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- PDB-7q5v: HIF PROLYL HYDROXYLASE 2 (PHD2/EGLN1) IN COMPLEX WITH N-OXALYLGLY... -

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Basic information

Entry
Database: PDB / ID: 7q5v
TitleHIF PROLYL HYDROXYLASE 2 (PHD2/EGLN1) IN COMPLEX WITH N-OXALYLGLYCINE (NOG) AND HIF-2 ALPHA CODD (523-542)
Components
  • Egl nine homolog 1
  • Endothelial PAS domain-containing protein 1
KeywordsOXIDOREDUCTASE / PHD2 / HIF-2Alpha / Complex / Hypoxia
Function / homology
Function and homology information


myoblast fate commitment / peptidyl-proline 4-dioxygenase activity / hypoxia-inducible factor-proline dioxygenase activity / hypoxia-inducible factor-proline dioxygenase / peptidyl-proline dioxygenase activity / negative regulation of cyclic-nucleotide phosphodiesterase activity / Cellular response to hypoxia / regulation protein catabolic process at postsynapse / regulation of protein neddylation / Transcriptional regulation of pluripotent stem cells ...myoblast fate commitment / peptidyl-proline 4-dioxygenase activity / hypoxia-inducible factor-proline dioxygenase activity / hypoxia-inducible factor-proline dioxygenase / peptidyl-proline dioxygenase activity / negative regulation of cyclic-nucleotide phosphodiesterase activity / Cellular response to hypoxia / regulation protein catabolic process at postsynapse / regulation of protein neddylation / Transcriptional regulation of pluripotent stem cells / PTK6 Expression / intracellular oxygen homeostasis / labyrinthine layer development / cardiac muscle tissue morphogenesis / norepinephrine metabolic process / heart trabecula formation / regulation of modification of postsynaptic structure / 2-oxoglutarate-dependent dioxygenase activity / surfactant homeostasis / L-ascorbic acid binding / epithelial cell maturation / Regulation of gene expression by Hypoxia-inducible Factor / response to nitric oxide / ventricular septum morphogenesis / embryonic placenta development / blood vessel remodeling / regulation of angiogenesis / regulation of heart rate / visual perception / Pexophagy / erythrocyte differentiation / mitochondrion organization / RNA polymerase II transcription regulatory region sequence-specific DNA binding / lung development / mRNA transcription by RNA polymerase II / ferrous iron binding / negative regulation of DNA-binding transcription factor activity / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / transcription coactivator binding / multicellular organismal-level iron ion homeostasis / positive regulation of cold-induced thermogenesis / Neddylation / cellular response to hypoxia / DNA-binding transcription activator activity, RNA polymerase II-specific / angiogenesis / intracellular iron ion homeostasis / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / response to oxidative stress / postsynaptic density / 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 / intracellular membrane-bounded organelle / glutamatergic synapse / chromatin / regulation of transcription by RNA polymerase II / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol / 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 / Prolyl 4-hydroxylase alpha subunit, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / Prolyl 4-hydroxylase, alpha subunit / Prolyl 4-hydroxylase alpha subunit homologues. ...: / 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 / Prolyl 4-hydroxylase alpha subunit, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / Prolyl 4-hydroxylase, alpha subunit / Prolyl 4-hydroxylase alpha subunit homologues. / MYND finger / Zinc finger, MYND-type / Zinc finger MYND-type signature. / Zinc finger MYND-type profile. / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile. / 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
FORMIC ACID / : / N-OXALYLGLYCINE / DI(HYDROXYETHYL)ETHER / Endothelial PAS domain-containing protein 1 / Egl nine homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.17 Å
AuthorsFigg Jr, W.D. / McDonough, M.A. / Chowdhury, R. / Nakashima, Y. / Schofield, C.J.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust106244/Z/14/Z United Kingdom
Cancer Research UK United Kingdom
CitationJournal: Proteins / Year: 2023
Title: Structural basis for binding of the renal carcinoma target hypoxia-inducible factor 2 alpha to prolyl hydroxylase domain 2.
Authors: Figg Jr., W.D. / Fiorini, G. / Chowdhury, R. / Nakashima, Y. / Tumber, A. / McDonough, M.A. / Schofield, C.J.
History
DepositionNov 4, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Egl nine homolog 1
B: Endothelial PAS domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,20515
Polymers28,3462
Non-polymers85913
Water4,720262
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint-46 kcal/mol
Surface area11310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.914, 38.322, 42.880
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Egl nine homolog 1 / Hypoxia-inducible factor prolyl hydroxylase 2 / HPH-2 / Prolyl hydroxylase domain-containing ...Hypoxia-inducible factor prolyl hydroxylase 2 / HPH-2 / Prolyl hydroxylase domain-containing protein 2 / PHD2 / SM-20


Mass: 26036.582 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EGLN1, C1orf12, PNAS-118, PNAS-137 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9GZT9, hypoxia-inducible factor-proline dioxygenase
#2: Protein/peptide 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 / HIF-2-alpha / HIF2-alpha / Member of PAS protein 2 / PAS domain-containing protein 2


Mass: 2309.544 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q99814

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Non-polymers , 8 types, 275 molecules

