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- PDB-4xt2: Crystal structure of the high affinity heterodimer of HIF2 alpha ... -

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Basic information

Entry
Database: PDB / ID: 4xt2
TitleCrystal structure of the high affinity heterodimer of HIF2 alpha and ARNT C-terminal PAS domains in complex with a tetrazole-containing antagonist
Components
  • Aryl hydrocarbon receptor nuclear translocator
  • Endothelial PAS domain-containing protein 1
KeywordsTRANSCRIPTION / transcription factor / Hypoxia Inducible Factor / inhibitor / cancer
Function / homology
Function and homology information


myoblast fate commitment / nuclear aryl hydrocarbon receptor complex / Aryl hydrocarbon receptor signalling / positive regulation of hormone biosynthetic process / aryl hydrocarbon receptor complex / Cellular response to hypoxia / Transcriptional regulation of pluripotent stem cells / regulation of protein neddylation / PTK6 Expression / positive regulation of protein sumoylation ...myoblast fate commitment / nuclear aryl hydrocarbon receptor complex / Aryl hydrocarbon receptor signalling / positive regulation of hormone biosynthetic process / aryl hydrocarbon receptor complex / Cellular response to hypoxia / Transcriptional regulation of pluripotent stem cells / regulation of protein neddylation / PTK6 Expression / positive regulation of protein sumoylation / norepinephrine metabolic process / Xenobiotics / surfactant homeostasis / Phase I - Functionalization of compounds / positive regulation of vascular endothelial growth factor receptor signaling pathway / epithelial cell maturation / Regulation of gene expression by Hypoxia-inducible Factor / aryl hydrocarbon receptor binding / blood vessel remodeling / positive regulation of vascular endothelial growth factor production / Endogenous sterols / embryonic placenta development / cis-regulatory region sequence-specific DNA binding / positive regulation of endothelial cell proliferation / NPAS4 regulates expression of target genes / visual perception / regulation of heart rate / Pexophagy / erythrocyte differentiation / positive regulation of erythrocyte differentiation / positive regulation of glycolytic process / RNA polymerase II transcription regulatory region sequence-specific DNA binding / mitochondrion organization / lung development / mRNA transcription by RNA polymerase II / transcription coactivator binding / PPARA activates gene expression / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / multicellular organismal-level iron ion homeostasis / negative regulation of inflammatory response / RNA polymerase II transcription regulator complex / nuclear receptor activity / sequence-specific double-stranded DNA binding / Neddylation / positive regulation of cold-induced thermogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / cellular response to oxidative stress / angiogenesis / cellular response to hypoxia / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / response to oxidative stress / sequence-specific DNA binding / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / response to hypoxia / nuclear speck / nuclear body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / DNA-binding transcription factor activity / regulation of transcription by RNA polymerase II / chromatin / signal transduction / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Hypoxia-inducible factor 1-alpha bHLH 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 ...Hypoxia-inducible factor 1-alpha bHLH 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 / 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 / Beta-Lactamase / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-43L / Aryl hydrocarbon receptor nuclear translocator / Endothelial PAS domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.698 Å
AuthorsScheuermann, T.H. / Gardner, K.H.
Funding support United States, 3items
OrganizationGrant numberCountry
Cancer Prevention and Research Institute of Texas (CPRIT)RP130513 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P01 CA95471 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RP100846 United States
CitationJournal: J.Med.Chem. / Year: 2015
Title: Isoform-Selective and Stereoselective Inhibition of Hypoxia Inducible Factor-2.
Authors: Scheuermann, T.H. / Stroud, D. / Sleet, C.E. / Bayeh, L. / Shokri, C. / Wang, H. / Caldwell, C.G. / Longgood, J. / MacMillan, J.B. / Bruick, R.K. / Gardner, K.H. / Tambar, U.K.
History
DepositionJan 22, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2015Group: Refinement description
Revision 1.2Sep 6, 2017Group: Advisory / Author supporting evidence / Derived calculations
Category: pdbx_audit_support / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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
B: Aryl hydrocarbon receptor nuclear translocator
D: Aryl hydrocarbon receptor nuclear translocator
A: Endothelial PAS domain-containing protein 1
C: Endothelial PAS domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4336
Polymers55,5634
Non-polymers8702
Water5,585310
1
B: Aryl hydrocarbon receptor nuclear translocator
A: Endothelial PAS domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2173
Polymers27,7812
Non-polymers4351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-9 kcal/mol
Surface area11130 Å2
MethodPISA
2
D: Aryl hydrocarbon receptor nuclear translocator
C: Endothelial PAS domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2173
Polymers27,7812
Non-polymers4351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-12 kcal/mol
Surface area11060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.253, 84.390, 82.784
Angle α, β, γ (deg.)90.00, 104.39, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Aryl hydrocarbon receptor nuclear translocator / ARNT protein / Class E basic helix-loop-helix protein 2 / bHLHe2 / Dioxin receptor / nuclear ...ARNT protein / Class E basic helix-loop-helix protein 2 / bHLHe2 / Dioxin receptor / nuclear translocator / Hypoxia-inducible factor 1-beta / HIF1-beta


