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- PDB-6yw3: HIF PROLYL HYDROXYLASE 2 (PHD2/ EGLN1) in complex with N-Oxalyl G... -

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Basic information

Entry
Database: PDB / ID: 6yw3
TitleHIF PROLYL HYDROXYLASE 2 (PHD2/ EGLN1) in complex with N-Oxalyl Glycine (NOG), HIF-1ALPHA CODD (556-574) and a RaPID-derived cyclic peptide 3C (14-mer)
Components
  • Egl nine homolog 1
  • Hypoxia-inducible factor 1-alpha
  • PHD2-SPECIFIC RaPID CYCLIC PEPTIDE 3C (14-MER)
KeywordsOXIDOREDUCTASE / NON-HEME DIOXYGENASE / IRON / 2-OXOGLUTARATE / HYPOXIA-INDUCIBLE FACTOR / HIF / HIF PROLYL HYDROXYLASE DOMAIN 2 / PHD2 / EGLN1 / OXYGENASE / HYPOXIA / DNA-BINDING / METAL-BINDING / TRANSCRIPTION / HELIX-LOOP-HELIX-BETA / DSBH / FACIAL TRIAD / CYTOPLASM / TRANSCRIPTION/EPIGENETIC REGULATION / SIGNALING / DEVELOPMENT / CELL STRUCTURE / BETA-HYDROXYLATION / TRANSCRIPTION ACTIVATOR/INHIBITOR / UBL CONJUGATION / POLYMORPHISM / VITAMIN C / ZINC-FINGER / FAMILIAL ERYTHROCYTOSIS / BREAST CANCER / TRANSCRIPTION COMPLEX
Function / homology
Function and homology information


