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- PDB-8q6d: Anaerobic crystal structure of HIF prolyl hydroxylase 2 (PHD2 181... -

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Basic information

Entry
Database: PDB / ID: 8q6d
TitleAnaerobic crystal structure of HIF prolyl hydroxylase 2 (PHD2 181-407) in complex with HIF2alpha-CODD peptide (523-542), Fe(II) and 2-oxoglutarate (2OG)
Components
  • Egl nine homolog 1
  • Endothelial PAS domain-containing protein 1
KeywordsOXIDOREDUCTASE / 2OG oxygenases / oxygen sensor / jelly-roll
Function / homology
Function and homology information


myoblast fate commitment / hypoxia-inducible factor-proline dioxygenase activity / hypoxia-inducible factor-proline dioxygenase / peptidyl-proline 4-dioxygenase activity / peptidyl-proline dioxygenase activity / negative regulation of cyclic-nucleotide phosphodiesterase activity / regulation protein catabolic process at postsynapse / Cellular response to hypoxia / regulation of protein neddylation / Transcriptional regulation of pluripotent stem cells ...myoblast fate commitment / hypoxia-inducible factor-proline dioxygenase activity / hypoxia-inducible factor-proline dioxygenase / peptidyl-proline 4-dioxygenase activity / peptidyl-proline dioxygenase activity / negative regulation of cyclic-nucleotide phosphodiesterase activity / regulation protein catabolic process at postsynapse / Cellular response to hypoxia / regulation of protein neddylation / Transcriptional regulation of pluripotent stem cells / PTK6 Expression / intracellular oxygen homeostasis / labyrinthine layer development / norepinephrine metabolic process / 2-oxoglutarate-dependent dioxygenase activity / cardiac muscle tissue morphogenesis / heart trabecula formation / regulation of modification of postsynaptic structure / surfactant homeostasis / L-ascorbic acid binding / epithelial cell maturation / Regulation of gene expression by Hypoxia-inducible Factor / embryonic placenta development / response to nitric oxide / ventricular septum morphogenesis / blood vessel remodeling / regulation of angiogenesis / visual perception / Pexophagy / regulation of heart rate / erythrocyte differentiation / lung development / mitochondrion organization / mRNA transcription by RNA polymerase II / RNA polymerase II transcription regulatory region sequence-specific DNA binding / ferrous iron binding / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / negative regulation of DNA-binding transcription factor activity / transcription coactivator binding / multicellular organismal-level iron ion homeostasis / cellular response to hypoxia / Neddylation / positive regulation of cold-induced thermogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / angiogenesis / intracellular iron ion homeostasis / RNA polymerase II-specific DNA-binding transcription factor binding / response to oxidative stress / postsynaptic density / DNA-binding transcription factor activity, RNA polymerase II-specific / response to hypoxia / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / intracellular membrane-bounded organelle / glutamatergic synapse / regulation of transcription by RNA polymerase II / chromatin / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm / cytosol
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 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. / 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: 1.4 Å
AuthorsFiorini, G. / Figg Jr, W.D. / Schofield, C.J.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
University of Oxford, Medical Sciences Internal Fund (MSIF) United Kingdom
Cancer Research UK United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: To Be Published
Title: HIF prolyl hydroxylase 2 in complex with HIF2alpha-CODD
Authors: Fiorini, G. / Figg Jr, W.D. / Schofield, C.J.
History
DepositionAug 11, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2024Provider: 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: Endothelial PAS domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5484
Polymers28,3462
Non-polymers2022
Water4,216234
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2980 Å2
ΔGint-24 kcal/mol
Surface area10780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.070, 42.630, 130.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

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Components

#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-Gold(DE3)pLysS AG' (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
#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: isolated from a natural source / Formula: C5H6O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.86 Å3/Da / Density % sol: 34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 10-35% PEG 4K, 0.2 ammonium acetate, 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: I24 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 17, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.4→38.07 Å / Num. obs: 42651 / % possible obs: 99.4 % / Redundancy: 12.6 % / CC1/2: 1 / Net I/σ(I): 19.7
Reflection shellResolution: 1.4→1.42 Å / Num. unique obs: 1834 / CC1/2: 0.8