Mass: 14243.098 Da / Num. of mol.: 2 / Fragment: C-terminal PAS domain (UNP residues 342-456) / Mutation: E362R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARNT, BHLHE2 / Plasmid: pHIS-GB1 Con29 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P27540
#2: Protein Endothelial PAS domain-containing protein 1 / EPAS-1 / Basic-helix-loop-helix-PAS protein MOP2 / Class E basic helix-loop-helix protein 73 / ...EPAS-1 / Basic-helix-loop-helix-PAS protein MOP2 / Class E basic helix-loop-helix protein 73 / bHLHe73 / HIF-1-alpha-like factor / HLF / Hypoxia-inducible factor 2-alpha / HIF2-alpha / Member of PAS protein 2 / PAS domain-containing protein 2


Mass: 13538.300 Da / Num. of mol.: 2 / Fragment: C-terminal PAS domain (UNP residues 239-350) / Mutation: R247E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPAS1, BHLHE73, HIF2A, MOP2, PASD2 / Plasmid: pHIS-GB1 Con30 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q99814
#3: Chemical ChemComp-43L / (5S,7R)-5,7-bis(3-bromophenyl)-4,5,6,7-tetrahydrotetrazolo[1,5-a]pyrimidine


Mass: 435.116 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H13Br2N5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.59 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2 uL 500 uM protein against 100 mM Bis-Tris, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 15, 2011
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.698→50 Å / Num. obs: 54343 / % possible obs: 99.8 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 18.3
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 3 % / Rmerge(I) obs: 0.562 / Mean I/σ(I) obs: 2.8 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000v704data reduction
HKL-2000v704data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3F1P

