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- PDB-8ruv: HIF prolyl hydroxylase 2 (PHD2) T387I variant bound to Fe(III), 2... -

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Basic information

Entry
Database: PDB / ID: 8ruv
TitleHIF prolyl hydroxylase 2 (PHD2) T387I variant bound to Fe(III), 2-oxoglutarate (2OG) and Hypoxia-inducible Factor 2alpha (HIF2alpha)
Components
  • Egl nine homolog 1
  • Hypoxia-inducible Factor-2alpha
KeywordsOXIDOREDUCTASE / 2OG oxygenase / Prolyl hydroxylase / Oxygen sensing / 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 / Transcriptional regulation of pluripotent stem cells / regulation of protein neddylation / PTK6 Expression ...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 / Transcriptional regulation of pluripotent stem cells / regulation of protein neddylation / PTK6 Expression / intracellular oxygen homeostasis / labyrinthine layer development / regulation protein catabolic process at postsynapse / 2-oxoglutarate-dependent dioxygenase activity / norepinephrine metabolic process / heart trabecula formation / regulation of modification of postsynaptic structure / cardiac muscle tissue morphogenesis / surfactant homeostasis / L-ascorbic acid binding / epithelial cell maturation / Regulation of gene expression by Hypoxia-inducible Factor / response to nitric oxide / ventricular septum morphogenesis / blood vessel remodeling / regulation of angiogenesis / embryonic placenta development / regulation of neuron apoptotic process / visual perception / regulation of heart rate / Pexophagy / erythrocyte differentiation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / mitochondrion organization / negative regulation of DNA-binding transcription factor activity / lung development / mRNA transcription by RNA polymerase II / transcription coactivator binding / ferrous iron binding / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / multicellular organismal-level iron ion homeostasis / Neddylation / positive regulation of cold-induced thermogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / angiogenesis / cellular response to hypoxia / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / response to oxidative stress / intracellular iron ion homeostasis / DNA-binding transcription factor activity, RNA polymerase II-specific / response to hypoxia / postsynaptic density / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / intracellular membrane-bounded organelle / regulation of transcription by RNA polymerase II / chromatin / glutamatergic synapse / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / zinc ion binding / 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 / Prolyl 4-hydroxylase alpha subunit, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / Prolyl 4-hydroxylase, alpha subunit ...: / 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 / 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 signature. / Zinc finger, MYND-type / 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
2-OXOGLUTARIC ACID / : / Endothelial PAS domain-containing protein 1 / Egl nine homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsFiorini, G. / Schofield, C.J. / Arif, F. / Kibria, M.M.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R013829/1, BB/J001694/2, BB/L000121/1 United Kingdom
Cancer Research UKC8717/A18245 United Kingdom
Wellcome Trust091857/7/10/7 United Kingdom
Other governmentNewton Abraham Scholarship
CitationJournal: To Be Published
Title: Investigating gatekeeper residues in Prolyl hydroxylase 2
Authors: Fiorini, G. / Schofield, C.J.
History
DepositionJan 31, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release

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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: Hypoxia-inducible Factor-2alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8594
Polymers27,6572
Non-polymers2022
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.116, 42.956, 130.508
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Space group name HallP22ab(y,z,x)
Symmetry operation#1: x,y,z
#2: x+1/2,-y,-z+1/2
#3: -x,y,-z
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Egl nine homolog 1 / Hypoxia-inducible factor prolyl hydroxylase 2 / HIF-PH2 / HIF-prolyl hydroxylase 2 / HPH-2 / Prolyl ...Hypoxia-inducible factor prolyl hydroxylase 2 / HIF-PH2 / HIF-prolyl hydroxylase 2 / HPH-2 / Prolyl hydroxylase domain-containing protein 2 / PHD2 / SM-20


Mass: 25477.010 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 (E. coli)
References: UniProt: Q9GZT9, hypoxia-inducible factor-proline dioxygenase
#2: Protein/peptide Hypoxia-inducible Factor-2alpha / 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: 2180.430 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q99814
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 1.93 Å3/Da / Density % sol: 36.11 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop
Details: (10-35%) PEG 4K, 0.2 M ammonium acetate and 0.1 M sodium ammonium acetate trihydrate pH (4.1-5.6).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.66→65.25 Å / Num. obs: 26202 / % possible obs: 100 % / Redundancy: 13.2 % / Biso Wilson estimate: 20.68 Å2 / CC1/2: 1 / Net I/σ(I): 4.7
Reflection shellResolution: 1.66→1.69 Å / Num. unique obs: 1258 / CC1/2: 0.2