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
DIALSdata scaling
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→36.55 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1899 2097 4.92 %
Rwork0.1671 --
obs0.1682 42585 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→36.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1844 0 11 234 2089
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051954
X-RAY DIFFRACTIONf_angle_d0.8992659
X-RAY DIFFRACTIONf_dihedral_angle_d6.519283
X-RAY DIFFRACTIONf_chiral_restr0.074284
X-RAY DIFFRACTIONf_plane_restr0.011353
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.430.25991220.25342401X-RAY DIFFRACTION89
1.43-1.470.24251440.21392681X-RAY DIFFRACTION100
1.47-1.510.23341290.18942650X-RAY DIFFRACTION100
1.51-1.550.2071460.18222655X-RAY DIFFRACTION100
1.55-1.60.18261570.17132691X-RAY DIFFRACTION100
1.6-1.660.22161330.17432671X-RAY DIFFRACTION100
1.66-1.730.2171350.17382721X-RAY DIFFRACTION100
1.73-1.810.20931490.16952675X-RAY DIFFRACTION100
1.81-1.90.18641500.16372700X-RAY DIFFRACTION100
1.9-2.020.17751450.15782695X-RAY DIFFRACTION100
2.02-2.180.16191320.15292717X-RAY DIFFRACTION100
2.18-2.390.17511400.15222749X-RAY DIFFRACTION100
2.39-2.740.17941450.1652738X-RAY DIFFRACTION100
2.74-3.450.20091240.16812806X-RAY DIFFRACTION100
3.45-36.550.18551460.16632938X-RAY DIFFRACTION100
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)
18.52831.78490.18627.20570.42892.12750.2477-0.34831.09910.23260.12570.2319-0.6367-0.1964-0.39670.25370.05030.10850.24980.0330.3045-7.9163-6.1611-9.4118
21.9513-0.4845-0.14110.51280.05351.01680.14890.11240.44140.1198-0.0440.091-0.2631-0.0481-0.10580.18580.02650.04550.13420.03730.16343.5264-3.1106-17.6085
32.476-0.3164-1.26671.61350.12472.14450.0786-0.01210.20030.0901-0.0269-0.1343-0.17660.1555-0.06260.1322-0.00740.00630.13690.03470.128915.6015-8.1445-15.0762
43.7111.7133-1.36422.4256-1.47313.53870.1145-0.12830.02070.1067-0.11590.0317-0.07090.0328-0.02420.12630.03490.01830.0639-0.00780.13677.6584-13.2904-11.5058
51.29180.4308-0.33211.9983-1.40093.01310.00120.25240.0838-0.14270.03670.0873-0.01810.0022-0.00640.10580.00560.00670.15520.03390.12189.5887-11.2559-24.4803
67.91026.90011.8359.20560.9965.57840.0440.1835-0.1073-0.06960.03820.09170.0637-0.5737-0.06980.13310.0289-0.00180.2672-0.00430.1341-0.4013-19.6167-28.7998
71.95820.8383-0.5713.0029-0.52352.27860.03170.27570.0388-0.0496-0.05220.0955-0.1121-0.07740.02670.09080.021-0.00480.16150.02690.10214.8772-12.3557-24.4116
81.0759-1.32311.45776.3012-4.90115.47670.05620.0441-0.03350.0957-0.0305-0.06580.08550.1106-0.01470.13550.00670.00710.1514-0.00150.133913.5711-18.2651-10.432
96.8734.336-0.20013.7525-0.64832.2247-0.09580.4856-1.3282-0.81340.0689-0.67021.02170.0463-0.12130.33780.03790.00860.1956-0.05040.338216.6237-28.2832-23.8607
103.2932-3.3528-4.10983.45614.44336.6455-0.1987-0.56180.22760.50970.5502-0.41360.51521.002-0.29280.23070.0175-0.02920.2856-0.03950.211216.6499-16.1044-8.0221
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 187 through 197 )
2X-RAY DIFFRACTION2chain 'A' and (resid 198 through 231 )
3X-RAY DIFFRACTION3chain 'A' and (resid 232 through 282 )
4X-RAY DIFFRACTION4chain 'A' and (resid 283 through 304 )
5X-RAY DIFFRACTION5chain 'A' and (resid 305 through 342 )
6X-RAY DIFFRACTION6chain 'A' and (resid 343 through 353 )
7X-RAY DIFFRACTION7chain 'A' and (resid 354 through 381 )
8X-RAY DIFFRACTION8chain 'A' and (resid 382 through 406 )
9X-RAY DIFFRACTION9chain 'B' and (resid 523 through 529 )
10X-RAY DIFFRACTION10chain 'B' and (resid 530 through 542 )

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