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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 / 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 ...epithelial cell differentiation involved in mammary gland alveolus development / neural fold elevation formation / iris morphogenesis / 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 / cardiac ventricle morphogenesis / connective tissue replacement involved in inflammatory response wound healing / negative regulation of mesenchymal cell apoptotic process / negative regulation of growth / Aryl hydrocarbon receptor signalling / positive regulation of hormone biosynthetic process / aryl hydrocarbon receptor complex / intestinal epithelial cell maturation / retina vasculature development in camera-type eye / Cellular response to hypoxia / mesenchymal cell apoptotic process / regulation of protein neddylation / negative regulation of bone mineralization / PTK6 Expression / intracellular oxygen homeostasis / collagen metabolic process / B-1 B cell homeostasis / 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 / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / lactate metabolic process / positive regulation of cytokine production involved in inflammatory response / Phase I - Functionalization of compounds / negative regulation of TOR signaling / positive regulation of vascular endothelial growth factor receptor signaling pathway / insulin secretion involved in cellular response to glucose stimulus / response to iron ion / neural crest cell migration / Regulation of gene expression by Hypoxia-inducible Factor / embryonic hemopoiesis / regulation of glycolytic process / motile cilium / DNA-binding transcription repressor activity / muscle cell cellular homeostasis / digestive tract morphogenesis / DNA-binding transcription activator activity / PTK6 promotes HIF1A stabilization / response to muscle activity / positive regulation of neuroblast proliferation / axonal transport of mitochondrion / bone mineralization / E-box binding / intracellular glucose homeostasis / heart looping / outflow tract morphogenesis / aryl hydrocarbon receptor binding / TOR signaling / positive regulation of insulin secretion involved in cellular response to glucose stimulus / positive regulation of macroautophagy / cellular response to interleukin-1 / positive regulation of epithelial cell migration / positive regulation of vascular endothelial growth factor production / neuroblast proliferation / positive regulation of blood vessel endothelial cell migration / epithelial to mesenchymal transition / chondrocyte differentiation / Endogenous sterols / embryonic placenta development / cis-regulatory region sequence-specific DNA binding / positive regulation of chemokine production / positive regulation of endothelial cell proliferation / lactation / axon cytoplasm / NPAS4 regulates expression of target genes / positive regulation of nitric-oxide synthase activity / negative regulation of miRNA transcription / positive regulation of erythrocyte differentiation / positive regulation of glycolytic process / response to reactive oxygen species / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Hsp90 protein binding / euchromatin / transcription coactivator binding / PPARA activates gene expression / visual learning / cerebral cortex development / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / cellular response to virus / positive regulation of miRNA transcription / NOTCH1 Intracellular Domain Regulates Transcription / negative regulation of inflammatory response / histone deacetylase binding / RNA polymerase II transcription regulator complex
Similarity search - Function
Hypoxia-inducible factor-1 alpha / Hypoxia-inducible factor 1-alpha bHLH domain / HIF-1 alpha, transactivation domain, C-terminal / HIF-1 alpha C terminal transactivation domain / : / Hypoxia-inducible factor, alpha subunit-like / Hypoxia-inducible factor-1 / Nuclear translocator / PAS fold-3 / PAS fold ...Hypoxia-inducible factor-1 alpha / Hypoxia-inducible factor 1-alpha bHLH domain / HIF-1 alpha, transactivation domain, C-terminal / HIF-1 alpha C terminal transactivation 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: Closson, J.D. / Xu, X. / Zhang, M. / Tiyani, T.T. / Marcelino, L.P. / Isiorho, E.A. / Nagati, J.S. / Garcia, J.A. / Gardner, K.H.
History
DepositionApr 30, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


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: 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) / References: GenBank: 405188
#2: 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) / References: GenBank: 405188
#3: 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
#4: 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
Has protein modificationN

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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: all / 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
2Leginon3.7image acquisition
4Warp1.0.9CTF correction
7UCSF ChimeraX1.9model fitting
11cryoSPARC4.7.0classification
12cryoSPARC4.7.03D reconstruction
13PHENIX1.20.1_4487:model refinement
14Coot0.9.6.1.1model 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_d0.00610398
ELECTRON MICROSCOPYf_angle_d0.63314308
ELECTRON MICROSCOPYf_dihedral_angle_d21.8211812
ELECTRON MICROSCOPYf_chiral_restr0.0391598
ELECTRON MICROSCOPYf_plane_restr0.0051577

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