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- PDB-8rv1: HIF prolyl hydroxylase 2 (PHD2) T387S variant bound to acetate (A... -

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Basic information

Entry
Database: PDB / ID: 8rv1
TitleHIF prolyl hydroxylase 2 (PHD2) T387S variant bound to acetate (ACT) and hydroxylated Hypoxia-inducible Factor 2alpha (HIF2alpha)
Components
  • Egl nine homolog 1
  • Endothelial PAS domain-containing protein 1
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
ACETATE ION / Endothelial PAS domain-containing protein 1 / Egl nine homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 Å
AuthorsFiorini, G. / Schofield, C.J.
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 hydroxyalse 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

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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)27,8954
Polymers27,7762
Non-polymers1182
Water4,900272
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)130.760, 38.120, 42.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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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: 25450.930 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 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: 2325.544 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q99814
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / Source method: isolated from a natural source / Formula: H2O
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: 35.34 %
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: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.39→43.59 Å / Num. obs: 43632 / % possible obs: 100 % / Redundancy: 12.4 % / Biso Wilson estimate: 18.54 Å2 / CC1/2: 1 / Net I/σ(I): 14.5
Reflection shellResolution: 1.39→1.41 Å / Num. unique obs: 2103 / CC1/2: 0.3

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
xia2data reduction
d*TREKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.39→42.4 Å / SU ML: 0.1734 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.8175
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1914 2143 4.92 %
Rwork0.1728 41425 -
obs0.1737 43568 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.03 Å2
Refinement stepCycle: LAST / Resolution: 1.39→42.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1841 0 8 272 2121
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01181943
X-RAY DIFFRACTIONf_angle_d1.30612639
X-RAY DIFFRACTIONf_chiral_restr0.0939282
X-RAY DIFFRACTIONf_plane_restr0.0132348
X-RAY DIFFRACTIONf_dihedral_angle_d6.5158279
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.39-1.420.35471440.31782652X-RAY DIFFRACTION97.76
1.42-1.460.32011510.27452719X-RAY DIFFRACTION100
1.46-1.50.26741240.23882726X-RAY DIFFRACTION100
1.5-1.540.26471460.22872716X-RAY DIFFRACTION100
1.54-1.590.25461380.20782733X-RAY DIFFRACTION100
1.59-1.650.25541470.20212718X-RAY DIFFRACTION100
1.65-1.710.23661240.1882746X-RAY DIFFRACTION100
1.71-1.790.21661550.17692749X-RAY DIFFRACTION100
1.79-1.890.20721420.16512737X-RAY DIFFRACTION100
1.89-20.18161380.16652770X-RAY DIFFRACTION100
2-2.160.21551370.15742765X-RAY DIFFRACTION100
2.16-2.380.19151630.16082779X-RAY DIFFRACTION99.97
2.38-2.720.17031240.16812813X-RAY DIFFRACTION99.9
2.72-3.430.18061500.1652817X-RAY DIFFRACTION100
3.43-42.40.15661600.16132985X-RAY DIFFRACTION99.87
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)
11.25747416834-1.04370958266-0.04805857714673.094748675731.695636650674.3013251354-0.151233660169-0.0985232250371-0.1846435977540.2454191966520.06740645603550.02856949357220.2789854983310.3534615264230.09138525243790.1326672749250.01465945615080.0257740856130.1508561455940.04414790630380.161749256792-14.3971036206-5.71652814913-9.52082323087
21.18460241677-0.0597069479741.396648534727.7511779755-4.275559441574.15053053972-0.100814050472-0.270827571260.05934973149990.7414109336230.2068304040250.06497728006210.09398525649780.173550918398-0.154991515470.301746854180.04525276430560.06528131867520.245282959572-0.02608845401140.119807801512-18.496651112.58451997455.81111407406
