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- PDB-4zqd: Crystal Structure of the Heterodimeric HIF-2a:ARNT Complex with t... -

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Basic information

Entry
Database: PDB / ID: 4zqd
TitleCrystal Structure of the Heterodimeric HIF-2a:ARNT Complex with the Benzoxadiazole Antagonist 0X3
Components
  • Aryl hydrocarbon receptor nuclear translocator
  • Endothelial PAS domain-containing protein 1
KeywordsPROTEIN TRANSPORT/TRANSCRIPTION / ARNT / HIF-2a / 0X3 / bHLH-PAS / PROTEIN TRANSPORT-TRANSCRIPTION complex
Function / homology
Function and homology information


Cellular response to hypoxia / Xenobiotics / Aryl hydrocarbon receptor signalling / Phase I - Functionalization of compounds / NPAS4 regulates expression of target genes / Regulation of gene expression by Hypoxia-inducible Factor / myoblast fate commitment / Endogenous sterols / nuclear aryl hydrocarbon receptor complex / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha ...Cellular response to hypoxia / Xenobiotics / Aryl hydrocarbon receptor signalling / Phase I - Functionalization of compounds / NPAS4 regulates expression of target genes / Regulation of gene expression by Hypoxia-inducible Factor / myoblast fate commitment / Endogenous sterols / nuclear aryl hydrocarbon receptor complex / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / positive regulation of hormone biosynthetic process / regulation of protein neddylation / positive regulation of protein sumoylation / Neddylation / norepinephrine metabolic process / surfactant homeostasis / epithelial cell maturation / aryl hydrocarbon receptor binding / hemopoiesis / positive regulation of vascular endothelial growth factor production / blood vessel remodeling / embryonic placenta development / cis-regulatory region sequence-specific DNA binding / visual perception / regulation of heart rate / lung development / positive regulation of glycolytic process / erythrocyte differentiation / mitochondrion organization / mRNA transcription by RNA polymerase II / multicellular organismal-level iron ion homeostasis / response to toxic substance / negative regulation of inflammatory response / transcription coactivator binding / RNA polymerase II transcription regulator complex / nuclear receptor activity / sequence-specific double-stranded DNA binding / positive regulation of cold-induced thermogenesis / cellular response to oxidative stress / response to oxidative stress / DNA-binding transcription activator activity, RNA polymerase II-specific / angiogenesis / transcription regulator complex / cellular response to hypoxia / gene expression / sequence-specific DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / cell differentiation / response to hypoxia / nuclear speck / nuclear body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein heterodimerization activity / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus / cytoplasm
Similarity search - Function
HIF-1 alpha, transactivation domain, C-terminal / HIF-1 alpha C terminal transactivation domain / : / Hypoxia-inducible factor 1-alpha bHLH domain / Hypoxia-inducible factor, alpha subunit-like / Hypoxia-inducible factor-1 / Nuclear translocator / PAS fold / Helix-loop-helix DNA-binding domain / PAC motif ...HIF-1 alpha, transactivation domain, C-terminal / HIF-1 alpha C terminal transactivation domain / : / Hypoxia-inducible factor 1-alpha bHLH domain / Hypoxia-inducible factor, alpha subunit-like / Hypoxia-inducible factor-1 / Nuclear translocator / 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
Chem-0X3 / Aryl hydrocarbon receptor nuclear translocator / Endothelial PAS domain-containing protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.87 Å
AuthorsWu, D. / Potluri, N. / Lu, J. / Kim, Y. / Rastinejad, F.
CitationJournal: Nature / Year: 2015
Title: Structural integration in hypoxia-inducible factors.
Authors: Wu, D. / Potluri, N. / Lu, J. / Kim, Y. / Rastinejad, F.
History
DepositionMay 9, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2015Group: Database references
Revision 1.2Aug 26, 2015Group: Database references
Revision 1.3Nov 22, 2017Group: Database references / Derived calculations / Refinement description
Category: citation / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aryl hydrocarbon receptor nuclear translocator
B: Endothelial PAS domain-containing protein 1
C: Aryl hydrocarbon receptor nuclear translocator
D: Endothelial PAS domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,5855
Polymers169,2774
Non-polymers3091
Water00
1
A: Aryl hydrocarbon receptor nuclear translocator
B: Endothelial PAS domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,9473
Polymers84,6382
Non-polymers3091
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6380 Å2
ΔGint-46 kcal/mol
Surface area25780 Å2
MethodPISA
2
C: Aryl hydrocarbon receptor nuclear translocator
D: Endothelial PAS domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)84,6382
Polymers84,6382
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6390 Å2
ΔGint-47 kcal/mol
Surface area27010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.123, 76.334, 97.985
Angle α, β, γ (deg.)89.910, 89.990, 73.180
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and segid
21chain C and segid
12chain B and segid
22chain D and segid

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and segidA0
211chain C and segidC0
112chain B and segidB0
212chain D and segidD0

NCS ensembles :
ID
1
2

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Components

#1: Protein Aryl hydrocarbon receptor nuclear translocator / ARNT protein / Dioxin receptor / nuclear translocator / Hypoxia-inducible factor 1-beta / HIF1-beta