3f1p


Resolution: 1.698→41.688 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 17.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1916 2741 5.04 %
Rwork0.1593 --
obs0.161 54336 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.698→41.688 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3682 0 46 310 4038
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113923
X-RAY DIFFRACTIONf_angle_d1.3455322
X-RAY DIFFRACTIONf_dihedral_angle_d15.1421459
X-RAY DIFFRACTIONf_chiral_restr0.083564
X-RAY DIFFRACTIONf_plane_restr0.006687
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6983-1.72760.22571390.2232525X-RAY DIFFRACTION97
1.7276-1.7590.27681290.2152597X-RAY DIFFRACTION100
1.759-1.79290.29951350.19762531X-RAY DIFFRACTION100
1.7929-1.82950.20171500.19132592X-RAY DIFFRACTION100
1.8295-1.86920.20581440.17552541X-RAY DIFFRACTION100
1.8692-1.91270.23741340.16892585X-RAY DIFFRACTION100
1.9127-1.96060.20141430.15532578X-RAY DIFFRACTION100
1.9606-2.01360.20571430.15492575X-RAY DIFFRACTION100
2.0136-2.07280.15711270.14942588X-RAY DIFFRACTION100
2.0728-2.13970.18371450.14952563X-RAY DIFFRACTION100
2.1397-2.21620.19151230.14942581X-RAY DIFFRACTION100
2.2162-2.30490.22511300.15142591X-RAY DIFFRACTION100
2.3049-2.40980.19341490.14522580X-RAY DIFFRACTION100
2.4098-2.53680.17981200.1492598X-RAY DIFFRACTION100
2.5368-2.69580.1681380.15152590X-RAY DIFFRACTION100
2.6958-2.90390.19951480.16132577X-RAY DIFFRACTION100
2.9039-3.1960.17411300.16372590X-RAY DIFFRACTION100
3.196-3.65820.18561480.15662587X-RAY DIFFRACTION100
3.6582-4.6080.15281270.13252624X-RAY DIFFRACTION100
4.608-41.70040.20881390.18312602X-RAY DIFFRACTION98
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)
13.22660.4313-0.43898.0595-3.88266.2630.0720.13010.48020.1317-0.27330.0737-0.74250.18680.02150.2055-0.0164-0.00920.14380.03010.172914.7679-10.914315.7687
22.82350.0486-1.1664.1719-0.08214.36020.05220.2525-0.0726-0.144-0.04440.4804-0.0225-0.4562-0.07780.0828-0.0079-0.00750.1569-0.02260.167410.0598-19.224215.7742
37.33941.2325-3.23481.51230.02394.3814-0.2354-0.1483-0.2130.0432-0.06880.2820.3643-0.160.29030.1486-0.02950.01210.0994-0.01510.152416.4375-26.283514.769
41.958-0.53980.63186.43575.16966.8599-0.1506-0.4555-0.2420.31730.12660.08940.32280.1662-0.01340.1036-0.00560.0020.19040.05090.120126.3839-24.566721.5121
50.7042-0.0596-1.59864.3688-3.41517.50520.1452-0.7380.03030.3689-0.4602-0.0877-0.08960.8531-0.640.2118-0.009-0.010.4554-0.05980.0925.0195-14.269931.2931
62.7112-0.551-2.05252.4841-0.16321.9791-0.12170.215-0.2588-0.18850.09680.05650.0865-0.08990.04390.1105-0.021-0.00420.13180.01470.086620.395-20.8769.177
71.8624-0.1142-2.49461.05610.43433.40280.111-0.13660.07940.05170.11870.0619-0.15440.1009-0.1190.0829-0.0001-0.00050.14920.01670.090221.4795-16.263417.1216
80.4626-0.2071-1.0422.65113.84647.35310.05770.0598-0.0701-0.1596-0.091-0.09160.53850.30120.07350.34520.06030.08390.28010.02140.167512.9026-17.523238.6037
92.2451-0.4284-2.63662.7015-1.25386.96080.2484-0.05490.2356-0.00330.04640.0449-0.3408-0.0237-0.3140.0753-0.0202-0.0140.1035-0.00860.083821.3626-13.315514.7028
103.8083-0.5734-0.47036.39231.63267.22980.1004-0.1250.1468-0.0832-0.0286-0.2357-0.1159-0.0554-0.08890.0626-0.01790.020.1182-0.00610.10249.0531-17.345119.0095
111.5990.36680.01522.49651.32594.0371-0.0266-0.10790.03720.17320.068-0.3298-0.0060.6227-0.04830.0943-0.0054-0.02060.1856-0.01020.14656.2461-17.148824.6453
128.7571-0.9277-8.1580.81880.04328.9475-0.52940.2119-0.0776-0.0990.22450.08371.0777-0.13630.30830.2034-0.0155-0.00470.13570.01920.126448.2517-26.335824.2182
