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

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Basic information

Entry
Database: PDB / ID: 4zph
TitleCrystal Structure of the Heterodimeric HIF-2a:ARNT Complex with Proflavine
Components
  • Aryl hydrocarbon receptor nuclear translocator
  • Endothelial PAS domain-containing protein 1
KeywordsPROTEIN TRANSPORT/TRANSCRIPTION / HIF-2a / ARNT / bHLH-PAS / Proflavine / 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 / negative regulation of inflammatory response / response to toxic substance / RNA polymerase II transcription regulator complex / transcription coactivator binding / nuclear receptor activity / sequence-specific double-stranded DNA binding / positive regulation of cold-induced thermogenesis / response to oxidative stress / cellular response to oxidative stress / DNA-binding transcription activator activity, RNA polymerase II-specific / angiogenesis / cellular response to hypoxia / transcription regulator complex / 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
PROFLAVIN / 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: 2.8 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 7, 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 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)169,4865
Polymers169,2774
Non-polymers2091
Water39622
1
A: Aryl hydrocarbon receptor nuclear translocator
B: Endothelial PAS domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,8483
Polymers84,6382
Non-polymers2091
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7300 Å2
ΔGint-47 kcal/mol
Surface area26260 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
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6630 Å2
ΔGint-53 kcal/mol
Surface area26780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.896, 76.418, 98.345
Angle α, β, γ (deg.)89.830, 89.640, 73.210
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain C
12chain B
22chain D

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUVALVALchain AAA98 - 46418 - 384
21GLUGLUVALVALchain CCC98 - 46418 - 384
12ARGARGSERSERchain BBB26 - 36125 - 360
22CYSCYSSERSERchain DDD25 - 36124 - 360

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-PRL / PROFLAVIN


Mass: 209.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H11N3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O

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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: 40.82 %
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: 0.5
ReflectionResolution: 2.8→50 Å / Num. obs: 33408 / % possible obs: 98.5 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.042 / Rrim(I) all: 0.069 / Χ2: 0.694 / Net I/av σ(I): 16.967 / Net I/σ(I): 10.7 / Num. measured all: 79567
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.8-2.852.20.69316800.490.580.9080.88597.6
2.85-2.92.20.60316950.5930.490.7810.94398.1
2.9-2.962.30.51316140.6620.4120.6620.89398.1
2.96-3.022.40.44516710.7290.350.5690.90698.4
3.02-3.082.40.38916910.80.3050.4970.91798.3
3.08-3.152.40.30416380.8740.2330.3850.95398.4
3.15-3.232.40.2516890.8990.1920.3170.90498.5
3.23-3.322.40.20516390.9290.1590.2610.88697.9
3.32-3.422.40.14816730.950.1140.1880.86298.9
3.42-3.532.40.1117070.9720.0840.140.82998.9
3.53-3.652.40.08416570.9760.0660.1080.75798.6
3.65-3.82.40.06716880.9870.0510.0850.65598.8
3.8-3.972.40.04816380.9880.0370.060.55598.7
3.97-4.182.40.03716890.990.0290.0470.48299.3
4.18-4.442.40.02916930.9920.0220.0370.41598.9
4.44-4.792.40.02516730.9930.0190.0320.37798.8
4.79-5.272.40.02616640.9920.020.0330.37799.2
5.27-6.032.40.02516920.9860.0190.0310.42599.1
6.03-7.592.40.02116670.9890.0160.0270.32298.9
7.59-502.40.02616500.9850.020.0330.62897.2

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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
Cootmodel building
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4ZP4

4zp4


Resolution: 2.8→49.172 Å / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 22.98 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2206 1636 5.19 %
Rwork0.1847 29893 -
obs0.189 31508 92.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 138.23 Å2 / Biso mean: 45.1453 Å2 / Biso min: 19.79 Å2
Refinement stepCycle: final / Resolution: 2.8→49.172 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8827 0 16 22 8865
Biso mean--56.53 48.44 -
Num. residues----1092
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.019016
X-RAY DIFFRACTIONf_angle_d1.52512153
X-RAY DIFFRACTIONf_chiral_restr0.0631376
X-RAY DIFFRACTIONf_plane_restr0.0071529
X-RAY DIFFRACTIONf_dihedral_angle_d15.6053343
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2302X-RAY DIFFRACTION7.919TORSIONAL
12C2302X-RAY DIFFRACTION7.919TORSIONAL
21B2626X-RAY DIFFRACTION7.919TORSIONAL
22D2626X-RAY DIFFRACTION7.919TORSIONAL
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 (%)
2.7937-2.88380.2931710.24821683175454
2.8838-2.98690.31891190.21582381250078
2.9869-3.10640.27171380.20692827296593
3.1064-3.24780.24341610.19372880304193
3.2478-3.41890.23821640.18592850301493
3.4189-3.6330.20361690.16892875304493
3.633-3.91330.18631430.17722891303494
3.9133-4.30670.22581460.16592882302894
4.3067-4.9290.17751570.15372882303994
4.929-6.20650.22351610.20222882304394
6.2065-40.79280.25521430.20842860300393
Refinement TLS params.Method: refined / Origin x: 186.3584 Å / Origin y: -88.6733 Å / Origin z: -136.7026 Å
111213212223313233
T0.1278 Å20.0543 Å2-0.0264 Å2-0.2922 Å20.0363 Å2--0.3153 Å2
L0.0893 °20.2602 °2-0.326 °2-0.3332 °2-0.1719 °2--1.0401 °2
S0.0041 Å °-0.0328 Å °0.0307 Å °0.0147 Å °0.0236 Å °-0.0464 Å °0.0275 Å °0.0439 Å °-0.0315 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA98 - 464
2X-RAY DIFFRACTION1allB26 - 361
3X-RAY DIFFRACTION1allC98 - 464
4X-RAY DIFFRACTION1allD25 - 361
5X-RAY DIFFRACTION1allE501
6X-RAY DIFFRACTION1allF1 - 26

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