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
xia2data reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.66→65.25 Å / SU ML: 0.3229 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.5202
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2572 1285 4.95 %
Rwork0.238 24687 -
obs0.239 25972 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.44 Å2
Refinement stepCycle: LAST / Resolution: 1.66→65.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1827 0 11 135 1973
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00431943
X-RAY DIFFRACTIONf_angle_d0.75542647
X-RAY DIFFRACTIONf_chiral_restr0.0483282
X-RAY DIFFRACTIONf_plane_restr0.0055353
X-RAY DIFFRACTIONf_dihedral_angle_d6.2803283
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.66-1.730.45161460.46412534X-RAY DIFFRACTION94.33
1.73-1.810.40971490.41252704X-RAY DIFFRACTION99.83
1.81-1.90.33921150.35072724X-RAY DIFFRACTION99.68
1.9-2.020.32721360.28882724X-RAY DIFFRACTION99.9
2.02-2.180.2441410.23382735X-RAY DIFFRACTION99.9
2.18-2.390.2651480.21622759X-RAY DIFFRACTION99.86
2.39-2.740.22421380.22062774X-RAY DIFFRACTION99.97
2.74-3.450.27071500.21052777X-RAY DIFFRACTION99.97
3.45-65.250.2041620.19242956X-RAY DIFFRACTION99.97
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)
11.461728406860.1816568962150.2388990140541.510240643430.4264883809761.5627719405-0.0913195579957-0.0386076435631-0.136733218908-0.1477207259550.269566551372-0.1053254473590.0266090211198-0.0295321570517-0.1695632536540.188208159779-0.0137590833685-0.02184548238490.3567163481990.02870097628340.222273741215-7.7250148676611.882945051412.6428005115
20.57921187290.3674973268960.2273172449140.3719223457040.06293255440940.4568458986630.06055896360070.0192865746468-0.2483027664360.0368855874933-0.0253500023766-0.0135058168914-0.0009315540239650.140788080993-0.03676497486640.1809480889520.00626552157095-0.01529123355170.2357754831780.03195352598710.2288287234827.50498665799-2.2047000539318.2853113076
30.723052346336-0.323623613584-0.1779340572341.12191993840.1375377493751.213562020640.02272131847410.0540636989398-0.0138548874463-0.0294148237758-0.0361273556649-0.05612715145660.05245199038950.1531371708540.03904694527380.1555145337560.004987782369140.002386353485270.2658539592110.02766010750490.17662305271413.59102547049.3192877964813.9297597615
40.62998024266-0.03615447924650.1222824772320.756495050131-0.4409218049351.24145532761-0.0213002888741-0.191568488485-0.05384101941950.09462778807470.05897544387930.01053072847070.01443380354610.00704606115907-0.02271444832130.1556531509863.08598186056E-5-0.005526964151720.2931698325880.0146463262820.1733637691099.8013293555311.118242102424.4070496221
53.67014024891-1.70906340164-0.5769990202482.411707402470.5723529503062.122815731080.123547991293-0.724408610744-0.141470460792-0.007281524745010.1594734634790.638907776802-0.0248192558732-0.687240360566-0.1614293978780.2192910360090.02814998628460.0150836198140.4401448478810.02597706183170.244593815098-0.30415524202819.56733315228.7083564102
60.717902456496-0.4183324036710.02887412645790.497863627953-0.003064126099820.487778159599-0.0388510393199-0.1351490957420.02754502890790.0256553406723-0.0297759824046-0.01640715515580.007808401824160.0322260321940.05799265514010.176976605647-0.0268432038773-0.02507054362470.228881182120.007214657815760.1780539967665.112829289512.359927588724.3358899612
70.557878399995-0.0126630307612-0.3519477738471.25163465702-1.048458771011.111765221340.06307175811990.04668777813510.0400168172605-0.02399769954470.04652754542120.09768403648330.0278514103082-0.0133960927009-0.05995760795930.18683173148-0.019454150525-0.001330030405970.2562090081040.01511829949360.1835127970613.6193565217.902727901910.4160793893
82.54201538144-0.1621357439090.3088099790521.12261736676-0.7062920798132.48985485193-0.0323733651816-0.5099209752650.6218806361360.03704250755660.01989089163320.0110754082273-0.524929094808-0.09108573360810.04148511185250.237017572885-0.021501055407-0.001718620438640.525378478613-0.005649364758360.30433269665217.449261259326.370951377122.5599387774
90.234093817090.106155839063-0.5828097576690.7086646560.282134228141.94529011828-0.1407738079720.18217483586-0.25492869182-0.3641903864460.302368283491-0.315877150919-0.5208077413430.124433227063-0.1115393405770.210514163053-0.02374458190650.01774629066130.3828954341770.004657780815930.22516030741816.757711886815.4755181897.57943716649
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 189 through 205 )AA189 - 2051 - 17
22chain 'A' and (resid 206 through 231 )AA206 - 23118 - 43
33chain 'A' and (resid 232 through 304 )AA232 - 30444 - 116
44chain 'A' and (resid 305 through 342 )AA305 - 342117 - 154
55chain 'A' and (resid 343 through 353 )AA343 - 353155 - 165
66chain 'A' and (resid 354 through 381 )AA354 - 381166 - 193
77chain 'A' and (resid 382 through 406 )AA382 - 406194 - 218
88chain 'B' and (resid 524 through 529 )BB524 - 5291 - 6
99chain 'B' and (resid 530 through 542 )BB530 - 5427 - 19

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