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- PDB-6yw1: HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with 2OG and Ra... -

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Basic information

Entry
Database: PDB / ID: 6yw1
TitleHIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with 2OG and RaPID-derived silent allosteric cyclic peptide 3C (14-mer)
Components
  • Egl nine homolog 1
  • 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


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 / intracellular oxygen homeostasis / labyrinthine layer development / regulation protein catabolic process at postsynapse / cardiac muscle tissue morphogenesis / 2-oxoglutarate-dependent dioxygenase activity ...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 / intracellular oxygen homeostasis / labyrinthine layer development / regulation protein catabolic process at postsynapse / cardiac muscle tissue morphogenesis / 2-oxoglutarate-dependent dioxygenase activity / heart trabecula formation / regulation of modification of postsynaptic structure / L-ascorbic acid binding / response to nitric oxide / ventricular septum morphogenesis / regulation of angiogenesis / regulation of neuron apoptotic process / negative regulation of DNA-binding transcription factor activity / ferrous iron binding / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / cellular response to hypoxia / intracellular iron ion homeostasis / response to hypoxia / postsynaptic density / intracellular membrane-bounded organelle / glutamatergic synapse / enzyme binding / positive regulation of transcription by RNA polymerase II / nucleus / cytosol / cytoplasm
Similarity search - Function
: / 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.
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / BICARBONATE ION / : / Egl nine homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 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)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1005
Polymers27,8382
Non-polymers2623
Water4,396244
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-18 kcal/mol
Surface area10710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.531, 46.531, 202.345
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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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
Details: CATALYTIC DOMAIN (aa 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
#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)

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Non-polymers , 4 types, 247 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-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 2.53 Å3/Da / Density % sol: 51.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Sample: 1.0 mM PHD2, 1.5 mM MnCl2, 2.0 mM compound, 1.0 mM 3C; Reservoir: 0.1 M Bis-Tris pH 6.5, 15.0 % PEG 3350, 0.002 M MnCl2; Sitting drop (300 nl), protein-to-well ratio, 1:2

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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-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: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.46→50 Å / Num. obs: 42887 / % possible obs: 100 % / Redundancy: 7.6 % / Biso Wilson estimate: 20.9 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.024 / Rrim(I) all: 0.064 / Χ2: 1.072 / Net I/σ(I): 28.4
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allΧ2Rrim(I) all
1.46-1.517.21.1081.4542500.6170.5371.197
1.51-1.577.20.91642770.8410.3661.140.987
1.57-1.647.70.71442990.8870.2731.1170.765
1.64-1.737.70.46242880.9520.1781.0690.495
1.73-1.847.50.30742520.9690.121.0080.33
1.84-1.987.60.18542770.9880.0721.0120.199
1.98-2.1880.11542940.9950.0431.0430.122
2.18-2.57.70.07842750.9970.031.0770.083
2.5-3.157.80.05143210.9990.0191.0380.055
3.15-507.80.03543540.9990.0131.0330.037

