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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: To Be Published
Title: Context-Dependent Variability Of HIF Heterodimers Influences Interactions With Macromolecular And Small Molecule Partners
Authors: Isiorho, E.T. / Xu, X. / Gardner, K.H.
History
DepositionMay 19, 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
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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