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- EMDB-70443: Dimer of HIF-1a-ARNT Heterodimers Complexed on 52-bp HRE/HAS -

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Basic information

Entry
Database: EMDB / ID: EMD-70443
TitleDimer of HIF-1a-ARNT Heterodimers Complexed on 52-bp HRE/HAS
Map data
Sample
  • Complex: Dimer of two HIF-1a-ARNT heterodimers complexed on 52-bp HRE
    • DNA: 52-nt Hypoxia Response Element (Forward)
    • DNA: 52-nt Hypoxia Response Element (Reverse)
    • Protein or peptide: Hypoxia-inducible factor 1-alpha
    • Protein or peptide: Aryl hydrocarbon receptor nuclear translocator
KeywordsComplex / Hypoxia / Transcription / Cancer / Dimer / Higher-ordered / DNA BINDING PROTEIN
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
Aryl hydrocarbon receptor nuclear translocator / Hypoxia-inducible factor 1-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsClosson JD / Tiyani TT / Xu X / Gardner KH
Funding support United States, 3 items
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 JD / Xu X / Zhang M / Tiyani TT / Marcelino LP / Isiorho EA / Nagati JS / Garcia JA / Gardner KH
History
DepositionApr 30, 2025-
Header (metadata) releaseJun 11, 2025-
Map releaseJun 11, 2025-
UpdateJun 11, 2025-
Current statusJun 11, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70443.png

Downloads & links

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Map

FileDownload / File: emd_70443.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 400 pix.
= 332. Å		0.83 Å/pix.
x 400 pix.
= 332. Å		0.83 Å/pix.
x 400 pix.
= 332. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 7.77
Minimum - Maximum-54.40746 - 70.050899999999999
Average (Standard dev.)-0.000000000003842 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 332.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_70443_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_70443_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Dimer of two HIF-1a-ARNT heterodimers complexed on 52-bp HRE

EntireName: Dimer of two HIF-1a-ARNT heterodimers complexed on 52-bp HRE
Components
  • Complex: Dimer of two HIF-1a-ARNT heterodimers complexed on 52-bp HRE
    • DNA: 52-nt Hypoxia Response Element (Forward)
    • DNA: 52-nt Hypoxia Response Element (Reverse)
    • Protein or peptide: Hypoxia-inducible factor 1-alpha
    • Protein or peptide: Aryl hydrocarbon receptor nuclear translocator

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Supramolecule #1: Dimer of two HIF-1a-ARNT heterodimers complexed on 52-bp HRE

SupramoleculeName: Dimer of two HIF-1a-ARNT heterodimers complexed on 52-bp HRE
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 205 KDa

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Macromolecule #1: 52-nt Hypoxia Response Element (Forward)

MacromoleculeName: 52-nt Hypoxia Response Element (Forward) / type: dna / ID: 1 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.821092 KDa
SequenceString: (DT)(DG)(DG)(DG)(DC)(DC)(DC)(DT)(DA)(DC) (DG)(DT)(DG)(DC)(DT)(DG)(DT)(DC)(DT)(DC) (DA)(DC)(DA)(DC)(DA)(DG)(DC)(DC)(DT) (DG)(DT)(DC)(DT)(DG)(DA)(DC)(DC)(DT)(DC) (DT) (DC)(DG)(DA)(DC)(DC)(DC) ...String:
(DT)(DG)(DG)(DG)(DC)(DC)(DC)(DT)(DA)(DC) (DG)(DT)(DG)(DC)(DT)(DG)(DT)(DC)(DT)(DC) (DA)(DC)(DA)(DC)(DA)(DG)(DC)(DC)(DT) (DG)(DT)(DC)(DT)(DG)(DA)(DC)(DC)(DT)(DC) (DT) (DC)(DG)(DA)(DC)(DC)(DC)(DT)(DA) (DC)(DC)(DG)(DG)

GENBANK: GENBANK: L16588.1

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Macromolecule #2: 52-nt Hypoxia Response Element (Reverse)

MacromoleculeName: 52-nt Hypoxia Response Element (Reverse) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.226375 KDa
SequenceString: (DC)(DC)(DG)(DG)(DT)(DA)(DG)(DG)(DG)(DT) (DC)(DG)(DA)(DG)(DA)(DG)(DG)(DT)(DC)(DA) (DG)(DA)(DC)(DA)(DG)(DG)(DC)(DT)(DG) (DT)(DG)(DT)(DG)(DA)(DG)(DA)(DC)(DA)(DG) (DC) (DA)(DC)(DG)(DT)(DA)(DG) ...String:
(DC)(DC)(DG)(DG)(DT)(DA)(DG)(DG)(DG)(DT) (DC)(DG)(DA)(DG)(DA)(DG)(DG)(DT)(DC)(DA) (DG)(DA)(DC)(DA)(DG)(DG)(DC)(DT)(DG) (DT)(DG)(DT)(DG)(DA)(DG)(DA)(DC)(DA)(DG) (DC) (DA)(DC)(DG)(DT)(DA)(DG)(DG)(DG) (DC)(DC)(DC)(DA)