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5L9R

5l9r


Resolution: 1.46→40.297 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1746 2152 5.03 %
Rwork0.1642 --
obs0.1648 42753 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT MODEL / Bsol: 45.3 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso max: 122.17 Å2 / Biso mean: 34.1839 Å2 / Biso min: 15.6 Å2
Refinement stepCycle: final / Resolution: 1.46→40.297 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1765 0 20 245 2030
Biso mean--34.37 40.11 -
Num. residues----223
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONf_bond_d0.0090.0661928
X-RAY DIFFRACTIONf_angle_d0.999.2842623
X-RAY DIFFRACTIONf_dihedral_angle_d7.233179.5481065
X-RAY DIFFRACTIONf_chiral_restr0.0810.318273
X-RAY DIFFRACTIONf_plane_restr0.0080.052347
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.46-1.4940.3561570.34162683
1.494-1.53130.32331380.30342659
1.5313-1.57280.27661330.2652740
1.5728-1.6190.27091490.23842711
1.619-1.67130.22891640.22712675
1.6713-1.7310.23741360.20482741
1.731-1.80030.22781190.19412706
1.8003-1.88230.17551500.18242690
1.8823-1.98150.17381240.16772713
1.9815-2.10560.19931330.16332745
2.1056-2.26820.17011640.15652678
2.2682-2.49640.16771270.15452707
2.4964-2.85760.1581190.15552768
2.8576-3.59990.16141860.14672671
3.5999-40.2970.14641530.14232714
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)
10.175-0.13380.18690.1676-0.00780.8424-0.0209-0.0988-0.1107-0.069-0.0891-0.03-0.1858-0.4411-0.05020.08590.00410.0290.35420.0120.2656-31.450611.1908-3.5059
20.2476-0.0816-0.18080.050.04990.1005-0.0823-0.1379-0.06220.24350.20310.2072-0.0575-0.116900.20020.05160.00930.23550.01730.206-22.95710.56280.7296
30.06610.0080.08260.53710.6440.8514-0.0143-0.1392-0.26870.5670.4974-0.22440.38210.38280.93430.39050.3019-0.17310.05570.03330.4631-8.6382-2.70251.3918
40.3697-0.24070.24750.70090.31970.7896-0.09220.4644-0.1588-0.15880.3933-0.3110.17090.6077-0.03760.22120.0958-0.01690.3951-0.15450.335-3.39185.3374-9.8877
50.23410.1682-0.17610.14820.02130.30370.04450.1672-0.4036-0.0509-0.04170.07780.3302-0.2274-00.2469-0.0145-0.01230.2512-0.04260.335-21.74481.0465-8.6182
60.1460.01890.00860.06780.03780.03570.00250.7680.0954-0.36-0.0450.114-0.0521-0.31840.00280.23870.0282-0.03710.5145-0.02850.2464-29.066812.8533-16.7132
70.29240.1975-0.2430.1622-0.17490.20190.11250.1261-0.2534-0.02110.0982-0.17570.24980.30430.02940.13720.0781-0.03580.2972-0.11780.2448-7.16378.4867-7.5189
80.20810.2027-0.18110.2024-0.08610.1291-0.02540.35520.1223-0.05080.1462-0.1046-0.07090.50540.00030.2057-0.00540.00550.2962-0.01550.2122-8.986221.166-10.6329
90.87510.7224-0.16680.55660.02450.1880.08840.0604-0.1860.140.0318-0.08190.0710.01650.00010.16540.0332-0.01890.2088-0.01820.1813-13.811710.2799-1.4429
100.25790.1102-0.09560.30650.26120.2471-0.0285-0.16520.03870.21970.17040.0915-0.3770.02370.00020.25240.0521-0.01770.2167-0.02880.2216-13.63522.91171.2641
110.1249-0.0466-0.070.03790.09810.2509-0.1109-0.48290.04470.30530.22290.2141-0.0986-0.1685-0.04040.23570.0893-0.01660.2277-0.03990.2298-15.884416.58474.3771
120.0810.0916-0.04790.19080.0219-0.0066-0.03260.02130.02090.16030.15950.0738-0.1081-0.23410.00020.17760.06470.00470.23590.00910.1847-19.549618.6536-8.2858
130.21060.1619-0.10.1236-0.02050.09660.16420.1046-0.0636-0.0280.0731-0.042-0.02220.16820.00490.16470.0161-0.02180.2503-0.04430.2065-7.682220.1774-0.249
140.65810.4877-0.14460.5847-0.20120.6290.02180.2749-0.13530.04170.1948-0.18790.0810.08020.09230.14640.0588-0.02710.2398-0.07730.2165-13.05279.8549-8.6528
150.0041-0.0244-0.00340.3601-0.02080.0005-0.12690.2575-0.0144-0.29990.2683-0.1690.1029-0.3580.00240.3535-0.13050.00240.46750.01140.2055-16.783615.9433-26.2119
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 393:403)A393 - 403

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