epithelial cell differentiation involved in mammary gland alveolus development / neural fold elevation formation / iris morphogenesis / intestinal epithelial cell maturation / : / hypoxia-inducible factor-1alpha signaling pathway / positive regulation of chemokine-mediated signaling pathway / elastin metabolic process / regulation of transforming growth factor beta2 production / glandular epithelial cell maturation ...epithelial cell differentiation involved in mammary gland alveolus development / neural fold elevation formation / iris morphogenesis / intestinal epithelial cell maturation / : / hypoxia-inducible factor-1alpha signaling pathway / positive regulation of chemokine-mediated signaling pathway / elastin metabolic process / regulation of transforming growth factor beta2 production / glandular epithelial cell maturation / peptidyl-proline 4-dioxygenase activity / hypoxia-inducible factor-proline dioxygenase activity / hypoxia-inducible factor-proline dioxygenase / negative regulation of hypoxia-inducible factor-1alpha signaling pathway / peptidyl-proline dioxygenase activity / hemoglobin biosynthetic process / negative regulation of mesenchymal cell apoptotic process / cardiac ventricle morphogenesis / connective tissue replacement involved in inflammatory response wound healing / negative regulation of growth / positive regulation of hormone biosynthetic process / Cellular response to hypoxia / retina vasculature development in camera-type eye / mesenchymal cell apoptotic process / regulation of protein neddylation / regulation protein catabolic process at postsynapse / PTK6 Expression / negative regulation of bone mineralization / intracellular oxygen homeostasis / B-1 B cell homeostasis / collagen metabolic process / vascular endothelial growth factor production / regulation of modification of postsynaptic structure / labyrinthine layer development / dopaminergic neuron differentiation / 2-oxoglutarate-dependent dioxygenase activity / transcription regulator activator activity / heart trabecula formation / cardiac muscle tissue morphogenesis / STAT3 nuclear events downstream of ALK signaling / lactate metabolic process / negative regulation of thymocyte apoptotic process / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / positive regulation of cytokine production involved in inflammatory response / L-ascorbic acid binding / negative regulation of TOR signaling / insulin secretion involved in cellular response to glucose stimulus / positive regulation of vascular endothelial growth factor receptor signaling pathway / response to iron ion / Regulation of gene expression by Hypoxia-inducible Factor / neural crest cell migration / embryonic hemopoiesis / regulation of glycolytic process / motile cilium / DNA-binding transcription repressor activity / response to nitric oxide / PTK6 promotes HIF1A stabilization / DNA-binding transcription activator activity / muscle cell cellular homeostasis / ventricular septum morphogenesis / positive regulation of neuroblast proliferation / digestive tract morphogenesis / response to muscle activity / axonal transport of mitochondrion / heart looping / bone mineralization / intracellular glucose homeostasis / E-box binding / TOR signaling / outflow tract morphogenesis / positive regulation of vascular endothelial growth factor production / positive regulation of macroautophagy / positive regulation of epithelial cell migration / epithelial to mesenchymal transition / cellular response to interleukin-1 / positive regulation of blood vessel endothelial cell migration / neuroblast proliferation / enzyme inhibitor activity / regulation of angiogenesis / chondrocyte differentiation / embryonic placenta development / positive regulation of insulin secretion involved in cellular response to glucose stimulus / cis-regulatory region sequence-specific DNA binding / positive regulation of chemokine production / regulation of neuron apoptotic process / lactation / positive regulation of endothelial cell proliferation / axon cytoplasm / negative regulation of miRNA transcription / positive regulation of erythrocyte differentiation / positive regulation of glycolytic process / nuclear receptor binding / transcription corepressor binding / response to reactive oxygen species / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Hsp90 protein binding / ferrous iron binding / euchromatin / cerebral cortex development / visual learning
Similarity search - Function
Hypoxia-inducible factor-1 alpha / : / HIF-1 alpha, transactivation domain, C-terminal / HIF-1 alpha C terminal transactivation domain / Hypoxia-inducible factor 1-alpha bHLH domain / Hypoxia-inducible factor, alpha subunit-like / Hypoxia-inducible factor-1 / PAS fold-3 / Prolyl 4-hydroxylase alpha subunit, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily ...Hypoxia-inducible factor-1 alpha / : / HIF-1 alpha, transactivation domain, C-terminal / HIF-1 alpha C terminal transactivation domain / Hypoxia-inducible factor 1-alpha bHLH domain / Hypoxia-inducible factor, alpha subunit-like / Hypoxia-inducible factor-1 / PAS fold-3 / Prolyl 4-hydroxylase alpha subunit, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / PAS fold / 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) / 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
: / N-OXALYLGLYCINE / Hypoxia-inducible factor 1-alpha / Egl nine homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.279 Å
AuthorsChowdhury, R. / Schofield, C.J.
Citation
Journal: Sci Rep / Year: 2020
Title: Use of cyclic peptides to induce crystallization: case study with prolyl hydroxylase domain 2.
Authors: Chowdhury, R. / Abboud, M.I. / McAllister, T.E. / Banerji, B. / Bhushan, B. / Sorensen, J.L. / Kawamura, A. / Schofield, C.J.
#1: Journal: Nat Commun / Year: 2016
Title: Structural basis for oxygen degradation domain selectivity of the HIF prolyl hydroxylases.
Authors: Chowdhury, R. / Leung, I.K. / Tian, Y.M. / Abboud, M.I. / Ge, W. / Domene, C. / Cantrelle, F.X. / Landrieu, I. / Hardy, A.P. / Pugh, C.W. / Ratcliffe, P.J. / Claridge, T.D. / Schofield, C.J.
History
DepositionApr 29, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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
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: Egl nine homolog 1
B: PHD2-SPECIFIC RaPID CYCLIC PEPTIDE 3C (14-MER)
S: Hypoxia-inducible factor 1-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4827
Polymers30,0923
Non-polymers3904
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-32 kcal/mol
Surface area11570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.443, 81.285, 43.219
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 , 1 types, 1 molecules A

#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
Details: CATALYTIC DOMAIN (RESIDUES 181-407) / Source: (gene. exp.) Homo sapiens (human) / Gene: EGLN1, C1orf12, PNAS-118, PNAS-137 / Plasmid: PET28A(+) / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9GZT9, hypoxia-inducible factor-proline dioxygenase

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Protein/peptide , 2 types, 2 molecules BS

#2: Protein/peptide PHD2-SPECIFIC RaPID CYCLIC PEPTIDE 3C (14-MER)


