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- PDB-9opf: Context-Dependent Variability Of HIF Heterodimers Influences Inte... -

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Basic information

Entry
Database: PDB / ID: 9opf
TitleContext-Dependent Variability Of HIF Heterodimers Influences Interactions With Macromolecular And Small Molecule Partners
ComponentsTransforming acidic coiled-coil-containing protein 3
KeywordsPROTEIN BINDING / coiled-coiled / coactivator
Function / homology
Function and homology information


microtubule cytoskeleton organization involved in mitosis / metaphase/anaphase transition of mitotic cell cycle / nuclear migration / regulation of mitotic spindle organization / mitotic spindle organization / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulation of NOTCH4 signaling / cerebral cortex development / centriolar satellite / microtubule cytoskeleton organization ...microtubule cytoskeleton organization involved in mitosis / metaphase/anaphase transition of mitotic cell cycle / nuclear migration / regulation of mitotic spindle organization / mitotic spindle organization / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulation of NOTCH4 signaling / cerebral cortex development / centriolar satellite / microtubule cytoskeleton organization / spindle pole / mitotic spindle / ciliary basal body / cell division / intracellular membrane-bounded organelle / Golgi apparatus / cytosol / cytoplasm
Similarity search - Function
Transforming acidic coiled-coil-containing protein, C-terminal / TACC family / Transforming acidic coiled-coil-containing protein (TACC), C-terminal
Similarity search - Domain/homology
Transforming acidic coiled-coil-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsIsiorho, E.A. / Xu, X. / Gardner, K.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB1818148 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
DepositionMay 19, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transforming acidic coiled-coil-containing protein 3
B: Transforming acidic coiled-coil-containing protein 3


Theoretical massNumber of molelcules
Total (without water)18,7092
Polymers18,7092
Non-polymers00
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR relaxation study
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-27 kcal/mol
Surface area8680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)263.114, 23.826, 31.851
Angle α, β, γ (deg.)90.000, 91.818, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11B-902-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and ((resid 782 and (name N or name...
d_2ens_1(chain "B" and ((resid 782 and (name N or name...

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: GLU / End label comp-ID: GLU / Auth seq-ID: 782 - 836 / Label seq-ID: 25 - 79

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB

NCS oper: (Code: givenMatrix: (0.993825368803, 0.106985973238, 0.0294132258172), (0.105891882085, -0.993706269183, 0.0365343659428), (0.0331367715884, -0.0331941578672, -0.998899445516)Vector: -1. ...NCS oper: (Code: given
Matrix: (0.993825368803, 0.106985973238, 0.0294132258172), (0.105891882085, -0.993706269183, 0.0365343659428), (0.0331367715884, -0.0331941578672, -0.998899445516)
Vector: -1.25589918939, 13.4150367726, 14.7177435741)

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Components

#1: Protein Transforming acidic coiled-coil-containing protein 3 / ERIC-1


Mass: 9354.629 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TACC3, ERIC1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y6A5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
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: 2.67 Å3/Da / Density % sol: 53.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M imidazole, 50% (+/-)-2-Methyl-2,4-pentanediol (MPD)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 2.28→29.02 Å / Num. obs: 9247 / % possible obs: 98.37 % / Redundancy: 3.3 % / Biso Wilson estimate: 48.44 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.085 / Net I/σ(I): 7
Reflection shellResolution: 2.28→2.4 Å / Rmerge(I) obs: 0.63 / Num. unique obs: 1264 / CC1/2: 0.58

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419-000refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.28→29.02 Å / SU ML: 0.2818 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 29.7272
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2951 934 10.1 %
Rwork0.2662 8313 -
obs0.2693 9247 98.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 78.65 Å2
Refinement stepCycle: LAST / Resolution: 2.28→29.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms898 0 0 6 904
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0146896
X-RAY DIFFRACTIONf_angle_d1.65431192
X-RAY DIFFRACTIONf_chiral_restr0.0637142
X-RAY DIFFRACTIONf_plane_restr0.0161156
X-RAY DIFFRACTIONf_dihedral_angle_d17.9146374
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 2.32470545557 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.28-2.40.321280.27741136X-RAY DIFFRACTION96.05
2.4-2.550.33441290.27861153X-RAY DIFFRACTION100
2.55-2.750.31481310.25021204X-RAY DIFFRACTION99.48
2.75-3.030.2561300.25481196X-RAY DIFFRACTION99.1
3.03-3.460.31381330.26961195X-RAY DIFFRACTION99.1
3.47-4.360.25891340.22971203X-RAY DIFFRACTION98.53
4.36-29.020.3121490.29911226X-RAY DIFFRACTION96.49

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