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- PDB-4wn5: Crystal structure of the C-terminal Per-Arnt-Sim (PASb) of human ... -

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Basic information

Entry
Database: PDB / ID: 4wn5
TitleCrystal structure of the C-terminal Per-Arnt-Sim (PASb) of human HIF-3alpha9 bound to 18:1-1-monoacylglycerol
ComponentsHypoxia-inducible factor 3-alpha
KeywordsTRANSCRIPTION / HIF-3alpha / PAS domain / monoacylglycerol / lipid / fatty acid
Function / homology
Function and homology information


: / Transcriptional regulation of pluripotent stem cells / chromatin => GO:0000785 / Regulation of gene expression by Hypoxia-inducible Factor / post-translational protein modification / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Neddylation / angiogenesis / transcription by RNA polymerase II / protein ubiquitination ...: / Transcriptional regulation of pluripotent stem cells / chromatin => GO:0000785 / Regulation of gene expression by Hypoxia-inducible Factor / post-translational protein modification / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Neddylation / angiogenesis / transcription by RNA polymerase II / protein ubiquitination / protein dimerization activity / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / apoptotic process / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion / nucleoplasm / nucleus / plasma membrane / cytosol
Similarity search - Function
Hypoxia-inducible factor, alpha subunit-like / Hypoxia-inducible factor-1 / PAS fold-3 / PAS fold / 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 ...Hypoxia-inducible factor, alpha subunit-like / Hypoxia-inducible factor-1 / PAS fold-3 / PAS fold / 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. / 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
MONOVACCENIN / Hypoxia-inducible factor 3-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsFala, A.M. / Oliveira, J.F. / Dias, S.M. / Ambrosio, A.L.
Funding support Brazil, 4items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2012/14298-9 Brazil
Sao Paulo Research Foundation (FAPESP)2009/10875-9 Brazil
Sao Paulo Research Foundation (FAPESP)2010/13739-6 Brazil
Sao Paulo Research Foundation (FAPESP)2014/04927-4 Brazil
CitationJournal: Sci Rep / Year: 2015
Title: Unsaturated fatty acids as high-affinity ligands of the C-terminal Per-ARNT-Sim domain from the Hypoxia-inducible factor 3 alpha.
Authors: Fala, A.M. / Oliveira, J.F. / Adamoski, D. / Aricetti, J.A. / Dias, M.M. / Dias, M.V.B. / Sforca, M.L. / Lopes-de-Oliveira, P.S. / Rocco, S.A. / Caldana, C. / Dias, S.M.G. / Ambrosio, A.L.B.
History
DepositionOct 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Advisory / Data collection / Derived calculations
Category: diffrn_source / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 13, 2019Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 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
A: Hypoxia-inducible factor 3-alpha
B: Hypoxia-inducible factor 3-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,35911
Polymers25,0422
Non-polymers2,3179
Water5,314295
1
B: Hypoxia-inducible factor 3-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5385
Polymers12,5211
Non-polymers1,0174
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Hypoxia-inducible factor 3-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8216
Polymers12,5211
Non-polymers1,3005
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.650, 53.890, 67.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11A-405-

P6G

21B-403-

P6G

31B-404-

P6G

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Components

#1: Protein Hypoxia-inducible factor 3-alpha / HIF3-alpha / Basic-helix-loop-helix-PAS protein MOP7 / Class E basic helix-loop-helix protein 17 / ...HIF3-alpha / Basic-helix-loop-helix-PAS protein MOP7 / Class E basic helix-loop-helix protein 17 / bHLHe17 / HIF3-alpha-1 / Inhibitory PAS domain protein / IPAS / Member of PAS protein 7 / PAS domain-containing protein 7


Mass: 12520.955 Da / Num. of mol.: 2 / Fragment: unp residues 235-345
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIF3A, BHLHE17, MOP7, PASD7 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-2 / References: UniProt: Q9Y2N7
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MVC / MONOVACCENIN / 11.7 MAG


Mass: 356.540 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H40O4
#4: Chemical
ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 295 / 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: 1.92 Å3/Da / Density % sol: 36.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.9
Details: 3% PEG 400, 1.95 M ammonium sulfate, 0.1 M sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97724 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97724 Å / Relative weight: 1
ReflectionResolution: 1.15→28.5 Å / Num. obs: 68827 / % possible obs: 99.6 % / Redundancy: 9.8 % / Net I/σ(I): 11.5
Reflection shellResolution: 1.15→1.17 Å / Redundancy: 9.1 % / % possible all: 99.4

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4h6j

4h6j


Resolution: 1.15→28.5 Å / SU ML: 0.06 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 10.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1408 6669 5.07 %
Rwork0.1216 --
obs0.1226 68827 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.15→28.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1637 0 155 295 2087
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111871
X-RAY DIFFRACTIONf_angle_d1.7222494
X-RAY DIFFRACTIONf_dihedral_angle_d13.735737
X-RAY DIFFRACTIONf_chiral_restr0.433262
X-RAY DIFFRACTIONf_plane_restr0.007303
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.15-1.16310.14672170.1074190X-RAY DIFFRACTION99
1.1631-1.17680.11232020.10784151X-RAY DIFFRACTION98
1.1768-1.19110.13252050.1054174X-RAY DIFFRACTION99
1.1911-1.20620.14732140.1014130X-RAY DIFFRACTION99
1.2062-1.22210.1441900.10394192X-RAY DIFFRACTION99
1.2221-1.23880.12682450.10764145X-RAY DIFFRACTION99
1.2388-1.25650.12592160.10834166X-RAY DIFFRACTION99
1.2565-1.27520.13972600.10454163X-RAY DIFFRACTION100
1.2752-1.29520.12612330.10944104X-RAY DIFFRACTION99
1.2952-1.31640.14542410.1094153X-RAY DIFFRACTION99
1.3164-1.33910.1231730.10534152X-RAY DIFFRACTION99
1.3391-1.36350.12852410.10474191X-RAY DIFFRACTION99
1.3635-1.38970.14352300.10794163X-RAY DIFFRACTION99
1.3897-1.4180.11332170.10844178X-RAY DIFFRACTION99
1.418-1.44890.12632220.11014185X-RAY DIFFRACTION100
1.4489-1.48260.15292310.10474131X-RAY DIFFRACTION100
1.4826-1.51970.12672620.09794117X-RAY DIFFRACTION100
1.5197-1.56070.11972360.10284209X-RAY DIFFRACTION100
1.5607-1.60670.14032240.1094152X-RAY DIFFRACTION99
1.6067-1.65850.12152120.10744125X-RAY DIFFRACTION99
1.6585-1.71780.12842180.10784213X-RAY DIFFRACTION100
1.7178-1.78660.14832270.11264150X-RAY DIFFRACTION100
1.7866-1.86780.11822490.11614187X-RAY DIFFRACTION100
1.8678-1.96630.1362400.11614168X-RAY DIFFRACTION100
1.9663-2.08950.15021890.11764241X-RAY DIFFRACTION100
2.0895-2.25070.14712380.12044089X-RAY DIFFRACTION98
2.2507-2.47710.15092100.12794156X-RAY DIFFRACTION99
2.4771-2.83530.15461620.14514247X-RAY DIFFRACTION100
2.8353-3.57110.15862190.13784199X-RAY DIFFRACTION100
3.5711-28.50860.15052460.15294090X-RAY DIFFRACTION98

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