Mass: 1801.050 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein/peptide Hypoxia-inducible factor 1-alpha / HIF1-alpha / ARNT-interacting protein / Basic-helix-loop-helix-PAS protein MOP1 / Class E basic ...HIF1-alpha / ARNT-interacting protein / Basic-helix-loop-helix-PAS protein MOP1 / Class E basic helix-loop-helix protein 78 / bHLHe78 / Member of PAS protein 1 / PAS domain-containing protein 8


Mass: 2254.532 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q16665

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Non-polymers , 5 types, 120 molecules

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


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


Mass: 147.086 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H5NO5 / Feature type: SUBJECT OF INVESTIGATION
#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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.36 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Sample: 1.0 mM cPHD2, 1.5 mM MnCl2, 2.0 mM compound, 1.0 mM 3C, 2.0 mM CODD; Reservoir: 19-23% w/v polyethylene glycol 3350, 0.25 M lithium sulfate, 2 mM MnCl2; Sitting drop (2 ul), protein-to-well ratio, 1:1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 8, 2017 / Details: MIRRORS
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.279→55.686 Å / Num. obs: 12861 / % possible obs: 100 % / Redundancy: 9.1 % / Biso Wilson estimate: 30.4 Å2 / CC1/2: 0.996 / Rpim(I) all: 0.056 / Rrim(I) all: 0.174 / Rsym value: 0.164 / Net I/av σ(I): 4 / Net I/σ(I): 9.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allRsym value% possible all
2.28-2.491.0431.7718300.70.3621.1061.043100
2.4-2.559.60.764117540.2570.8070.764100
2.55-2.739.10.5451.416290.1890.5780.545100
2.73-2.949.30.3152.415340.1070.3330.315100
2.94-3.229.30.23.814080.0680.2120.2100
3.22-3.69.30.1215.913050.0410.1280.121100
3.6-4.169.10.0897.411440.030.0940.089100
4.16-5.19.20.0728.39950.0240.0760.072100
5.1-7.218.40.0767.87860.0270.0810.076100
7.21-76.44380.0747.14760.0280.0790.07499.9