#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-OGA / N-OXALYLGLYCINE


Mass: 147.086 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H5NO5 / Feature type: SUBJECT OF INVESTIGATION / Comment: inhibitor*YM
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 1.9 Å3/Da / Density % sol: 35.17 % / Description: Rod
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Sample: 1.0 mM PHD2, 1.2 mM MnCl2, 2.0 mM NOG, 2 mM 3C, 2-4 mM HIF-2alpha-CODD; Reservoir: 0.31 M Magnesium formate (range: 0.25-0.39 M), 16.6% w/v polyethylene glycol 3350 (range: 18-22%); ...Details: Sample: 1.0 mM PHD2, 1.2 mM MnCl2, 2.0 mM NOG, 2 mM 3C, 2-4 mM HIF-2alpha-CODD; Reservoir: 0.31 M Magnesium formate (range: 0.25-0.39 M), 16.6% w/v polyethylene glycol 3350 (range: 18-22%); Sitting drop (200 nl): protein-to-well ratio, 1:1; Cryo-protectant: 15% v/v dilution of reservoir with glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96861 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 9, 2019
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96861 Å / Relative weight: 1
ReflectionResolution: 1.17→43.64 Å / Num. obs: 73796 / % possible obs: 99.9 % / Redundancy: 23.9 % / Biso Wilson estimate: 13.75 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1467 / Rpim(I) all: 0.03 / Rrim(I) all: 0.15 / Net I/σ(I): 11.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) all% possible all
1.17-1.1915.43.8711.135400.390.7491.0464.26997.1
3.17-43.6723.637.340040.0140.07100

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.44 Å42.88 Å
Translation5.44 Å42.88 Å

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
xia20.5.769data reduction
DIALS1.12.5data scaling
PHASER2.8.2phasing
Coot0.9.6model building
MolProbity4.5.1model building
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HQR

3hqr


Resolution: 1.17→42.88 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 18.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1792 3747 5.09 %
Rwork0.157 69907 -
obs0.158 73654 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.29 Å2 / Biso mean: 23.6567 Å2 / Biso min: 6.54 Å2
Refinement stepCycle: final / Resolution: 1.17→42.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1909 0 94 277 2280
Biso mean--56.04 32.83 -
Num. residues----243
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.17-1.180.3071300.31092435256596
1.18-1.20.31881290.30912542267198
1.2-1.220.30681190.286925502669100
1.22-1.230.29731540.285125632717100
1.23-1.250.24391450.266925562701100
1.25-1.270.26861320.250225562688100
1.27-1.290.23791250.246825502675100
1.29-1.320.24821640.223225342698100
1.32-1.340.24741450.217825852730100
1.34-1.360.23241460.208125482694100
1.36-1.390.20791270.202625742701100
1.39-1.420.2041460.196825842730100
1.42-1.460.21331440.18625122656100
1.46-1.490.20971410.189725952736100
1.49-1.530.20751210.183826302751100
1.53-1.580.18081270.166825612688100
1.58-1.630.18741440.156725792723100
1.63-1.690.18691260.159126052731100
1.69-1.750.21211570.154825692726100
1.75-1.830.19111490.14526012750100
1.83-1.930.15141530.146125932746100
1.93-2.050.16261410.141326102751100
2.05-2.210.15351530.136626192772100
2.21-2.430.14361210.13326412762100
2.43-2.790.15931380.135726492787100
2.79-3.510.15881340.132227162850100
3.51-42.880.1611360.139528502986100
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)
16.95794.2682-3.58677.802-1.63482.1313-0.3015-0.91010.28930.96640.0480.0382-0.32890.17310.30170.25480.102-0.01880.2824-0.0680.22129.552526.725916.9036
21.322-0.58930.2152.0044-0.35171.2035-0.0582-0.1439-0.11420.15080.1007-0.03550.0707-0.0323-0.04130.07860.0064-0.0220.11770.00260.106418.86456.419413.9396
32.429-0.5775-0.02651.1761-0.13470.7089-0.0545-0.05330.0240.0540.06220.0349-0.0456-0.0844-0.00470.09080.0102-0.01440.0899-0.0070.091213.250311.46489.359
43.4010.66090.10182.1372-1.08694.3044-0.0164-0.05070.17490.11560.0057-0.2111-0.26140.1677-0.00610.0911-0.0066-0.03180.0649-0.03250.172530.056215.534612.1641
52.3613-0.76270.46121.556-0.59822.4077-0.0174-0.060.10640.0150.017-0.1769-0.11080.0799-0.00840.0841-0.0152-0.01750.0618-0.00940.113424.671514.11019.0196
64.52891.20573.84691.32970.94935.3005-0.05810.2062-0.1334-0.13640.08510.0380.0775-0.0439-0.05170.0855-0.01070.00650.0978-0.00980.096410.2435.03981.9494
74.92751.6357-2.58035.1947-4.57194.85190.00941.2414-0.013-1.42830.1017-0.41940.62010.7370.04460.3357-00.06160.3481-0.03360.195124.10912.9201-7.2898
85.75940.0934-2.20140.90940.03451.0438-0.33390.1698-0.87630.11370.01810.2580.1621-0.21190.30430.1179-0.0120.0260.1491-0.01630.21846.8311.72376.0215
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 185 through 197 )A185 - 197
2X-RAY DIFFRACTION2chain 'A' and (resid 198 through 266 )A198 - 266
3X-RAY DIFFRACTION3chain 'A' and (resid 267 through 329 )A267 - 329
4X-RAY DIFFRACTION4chain 'A' and (resid 330 through 353 )A330 - 353
5X-RAY DIFFRACTION5chain 'A' and (resid 354 through 381 )A354 - 381
6X-RAY DIFFRACTION6chain 'A' and (resid 382 through 407 )A382 - 407
7X-RAY DIFFRACTION7chain 'B' and (resid 523 through 529 )B523 - 529
8X-RAY DIFFRACTION8chain 'B' and (resid 530 through 542 )B530 - 542

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