocyte differentiation / Endogenous sterols / embryonic placenta development / positive regulation of insulin secretion involved in cellular response to glucose stimulus / cis-regulatory region sequence-specific DNA binding / positive regulation of chemokine production / lactation / positive regulation of endothelial cell proliferation / NPAS4 regulates expression of target genes / axon cytoplasm / negative regulation of miRNA transcription / positive regulation of erythrocyte differentiation / positive regulation of glycolytic process / response to reactive oxygen species / nuclear receptor binding / transcription corepressor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Hsp90 protein binding / euchromatin / PPARA activates gene expression / cerebral cortex development / visual learning / cellular response to virus / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / positive regulation of miRNA transcription / NOTCH1 Intracellular Domain Regulates Transcription / negative regulation of inflammatory response / RNA polymerase II transcription regulator complex / histone deacetylase binding / transcription coactivator binding
Similarity search - Function
Hypoxia-inducible factor-1 alpha / HIF-1 alpha, transactivation domain, C-terminal / HIF-1 alpha C terminal transactivation domain / : / Hypoxia-inducible factor 1-alpha bHLH domain / Hypoxia-inducible factor, alpha subunit-like / Hypoxia-inducible factor-1 / Nuclear translocator / PAS fold-3 / PAS fold ...Hypoxia-inducible factor-1 alpha / HIF-1 alpha, transactivation domain, C-terminal / HIF-1 alpha C terminal transactivation domain / : / Hypoxia-inducible factor 1-alpha bHLH domain / Hypoxia-inducible factor, alpha subunit-like / Hypoxia-inducible factor-1 / Nuclear translocator / PAS fold-3 / PAS fold / Helix-loop-helix DNA-binding domain / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Aryl hydrocarbon receptor nuclear translocator / Hypoxia-inducible factor 1-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsClosson, J.D. / Tiyani, T.T. / Xu, X. / Gardner, K.H.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)U54 CA132378 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)U54 C137788 United States
The G. Harold and Leila Y. Mathers FoundationMF-2112-02288 United States
CitationJournal: bioRxiv / Year: 2025
Title: CONTEXT-DEPENDENT VARIABILITY OF HIF HETERODIMERS INFLUENCES INTERACTIONS WITH MACROMOLECULAR AND SMALL MOLECULE PARTNERS.
Authors: Joseph D Closson / Xingjian Xu / Meiling Zhang / Tarsisius T Tiyani / Leandro Pimentel Marcelino / Eta A Isiorho / Jason S Nagati / Joseph A Garcia / Kevin H Gardner /
Abstract: Hypoxia inducible factors (HIFs) are transcription factors that coordinate cellular responses to low oxygen levels, functioning as an α/β heterodimer which binds a short hypoxia response element ...Hypoxia inducible factors (HIFs) are transcription factors that coordinate cellular responses to low oxygen levels, functioning as an α/β heterodimer which binds a short hypoxia response element (HRE) DNA sequence. Prior studies suggest HIF/HRE complexes are augmented by the binding of additional factors nearby, but those interactions are not well understood. Here, we integrated structural and biochemical approaches to investigate several functionally relevant HIF assemblies with other protein, small molecule, and DNA partners. First, we used cryo-electron microscopy (cryo-EM) to establish HIF-1 and HIF-2 form novel "dimer-of-heterodimers" (DoHD) complexes on extended human EPO enhancer sequences, showing that one heterodimer bound at a canonical HRE site with the second binding in an inverted fashion to an HRE-adjacent sequence (HAS) 8 bp away. Consistent with ARNT PAS-B domains predominating interactions within a DoHD, we found HIF-1 and HIF-2 assemble mixed DoHD complexes on the same DNA. Second, we saw substantial variability among ligands for isolated ARNT or HIF-2α PAS-B domains to bind larger complexes: for example, the ARNT PAS-B binding KG-548 and KG-279 ligands both bound the simpler HIF-2 heterodimer but exhibited differential binding to a HIF-2 DoHD. Finally, we combined cryo-EM and hydrogen-deuterium exchange by mass spectrometry (HDX-MS) to show how HIF-1 and HIF-2 heterodimers engage the transforming acidic coiled-coil containing protein 3 (TACC3) coactivator via both ARNT and HIF-α subunits, though this was unseen in the larger DoHD. Our findings highlight the importance of both molecular context and dynamics in biomolecular complex formation, adding to the complexities of potential regulation.
History
DepositionApr 30, 2025Deposition site: RCSB / Processing site: RCSB
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Description: Atomic clashes / Details: Re-refining to reduce clashscore and overfitting / Provider: author / Type: Coordinate replacement
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Item: _em_admin.last_update / _em_entity_assembly.entity_id_list ..._em_admin.last_update / _em_entity_assembly.entity_id_list / _em_software.fitting_id / _em_software.name / _em_software.version / _entity.details / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly.pdbx_strand_id / _entity_poly.type / _entity_src_gen.entity_id / _pdbx_entity_src_syn.entity_id / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.pdbx_strand_id / _struct_ref_seq.ref_id / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_ref_seq_dif.align_id / _struct_ref_seq_dif.pdbx_auth_seq_num / _struct_ref_seq_dif.pdbx_pdb_strand_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypoxia-inducible factor 1-alpha
B: Aryl hydrocarbon receptor nuclear translocator
C: Hypoxia-inducible factor 1-alpha
D: Aryl hydrocarbon receptor nuclear translocator
E: 52-nt Hypoxia Response Element (Forward)
F: 52-nt Hypoxia Response Element (Reverse)


