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

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Basic information

Entry
Database: PDB / ID: 4zpk
TitleCrystal Structure of the Heterodimeric HIF-2a:ARNT Complex with HRE DNA
Components
  • Aryl hydrocarbon receptor nuclear translocator
  • DNA (5'-D(*CP*AP*CP*GP*AP*CP*CP*CP*GP*CP*AP*CP*GP*TP*AP*CP*GP*CP*AP*GP*C)-3')
  • DNA (5'-D(*GP*GP*CP*TP*GP*CP*GP*TP*AP*CP*GP*TP*GP*CP*GP*GP*GP*TP*CP*GP*T)-3')
  • Endothelial PAS domain-containing protein 1
KeywordsPROTEIN TRANSPORT/TRANSCRIPTION/DNA / ARNT / HIF-2a / HRE / bHLH-PAS / PROTEIN TRANSPORT-TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


Cellular response to hypoxia / Phase I - Functionalization of compounds / Xenobiotics / Aryl hydrocarbon receptor signalling / NPAS4 regulates expression of target genes / myoblast fate commitment / norepinephrine biosynthetic process / Regulation of gene expression by Hypoxia-inducible Factor / Endogenous sterols / nuclear aryl hydrocarbon receptor complex ...Cellular response to hypoxia / Phase I - Functionalization of compounds / Xenobiotics / Aryl hydrocarbon receptor signalling / NPAS4 regulates expression of target genes / myoblast fate commitment / norepinephrine biosynthetic process / Regulation of gene expression by Hypoxia-inducible Factor / Endogenous sterols / nuclear aryl hydrocarbon receptor complex / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / positive regulation of dopamine biosynthetic process / positive regulation of hormone biosynthetic process / aryl hydrocarbon receptor complex / regulation of protein neddylation / positive regulation of protein sumoylation / Neddylation / norepinephrine metabolic process / surfactant homeostasis / epithelial cell maturation / cobalt ion binding / aryl hydrocarbon receptor binding / hemopoiesis / positive regulation of vascular endothelial growth factor production / embryonic placenta development / blood vessel remodeling / cis-regulatory region sequence-specific DNA binding / visual perception / regulation of heart rate / mitochondrion organization / erythrocyte differentiation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / lung development / mRNA transcription by RNA polymerase II / response to toxic substance / multicellular organismal-level iron ion homeostasis / transcription coactivator binding / negative regulation of inflammatory response / RNA polymerase II transcription regulator complex / nuclear receptor activity / sequence-specific double-stranded DNA binding / positive regulation of cold-induced thermogenesis / gene expression / cellular response to oxidative stress / cellular response to hypoxia / DNA-binding transcription activator activity, RNA polymerase II-specific / angiogenesis / RNA polymerase II-specific DNA-binding transcription factor binding / response to oxidative stress / transcription regulator complex / sequence-specific DNA binding / transcription by RNA polymerase II / cell differentiation / nuclear body / response to hypoxia / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear speck / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein-containing complex binding / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / 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, 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 ...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 / 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 DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / 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: 3.6 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 8, 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: DNA (5'-D(*GP*GP*CP*TP*GP*CP*GP*TP*AP*CP*GP*TP*GP*CP*GP*GP*GP*TP*CP*GP*T)-3')
D: DNA (5'-D(*CP*AP*CP*GP*AP*CP*CP*CP*GP*CP*AP*CP*GP*TP*AP*CP*GP*CP*AP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)97,5294
Polymers97,5294
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12610 Å2
ΔGint-82 kcal/mol
Surface area35240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.746, 65.746, 245.929
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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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.: 1 / 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.: 1 / 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: DNA chain DNA (5'-D(*GP*GP*CP*TP*GP*CP*GP*TP*AP*CP*GP*TP*GP*CP*GP*GP*GP*TP*CP*GP*T)-3')


Mass: 6527.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: HRE DNA sense strand / Source: (synth.) Mus musculus (house mouse)
#4: DNA chain DNA (5'-D(*CP*AP*CP*GP*AP*CP*CP*CP*GP*CP*AP*CP*GP*TP*AP*CP*GP*CP*AP*GP*C)-3')


Mass: 6363.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: HRE DNA antisense strand / Source: (synth.) Mus musculus (house mouse)

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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: 2.72 Å3/Da / Density % sol: 54.86 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 4% Tacsimate, pH 6.0, 10% 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 5, 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
ReflectionResolution: 3.6→50 Å / Num. obs: 12149 / % possible obs: 99.5 % / Redundancy: 3.7 % / Biso Wilson estimate: 116.97 Å2 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.059 / Rrim(I) all: 0.114 / Χ2: 1.128 / Net I/av σ(I): 12.909 / Net I/σ(I): 7.9 / Num. measured all: 45153
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.6-3.663.50.7226260.6810.4490.8521.28199.5
3.66-3.733.70.6445880.740.3920.7541.23799.5
3.73-3.83.70.6155900.7630.3720.721.36399.7
3.8-3.883.70.5066470.8650.3040.5911.22999.8
3.88-3.963.70.385700.8920.230.4451.24199.8
3.96-4.053.80.3056190.9430.1830.3561.25299.7
4.05-4.163.80.2685890.9580.160.3131.20199.8
4.16-4.273.80.1996020.9750.120.2331.23599.7
4.27-4.393.80.1556310.9840.0930.1821.1699.8
4.39-4.543.80.1375750.9810.0820.161.11299.7
4.54-4.73.80.1256440.9880.0750.1461.05899.7
4.7-4.893.80.1085780.9920.0650.1261.08799.7
4.89-5.113.80.1056200.990.0630.1231.0399.7
5.11-5.383.80.1046000.9910.0620.1211.05399.5
5.38-5.713.70.1046030.9870.0620.1211.02299.7
5.71-6.153.70.16070.9890.060.1161.03199.5
6.15-6.773.70.0886100.9890.0540.1041.07899.3
6.77-7.753.70.0696210.9920.0410.080.98899.4
7.75-9.753.60.0476080.9950.0280.0540.827100
9.75-503.60.0466210.9850.0290.0551.09697.3

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Phasing

PhasingMethod: molecular replacement

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Processing

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

4zp4


Resolution: 3.6→32.873 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 34.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3213 580 4.79 %
Rwork0.2341 11532 -
obs0.2381 12112 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 254.41 Å2 / Biso mean: 133.3382 Å2 / Biso min: 96.31 Å2
Refinement stepCycle: final / Resolution: 3.6→32.873 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4769 855 0 0 5624
Num. residues----631
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045814
X-RAY DIFFRACTIONf_angle_d0.8838013
X-RAY DIFFRACTIONf_chiral_restr0.034902
X-RAY DIFFRACTIONf_plane_restr0.003873
X-RAY DIFFRACTIONf_dihedral_angle_d21.2282228
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.5885-3.94910.35231350.303328572992100
3.9491-4.51930.36631460.261528873033100
4.5193-5.68910.34281640.25828773041100
5.6891-32.87440.27571350.19222911304699

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