133.1103-0.73381.75615.8578-4.29493.68920.1187-0.01-0.33-0.01310.15880.17250.2413-0.0682-0.28660.1045-0.03690.00230.13670.00410.165937.0261-23.868319.8848
140.6163-0.35120.2291.7599-1.57464.5025-0.0323-0.0531-0.07470.19370.14140.0234-0.1988-0.0604-0.08930.1007-0.03020.02150.1406-0.00490.105942.9189-17.552425.1198
150.1739-0.1818-0.51520.47920.64158.33130.05510.01920.06290.0972-0.00340.01280.1693-0.38110.00270.1043-0.02380.02070.1555-0.02020.092646.2143-14.933213.888
162.2162-0.5652-0.46834.64050.69044.42660.1110.0647-0.0081-0.1566-0.04090.5666-0.0341-0.4691-0.06140.134-0.0006-0.02620.1615-0.01320.24525.071-5.288526.4749
171.8981-2.3918-1.87034.92791.52793.0407-0.0951-0.26090.12440.09050.373-0.2492-0.21080.2951-0.19390.1503-0.0309-0.02020.1786-0.0290.15613.1081.643430.2313
183.5964-1.3950.13224.66611.47222.658-0.0045-0.10140.20720.31660.30710.4419-0.2681-0.2259-0.2610.18490.03410.04070.13740.05390.2147.8322-4.013231.1387
193.3249-1.2437-0.2064.68110.13022.10790.16520.3806-0.0712-0.3531-0.0053-0.37690.08310.3702-0.06860.1187-0.01980.00820.2191-0.03670.17857.2621-10.22817.4607
205.80960.6708-2.38513.97181.16593.70550.049-0.068-0.01830.25770.0078-0.3823-0.00140.2094-0.0640.1342-0.0535-0.03250.12960.0170.190158.7904-2.40615.0214
214.15490.87441.05195.1393-3.98737.9126-0.08560.17030.05420.0526-0.0399-0.2959-0.15440.08370.09240.1392-0.03030.01660.0864-0.01650.163256.34956.8512.1293
224.36091.6375-0.74213.5079-0.44232.4341-0.02370.05780.0955-0.18960.10340.2108-0.4075-0.1417-0.08750.17370.0136-0.01780.1493-0.00320.116949.54083.85035.4267
238.27492.2799-6.07073.3545-2.46886.5703-0.0143-0.01620.0999-0.13070.04990.018-0.07610.0878-0.05290.0968-0.0292-0.00750.1444-0.01690.098749.5097-2.38037.3852
243.1670.8628-1.88673.798-2.48476.5892-0.4482-1.0979-0.0381.08220.34630.82270.25280.7442-0.04640.362-0.00140.14720.8444-0.10240.424835.0292-4.023525.9368
253.7010.89870.36714.0178-0.39663.46170.0579-0.04930.2242-0.160.0811-0.3167-0.06420.3081-0.08140.1204-0.02350.0010.0995-0.03540.173153.8072-3.81937.7217
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 358 through 367 )
2X-RAY DIFFRACTION2chain 'B' and (resid 368 through 390 )
3X-RAY DIFFRACTION3chain 'B' and (resid 391 through 401 )
4X-RAY DIFFRACTION4chain 'B' and (resid 402 through 417 )
5X-RAY DIFFRACTION5chain 'B' and (resid 418 through 422 )
6X-RAY DIFFRACTION6chain 'B' and (resid 423 through 435 )
7X-RAY DIFFRACTION7chain 'B' and (resid 436 through 446 )
8X-RAY DIFFRACTION8chain 'B' and (resid 447 through 455 )
9X-RAY DIFFRACTION9chain 'B' and (resid 456 through 468 )
10X-RAY DIFFRACTION10chain 'D' and (resid 360 through 372 )
11X-RAY DIFFRACTION11chain 'D' and (resid 373 through 391 )
12X-RAY DIFFRACTION12chain 'D' and (resid 392 through 401 )
13X-RAY DIFFRACTION13chain 'D' and (resid 402 through 417 )
14X-RAY DIFFRACTION14chain 'D' and (resid 418 through 446 )
15X-RAY DIFFRACTION15chain 'D' and (resid 447 through 466 )
16X-RAY DIFFRACTION16chain 'A' and (resid 234 through 272 )
17X-RAY DIFFRACTION17chain 'A' and (resid 273 through 333 )
18X-RAY DIFFRACTION18chain 'A' and (resid 334 through 349 )
19X-RAY DIFFRACTION19chain 'C' and (resid 236 through 248 )
20X-RAY DIFFRACTION20chain 'C' and (resid 249 through 272 )
21X-RAY DIFFRACTION21chain 'C' and (resid 273 through 282 )
22X-RAY DIFFRACTION22chain 'C' and (resid 283 through 315 )
23X-RAY DIFFRACTION23chain 'C' and (resid 316 through 327 )
24X-RAY DIFFRACTION24chain 'C' and (resid 328 through 333 )
25X-RAY DIFFRACTION25chain 'C' and (resid 334 through 349 )

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