Theoretical massNumber of molelcules
Total (without water)204,0976
Polymers204,0976
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Hypoxia-inducible factor 1-alpha / HIF-1-alpha / HIF1-alpha / ARNT-interacting protein / Basic-helix-loop-helix-PAS protein MOP1 / ...HIF-1-alpha / HIF1-alpha / ARNT-interacting protein / Basic-helix-loop-helix-PAS protein MOP1 / Class E basic helix-loop-helix protein 78 / bHLHe78 / Member of PAS protein 1 / PAS domain-containing protein 8


Mass: 42962.926 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-terminal 14 residues (MGSSHHHHHHSQDP) are vector-derived
Source: (gene. exp.) Homo sapiens (human) / Gene: HIF1A, BHLHE78, MOP1, PASD8 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q16665
#2: Protein Aryl hydrocarbon receptor nuclear translocator / ARNT protein / Class E basic helix-loop-helix protein 2 / bHLHe2 / Dioxin receptor / nuclear ...ARNT protein / Class E basic helix-loop-helix protein 2 / bHLHe2 / Dioxin receptor / nuclear translocator / Hypoxia-inducible factor 1-beta / HIF-1-beta / HIF1-beta


Mass: 43061.820 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARNT, BHLHE2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P27540
#3: DNA chain 52-nt Hypoxia Response Element (Forward)


Mass: 15821.092 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: DNA chain 52-nt Hypoxia Response Element (Reverse)


Mass: 16226.375 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Dimer of two HIF-1a-ARNT heterodimers complexed on 52-bp HRE
Type: COMPLEX / Entity ID: #3-#4, #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.205 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21 (DE3)
Buffer solutionpH: 7.4 / Details: 50mM HEPES, 150mM NaCl, 5mM MgCl2
Buffer component
IDConc.NameFormulaBuffer-ID
150 mM2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acidC8H18N2O4S1
2150 mMSodium ChlorideNaCl1
35 mMMagnesium ChlorideMgCl21
SpecimenConc.: 1.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 4000 nm / Nominal defocus min: 300 nm / Cs: 2.7 mm
Image recordingElectron dose: 58.19 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 2 / Num. of real images: 4098

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Processing

EM software
IDNameVersionCategory
1Warp1.0.9particle selection
4Warp1.0.9CTF correction
7UCSF ChimeraX1.9model fitting
11cryoSPARC4.7.0classification
12cryoSPARC4.7.03D reconstruction
13PHENIX1.20.1_4487:model refinement
14Coot0.9.1.1model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 262568
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 71802 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingSource name: AlphaFold / Type: in silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01210403
ELECTRON MICROSCOPYf_angle_d0.73914305
ELECTRON MICROSCOPYf_dihedral_angle_d20.651807
ELECTRON MICROSCOPYf_chiral_restr0.0391604
ELECTRON MICROSCOPYf_plane_restr0.0061575

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