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- EMDB-70418: Dimer of HIF-2a-ARNT Heterodimers Complexed on 51-bp HRE/HAS -

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Basic information

Entry
Database: EMDB / ID: EMD-70418
TitleDimer of HIF-2a-ARNT Heterodimers Complexed on 51-bp HRE/HAS
Map data
Sample
  • Complex: Dimer of two HIF-2a-ARNT heterodimers complexed on 51-bp HRE
    • DNA: 51-nt Hypoxia Response Element (Forward)
    • DNA: 51-nt Hypoxia Response Element (Reverse)
    • Protein or peptide: Endothelial PAS domain-containing protein 1
    • Protein or peptide: Aryl hydrocarbon receptor nuclear translocator
KeywordsComplex / Hypoxia / Transcription / Cancer / Dimer / Higher-ordered / DNA BINDING PROTEIN
Function / homology
Function and homology information


myoblast fate commitment / nuclear aryl hydrocarbon receptor complex / Aryl hydrocarbon receptor signalling / positive regulation of hormone biosynthetic process / aryl hydrocarbon receptor complex / Cellular response to hypoxia / Transcriptional regulation of pluripotent stem cells / regulation of protein neddylation / PTK6 Expression / positive regulation of protein sumoylation ...myoblast fate commitment / nuclear aryl hydrocarbon receptor complex / Aryl hydrocarbon receptor signalling / positive regulation of hormone biosynthetic process / aryl hydrocarbon receptor complex / Cellular response to hypoxia / Transcriptional regulation of pluripotent stem cells / regulation of protein neddylation / PTK6 Expression / positive regulation of protein sumoylation / norepinephrine metabolic process / Xenobiotics / surfactant homeostasis / Phase I - Functionalization of compounds / positive regulation of vascular endothelial growth factor receptor signaling pathway / epithelial cell maturation / Regulation of gene expression by Hypoxia-inducible Factor / aryl hydrocarbon receptor binding / blood vessel remodeling / positive regulation of vascular endothelial growth factor production / Endogenous sterols / embryonic placenta development / cis-regulatory region sequence-specific DNA binding / positive regulation of endothelial cell proliferation / NPAS4 regulates expression of target genes / visual perception / regulation of heart rate / Pexophagy / erythrocyte differentiation / positive regulation of erythrocyte differentiation / positive regulation of glycolytic process / RNA polymerase II transcription regulatory region sequence-specific DNA binding / mitochondrion organization / lung development / mRNA transcription by RNA polymerase II / transcription coactivator binding / PPARA activates gene expression / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / multicellular organismal-level iron ion homeostasis / negative regulation of inflammatory response / RNA polymerase II transcription regulator complex / nuclear receptor activity / sequence-specific double-stranded DNA binding / Neddylation / positive regulation of cold-induced thermogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / cellular response to oxidative stress / angiogenesis / cellular response to hypoxia / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / response to oxidative stress / sequence-specific DNA binding / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / response to hypoxia / nuclear speck / nuclear body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / DNA-binding transcription factor activity / regulation of transcription by RNA polymerase II / chromatin / signal transduction / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
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 / Helix-loop-helix DNA-binding domain / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) ...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 / 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 / Endothelial PAS domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsClosson JD / 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 29, 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_70418.png

Downloads & links

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Map

FileDownload / File: emd_70418.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.)
0.84 Å/pix.
x 400 pix.
= 337.6 Å		0.84 Å/pix.
x 400 pix.
= 337.6 Å		0.84 Å/pix.
x 400 pix.
= 337.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.844 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-1.4034662 - 2.1493194
Average (Standard dev.)0.0017521584 (±0.037548907)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 337.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_70418_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_70418_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Dimer of two HIF-2a-ARNT heterodimers complexed on 51-bp HRE

EntireName: Dimer of two HIF-2a-ARNT heterodimers complexed on 51-bp HRE
Components
  • Complex: Dimer of two HIF-2a-ARNT heterodimers complexed on 51-bp HRE
    • DNA: 51-nt Hypoxia Response Element (Forward)
    • DNA: 51-nt Hypoxia Response Element (Reverse)
    • Protein or peptide: Endothelial PAS domain-containing protein 1
    • Protein or peptide: Aryl hydrocarbon receptor nuclear translocator

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Supramolecule #1: Dimer of two HIF-2a-ARNT heterodimers complexed on 51-bp HRE

SupramoleculeName: Dimer of two HIF-2a-ARNT heterodimers complexed on 51-bp HRE
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 202 KDa

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Macromolecule #1: 51-nt Hypoxia Response Element (Forward)

MacromoleculeName: 51-nt Hypoxia Response Element (Forward) / type: dna / ID: 1 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.82208 KDa
SequenceString:
(DA)(DG)(DG)(DG)(DG)(DT)(DG)(DG)(DA)(DG) (DG)(DG)(DG)(DG)(DC)(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)

GENBANK: GENBANK: M11319.1

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Macromolecule #2: 51-nt Hypoxia Response Element (Reverse)

MacromoleculeName: 51-nt Hypoxia Response Element (Reverse) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.608979 KDa
SequenceString:
(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)(DG)(DC)(DC) (DC) (DC)(DC)(DT)(DC)(DC)(DA)(DC)(DC) (DC)(DC)(DT)

GENBANK: GENBANK: M11319.1

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Macromolecule #3: Endothelial PAS domain-containing protein 1

MacromoleculeName: Endothelial PAS domain-containing protein 1 / type: protein_or_peptide / ID: 3
Details: N-terminal 21 residues (MGSSHHHHHHSQDPGKEKKRS) are vector-derived
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 42.684453 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSHHHHHH SQDPGKEKKR SSSERRKEKS RDAARCRRSK ETEVFYELAH ELPLPHSVSS HLDKASIMRL AISFLRTHKL LSSVCSENE SEAEADQQMD NLYLKALEGF IAVVTQDGDM IFLSENISKF MGLTQVELTG HSIFDFTHPC DHEEIRENLS L KNGSGFGK ...String:
MGSSHHHHHH SQDPGKEKKR SSSERRKEKS RDAARCRRSK ETEVFYELAH ELPLPHSVSS HLDKASIMRL AISFLRTHKL LSSVCSENE SEAEADQQMD NLYLKALEGF IAVVTQDGDM IFLSENISKF MGLTQVELTG HSIFDFTHPC DHEEIRENLS L KNGSGFGK KSKDMSTERD FFMRMKCTVT NRGRTVNLKS ATWKVLHCTG QVKVYNNCPP HNSLCGYKEP LLSCLIIMCE PI QHPSHMD IPLDSKTFLS RHSMDMKFTY CDDRITELIG YHPEELLGRS AYEFYHALDS ENMTKSHQNL CTKGQVVSGQ YRM LAKHGG YVWLETQGTV IYNPRNLQPQ CIMCVNYVLS EIEKNDVVFS MDQTES

UniProtKB: Endothelial PAS domain-containing protein 1

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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

Concentration4.2 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 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / 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
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 3 / Number real images: 10910 / Average electron dose: 58.94 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: 656778
CTF correctionSoftware - Name: Warp (ver. 1.0.9) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.0) / Number images used: 164352
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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