GENBANK: GENBANK: L16588.1

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Macromolecule #3: Hypoxia-inducible factor 1-alpha

MacromoleculeName: Hypoxia-inducible factor 1-alpha / type: protein_or_peptide / ID: 3
Details: N-terminal 14 residues (MGSSHHHHHHSQDP) are vector-derived
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 42.962926 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSHHHHHH SQDPGAGGAN DKKKISSERR KEKSRDAARS RRSKESEVFY ELAHQLPLPH NVSSHLDKAS VMRLTISYLR VRKLLDAGD LDIEDDMKAQ MNCFYLKALD GFVMVLTDDG DMIYISDNVN KYMGLTQFEL TGHSVFDFTH PCDHEEMREM L THRNGLVK ...String:
MGSSHHHHHH SQDPGAGGAN DKKKISSERR KEKSRDAARS RRSKESEVFY ELAHQLPLPH NVSSHLDKAS VMRLTISYLR VRKLLDAGD LDIEDDMKAQ MNCFYLKALD GFVMVLTDDG DMIYISDNVN KYMGLTQFEL TGHSVFDFTH PCDHEEMREM L THRNGLVK KGKEQNTQRS FFLRMKCTLT SRGRTMNIKS ATWKVLHCTG HIHVYDTNSN QPQCGYKKPP MTCLVLICEP IP HPSNIEI PLDSKTFLSR HSLDMKFSYC DERITELMGY EPEELLGRSI YEYYHALDSD HLTKTHHDMF TKGQVTTGQY RML AKRGGY VWVETQATVI YNTKNSQPQC IVCVNYVVSG IIQHDLIFSL QQTECVL

UniProtKB: Hypoxia-inducible factor 1-alpha

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Macromolecule #4: Aryl hydrocarbon receptor nuclear translocator

MacromoleculeName: Aryl hydrocarbon receptor nuclear translocator / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 43.06182 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MRENHSEIER RRRNKMTAYI TELSDMVPTC SALARKPDKL TILRMAVSHM KSLRGTGNTS TDGSYKPSFL TDQELKHLIL EAADGFLFI VSCETGRVVY VSDSVTPVLN QPQSEWFGST LYDQVHPDDV DKLREQLSTS ENALTGRILD LKTGTVKKEG Q QSSMRMCM ...String:
MRENHSEIER RRRNKMTAYI TELSDMVPTC SALARKPDKL TILRMAVSHM KSLRGTGNTS TDGSYKPSFL TDQELKHLIL EAADGFLFI VSCETGRVVY VSDSVTPVLN QPQSEWFGST LYDQVHPDDV DKLREQLSTS ENALTGRILD LKTGTVKKEG Q QSSMRMCM GSRRSFICRM RCGSSSVDPV SVNRLSFVRN RCRNGLGSVK DGEPHFVVVH CTGYIKAWPP AGVSLPDDDP EA GQGSKFC LVAIGRLQVT SSPNCTDMSN VCQPTEFISR HNIEGIFTFV DHRCVATVGY QPQELLGKNI VEFCHPEDQQ LLR DSFQQV VKLKGQVLSV MFRFRSKNQE WLWMRTSSFT FQNPYSDEIE YIICTNTNVK NSSQE

UniProtKB: Aryl hydrocarbon receptor nuclear translocator

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.2 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
50.0 mMC8H18N2O4S2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acid
150.0 mMNaClSodium Chloride
5.0 mMMgCl2Magnesium Chloride

Details: 50mM HEPES, 150mM NaCl, 5mM MgCl2
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK II

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Electron microscopy

MicroscopeTFS KRIOS
SoftwareName: Leginon (ver. 3.7)
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 2 / Number real images: 4098 / Average electron dose: 58.19 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 0.3 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 262568
CTF correctionSoftware - Name: Warp (ver. 1.0.9) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: AlphaFold2 model of human HIF-1
Final reconstructionNumber classes used: 1 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.0) / Number images used: 71802
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationNumber classes: 1 / Software - Name: cryoSPARC (ver. 4.7.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
SoftwareName: UCSF ChimeraX (ver. 1.9)
Output model

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

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