32.2673048741-1.721146341050.2111685679723.19211983127-0.1834954943851.85360167433-0.0288786281955-0.100115033750.1110611966560.1274215705740.0515256366498-0.0551067592853-0.09893414665270.0764081584438-0.002053248147620.0819007361088-0.01793694137140.02377322848330.1180481282210.002348771690860.109526568212-14.880479749315.464510866-8.16955979818
43.52841749334-2.58072065221-1.43502109224.870129270032.562716372022.235976404270.00398598516788-0.0357270479785-0.00243016315679-0.03632121412760.088929838926-0.148258871136-0.03651408614340.117377075695-0.1279331559570.1388951442510.0129876059246-0.005657280714330.1432337900130.04730653708350.0928694481174-11.4497857268.1227106097-13.5184289256
53.56683027607-0.468315113123-1.564591340081.358304401560.05134064917062.62401220219-0.0273281100475-0.0301372772549-0.01029277746070.08589365502510.01054003586790.2017888314130.0578968613734-0.1585193592770.01201724685820.103754507713-0.01861288897670.01159032371640.0919789533096-0.01103332274860.137166359339-24.60673694149.61394005193-11.1876360267
65.272745018010.9268303902871.029573865154.790148493994.364956328543.949250463550.02802253400140.236599259929-0.733886494547-0.411273186158-0.0710684663665-0.108199929578-0.0195930998252-0.2544515883940.05469923707130.188622520598-0.01016843281440.0216165932570.166899960966-0.0121257273240.289447213168-28.6075326670.0197671230763-19.6224126916
71.49836283175-0.2502704913010.338563586041.465726817570.3130125032324.125511604730.0175127854926-0.14637035913-0.07214334282870.1462596674420.05019100256310.1973339545910.106683961244-0.0414071771156-0.05988676737530.1405694222350.00563539938650.01539269754540.1150699558010.02172768063860.16729140039-21.70782354552.31250687596-9.86413339734
86.76021276446-3.33050899117-5.442835009964.426349831845.269155568598.767325116040.1512335250210.0893289639981-0.0728464973619-0.167550316927-0.1746814756380.371755975134-0.299633909604-0.2241386223050.003388248411840.1062817646130.01593310479420.01004982638980.1104215719490.04281180592120.167492030471-28.13881234878.52229220452-15.8923051569
95.920924593681.24913105216-5.655821580671.01831678933-1.28646208497.07486777517-0.02330424026840.1661294697730.185025921636-0.07008720084970.0924226428495-0.0155475334245-0.06808127665720.0272809469926-0.06905809797070.100062174401-0.0106054573616-0.01251935316310.1214810428720.007094163589630.12361144325-10.400323082213.6501186463-18.2890692149
106.10713737953-0.367280460086-2.232746787365.084319803864.198739471344.06951819732-0.09939243164161.12946078087-0.14819079005-1.498861081050.166126743790.172169491031-0.708793158481-0.5993977507020.118824040490.338656428672-0.0243224240212-0.0188014716340.2987423111160.0143292867260.184115857024-23.997551638416.7072965266-28.2021990836
115.69954298251-2.719752772423.802501810041.29723966242-1.841837541062.540137877-0.4119551389740.5515846905730.8924493975340.199502841443-0.118467184127-0.542474161705-0.3385735328240.4993909781010.4954540631510.177077121274-0.0253809600904-0.04823562527520.2157474270820.03651803904390.291865042379-8.1158022933416.3858489139-15.6304847072
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 188 through 215 )AA188 - 2151 - 28
22chain 'A' and (resid 216 through 231 )AA216 - 23129 - 44
33chain 'A' and (resid 232 through 283 )AA232 - 28345 - 96
44chain 'A' and (resid 284 through 304 )AA284 - 30497 - 117
55chain 'A' and (resid 305 through 342 )AA305 - 342118 - 155
66chain 'A' and (resid 343 through 353 )AA343 - 353156 - 166
77chain 'A' and (resid 354 through 369 )AA354 - 369167 - 182
88chain 'A' and (resid 370 through 381 )AA370 - 381183 - 194
99chain 'A' and (resid 382 through 406 )AA382 - 406195 - 219
1010chain 'B' and (resid 523 through 529 )BD523 - 5291 - 7
1111chain 'B' and (resid 530 through 542 )BD530 - 5428 - 20

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