Mass: 43437.391 Da / Num. of mol.: 2 / Fragment: UNP residues 82-464
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Arnt / Plasmid: pMKH / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P53762
#2: Protein Endothelial PAS domain-containing protein 1 / EPAS-1 / HIF-1-alpha-like factor / mHLF / HIF-related factor / HRF / Hypoxia-inducible factor 2- ...EPAS-1 / HIF-1-alpha-like factor / mHLF / HIF-related factor / HRF / Hypoxia-inducible factor 2-alpha / HIF2-alpha


Mass: 41200.953 Da / Num. of mol.: 2 / Fragment: UNP residues 3-361
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Epas1, Hif2a / Plasmid: pSJ2 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P97481
#3: Chemical ChemComp-0X3 / N-(3-chloro-5-fluorophenyl)-4-nitro-2,1,3-benzoxadiazol-5-amine


Mass: 308.652 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H6ClFN4O3

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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: 2.08 Å3/Da / Density % sol: 40.8 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2% Tacsimate, pH 7.0, 6% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 15, 2014
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.47
ReflectionResolution: 2.87→50 Å / Num. obs: 30404 / % possible obs: 97.9 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.089 / Rrim(I) all: 0.151 / Χ2: 1.459 / Net I/av σ(I): 8.924 / Net I/σ(I): 10.3 / Num. measured all: 77269
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.87-2.922.20.74713960.4440.590.9581.17391.1
2.92-2.972.30.76614470.3710.6020.981.25994
2.97-3.032.40.63214960.5470.4960.8091.22295.9
3.03-3.092.40.58915350.5240.4610.7531.24497.6
3.09-3.162.50.514980.6090.3930.641.26698.4
3.16-3.232.60.42215550.7280.3260.5371.29997.9
3.23-3.312.60.37115250.7620.2850.471.37798.5
3.31-3.42.60.2715230.8540.2080.3431.28798.3
3.4-3.52.60.22715410.8840.1750.2881.38998.2
3.5-3.622.60.18515010.920.1410.2341.40398.6
3.62-3.742.60.20715550.2070.1710.271.53798.7
3.74-3.892.60.13815390.9550.1030.1741.39298.8
3.89-4.072.60.11915480.9580.090.1511.56698.9
4.07-4.292.60.09315050.9810.0680.1151.17898.8
4.29-4.552.60.08215380.9660.060.1021.30299.3
4.55-4.912.60.07815530.9810.0570.0981.18199
4.91-5.42.60.08415440.9790.0610.1041.32599.2
5.4-6.182.60.08915400.9680.0650.1111.46299.4
6.18-7.782.60.09415410.9450.0690.1181.82499.4
7.78-502.60.10415240.9680.0740.1293.29498.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000phasing
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
SCALEPACKdata scaling
Cootmodel building
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZP4

4zp4


Resolution: 2.87→48.992 Å / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 27.04 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2542 1565 5.15 %
Rwork0.2122 28811 -
obs0.2179 30376 97.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 249.47 Å2 / Biso mean: 90.4041 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 2.87→48.992 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8695 0 21 0 8716
Biso mean--103.79 --
Num. residues----1074
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0128895
X-RAY DIFFRACTIONf_angle_d1.59211990
X-RAY DIFFRACTIONf_chiral_restr0.0661355
X-RAY DIFFRACTIONf_plane_restr0.0071508
X-RAY DIFFRACTIONf_dihedral_angle_d15.4143288
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2100X-RAY DIFFRACTION8.543TORSIONAL
12C2100X-RAY DIFFRACTION8.543TORSIONAL
21B2466X-RAY DIFFRACTION8.543TORSIONAL
22D2466X-RAY DIFFRACTION8.543TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8705-2.96310.39671310.34862379251084
2.9631-3.06890.41381360.33662601273791
3.0689-3.19170.35081380.31972605274393
3.1917-3.33680.34631500.30962616276693
3.3368-3.51250.33631280.28262692282094
3.5125-3.73220.27391340.24952619275394
3.7322-4.01990.24141390.22812669280894
4.0199-4.42350.20751270.1792676280394
4.4235-5.06150.19931500.1622635278594
5.0615-6.36880.23591450.19672683282894
6.3688-32.14270.25531530.16972636278994
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.76-0.1231-0.21080.5314-0.28050.23840.05680.06660.03340.04390.05950.11150.00580.25870.00020.62170.1145-0.07560.6521-0.06540.5585-170.2767115.7596-111.3744
20.5841-0.13530.19210.56280.27060.8657-0.0003-0.1216-0.12160.14970.03390.06620.01710.1-0.00020.53510.04630.00620.7608-0.02620.6023-177.8269103.7638-106.4762
30.4356-0.1817-0.15460.74030.04330.2116-0.006-0.0024-0.01980.0309-0.1110.14470.1369-0.1515-0.00010.55560.0392-0.04480.6664-0.0320.6239-196.73489.974-159.7387
40.4565-0.10820.31210.74770.04470.6227-0.0107-0.21920.1225-0.07330.1325-0.1240.0763-0.0097-0.00010.5135-0.0207-0.01330.6754-0.10720.7031-189.13100.8607-155.1251
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resseq 100:464)A100 - 464
2X-RAY DIFFRACTION2(chain B and resseq 26:361)B26 - 361
3X-RAY DIFFRACTION3(chain C and resseq 98:464)C98 - 464
4X-RAY DIFFRACTION4(chain D and resseq 25:361)D25 - 361

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