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5L9R

5l9r


Resolution: 2.279→55.686 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2082 617 4.81 %
Rwork0.1878 --
obs0.1898 12824 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT MODEL / Bsol: 40.2 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso max: 96.01 Å2 / Biso mean: 36.8484 Å2 / Biso min: 15.18 Å2
Refinement stepCycle: final / Resolution: 2.279→55.686 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1969 0 33 116 2118
Biso mean--31.52 36.31 -
Num. residues----254
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONf_bond_d0.0040.0459529
X-RAY DIFFRACTIONf_angle_d0.7956.90912945
X-RAY DIFFRACTIONf_dihedral_angle_d16.442179.965500
X-RAY DIFFRACTIONf_chiral_restr0.0480.1671356
X-RAY DIFFRACTIONf_plane_restr0.0050.0611691
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2792-2.36070.2721520.2526117699
2.3607-2.45520.2402650.24391181100
2.4552-2.56690.2901660.22891213100
2.5669-2.70230.2338750.22171195100
2.7023-2.87160.2708640.21321191100
2.8716-3.09330.1944670.20831202100
3.0933-3.40450.243580.1911226100
3.4045-3.89710.1844620.16951224100
3.8971-4.90940.1395580.13151255100
4.9094-55.6860.2114500.18631345100
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)
12.9125-1.97960.93613.9287-0.97873.1859-0.00890.0478-0.5226-0.3510.16830.5470.5638-0.0204-0.04260.296-0.03260.04470.2611-0.04880.339379.464211.006450.0979
22.8592-0.11590.83632.7204-1.20553.89490.1828-0.3198-0.2189-0.08340.13290.43870.1858-0.0285-0.33260.2291-0.0568-0.04630.1525-0.00010.24179.96617.586256.9509
34.10672.7012-0.77979.44820.54231.14540.0543-0.0510.2511.7118-0.0787-0.079-0.34850.51920.0950.5508-0.041-0.14910.46670.06480.239693.236423.363470.6847
45.8639-0.84110.44122.6634-0.48583.8058-0.0915-0.16230.64280.4049-0.1662-0.3606-0.56890.65850.25750.3273-0.1522-0.09850.40640.00770.402696.50535.333157.6966
55.15420.96881.07724.58562.08186.37790.26860.0048-0.40240.40340.0312-0.42860.73590.7526-0.27730.26090.0442-0.05830.25130.02550.244192.803914.27256.0993
65.48491.3464-0.35223.52330.23743.78690.01710.5901-0.0407-0.30370.0345-0.28440.73440.1276-0.20380.38920.06010.02650.3317-0.01880.278788.549515.520941.0071
72.43790.61440.66811.95590.35582.7066-0.025-0.53010.45940.31340.2663-0.5382-0.19220.5578-0.12790.2549-0.0443-0.06480.34580.00810.245892.61730.388959.0865
83.6848-1.1903-1.75215.22021.12635.5514-0.00430.15750.3371-0.1565-0.1464-0.1874-0.68830.24080.18620.2156-0.0818-0.04920.19710.05040.258686.46535.670548.7129
92.3243-0.5495-0.55313.34710.72543.16-0.2650.024-0.34920.5411-0.3110.0038-0.3367-0.01360.60410.2454-0.0182-0.04110.2160.0240.198184.65425.579359.378
102.6392-0.5041-0.65792.5041-0.7841.9579-0.02570.2511-0.11670.0515-0.10010.1370.4472-1.20180.23250.1781-0.074-0.05110.3295-0.02010.268875.229532.450555.8347
116.6308-3.11334.43626.5416-3.41417.040.1414-0.8331-0.28290.33760.22031.2544-0.102-0.9968-0.41710.258-0.03710.02740.2206-0.01010.322976.045126.603459.0726
122.5467-1.17870.592.5971-0.01112.27820.03350.2763-0.0009-0.2931-0.11240.22730.2250.21840.10320.2203-0.0443-0.01370.25580.00090.19482.655424.814548.4456
130.6522-0.4565-0.14582.03183.43077.8046-0.3318-0.01620.39320.0909-0.28170.51350.0045-0.38170.60090.2505-0.0154-0.00810.1820.01770.361580.111635.949157.3415
142.3711-0.1902-0.10553.64810.57632.45060.0060.19160.0291-0.01330.0404-0.3837-0.30270.17950.00650.1998-0.0074-0.00540.24860.0460.210890.507126.231155.3994
156.9056-0.7182-1.1143.3592-0.32837.05640.36780.36790.2588-0.1065-0.0017-0.3956-0.6102-0.7759-0.41430.2530.09510.05250.3753-0.01140.3599102.048930.065835.5906
162.07760.2423-1.07194.70841.13872.76520.11090.4875-0.0239-0.1765-0.2517-0.5696-0.23190.75130.01720.2507-0.063-0.0440.4272-0.03240.414297.052130.2147.0578
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 188:204)A188 - 204
2X-RAY DIFFRACTION2(chain A and resid 205:215)A205 - 215
3X-RAY DIFFRACTION3(chain A and resid 216:232)A216 - 232
4X-RAY DIFFRACTION4(chain A and resid 233:266)A233 - 266
5X-RAY DIFFRACTION5(chain A and resid 267:283)A267 - 283
6X-RAY DIFFRACTION6(chain A and resid 284:293)A284 - 293
7X-RAY DIFFRACTION7(chain A and resid 294:306)A294 - 306
8X-RAY DIFFRACTION8(chain A and resid 307:320)A307 - 320
9X-RAY DIFFRACTION9(chain A and resid 321:335)A321 - 335
10X-RAY DIFFRACTION10(chain A and resid 336:350)A336 - 350
11X-RAY DIFFRACTION11(chain A and resid 351:361)A351 - 361
12X-RAY DIFFRACTION12(chain A and resid 362:371)A362 - 371
13X-RAY DIFFRACTION13(chain A and resid 372:381)A372 - 381
14X-RAY DIFFRACTION14(chain A and resid 382:392)A382 - 392
15X-RAY DIFFRACTION15(chain A and resid 393:407)A393 - 407
16X-RAY DIFFRACTION16(chain S and resid 558:574)S558 - 574

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