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- PDB-6yw4: HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with N-oxalylgl... -

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Basic information

Entry
Database: PDB / ID: 6yw4
TitleHIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with N-oxalylglycine (NOG) and a 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 / negative regulation of hypoxia-inducible factor-1alpha signaling pathway / peptidyl-proline dioxygenase activity / regulation protein catabolic process at postsynapse / intracellular oxygen homeostasis / regulation of modification of postsynaptic structure / labyrinthine layer development / 2-oxoglutarate-dependent dioxygenase activity ...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 / regulation protein catabolic process at postsynapse / intracellular oxygen homeostasis / regulation of modification of postsynaptic structure / labyrinthine layer development / 2-oxoglutarate-dependent dioxygenase activity / heart trabecula formation / cardiac muscle tissue morphogenesis / L-ascorbic acid binding / response to nitric oxide / ventricular septum morphogenesis / enzyme inhibitor activity / regulation of angiogenesis / regulation of neuron apoptotic process / 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 / zinc ion binding / nucleus / cytoplasm / cytosol
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
: / N-OXALYLGLYCINE / Egl nine homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.528 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 20, 2021Group: Database references / Category: struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_isoform ..._struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_isoform / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details / _struct_ref_seq_dif.pdbx_seq_db_seq_num
Revision 1.2Jan 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)28,1146
Polymers27,7192
Non-polymers3944
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-43 kcal/mol
Surface area10650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.622, 46.622, 203.711
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: 25918.402 Da / Num. of mol.: 1 / Mutation: C201A/R398A
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, 197 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-OGA / N-OXALYLGLYCINE


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


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.56 Å3/Da / Density % sol: 51.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Sample: 1.0 mM cPHD2, 1.5 mM MnCl2, 2.0 mM compound, 1.0 mM 3C; Reservoir: 0.2 M lithium sulfate, 0.1 M Tris-HCl pH 8.5, 1.26 M ammonium sulfate; Sitting drop (300 nl), 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: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 17, 2015 / 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: 1.528→50 Å / Num. obs: 37807 / % possible obs: 100 % / Redundancy: 16 % / Biso Wilson estimate: 21.2 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.039 / Rrim(I) all: 0.129 / Χ2: 1.043 / Net I/σ(I): 20.07
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
1.53-1.5813.11.7331240.6530.5321.104100
1.58-1.6316.131700.7050.4981.099100
1.63-1.6815.731340.7810.4011.073100
1.68-1.7516.731290.9040.2641.065100
1.75-1.8317.331320.9330.1981.0411000.8140.838
1.83-1.931731550.9660.1321.0261000.5340.55
1.93-2.0516.431420.9790.0951.0171000.3760.388
2.05-2.2117.731620.9880.0661.0141000.2680.276
2.21-2.4317.331400.9940.0491.0241000.1970.203
2.43-2.7816.331560.9950.0371.00799.90.1450.15
2.78-3.515.531540.9970.0261.0341000.0960.099
3.5-5013.132090.9960.021.02299.90.0710.074

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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: 1.528→39.605 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.177 1841 4.89 %
Rwork0.162 --
obs0.1628 37652 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT MODEL / Bsol: 50.2 Å2 / ksol: 0.41 e/Å3
Displacement parametersBiso max: 118.95 Å2 / Biso mean: 34.4686 Å2 / Biso min: 15 Å2
Refinement stepCycle: final / Resolution: 1.528→39.605 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1756 0 24 193 1973
Biso mean--54.01 40.69 -
Num. residues----224
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONf_bond_d0.0160.1271854
X-RAY DIFFRACTIONf_angle_d1.40710.5082513
X-RAY DIFFRACTIONf_dihedral_angle_d11.882160.6331081
X-RAY DIFFRACTIONf_chiral_restr0.0870.295264
X-RAY DIFFRACTIONf_plane_restr0.0120.06326
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.528-1.56920.28221210.2731270598
1.5692-1.61530.28281390.24722814100
1.6153-1.66750.25211420.23052759100
1.6675-1.72710.26261570.19982743100
1.7271-1.79620.22011200.18752774100
1.7962-1.8780.19991370.16132740100
1.878-1.9770.17281620.15072730100
1.977-2.10080.18251300.15262775100
2.1008-2.2630.16441260.14432770100
2.263-2.49080.18261660.1442725100
2.4908-2.85110.16751400.15042764100
2.8511-3.59170.151450.15772761100
3.5917-39.6050.16821560.15972751100
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)
10.01430.03020.03650.13490.11531.2422-0.0884-0.0224-0.2097-0.0752-0.02320.0529-0.1132-0.5336-0.02760.11380.0076-0.00340.3986-0.00350.2799-31.034211.1408-3.3499
20.0144-0.0663-0.01090.4176-0.06150.10950.0101-0.2219-0.0642-0.14410.09040.2960.0275-0.31960.00660.13930.02980.00820.27160.01270.1862-22.462710.53920.8719
30.11460.10570.14980.40.61650.93530.1693-0.0558-0.21470.25040.2349-0.27130.3570.20210.14510.36620.1194-0.11510.2760.00650.3866-6.9375-2.21920.6227
40.11150.1070.25680.51720.06910.5691-0.02330.0944-0.4281-0.38450.2025-0.30380.16630.53730.04650.22720.07080.00960.4165-0.14530.3883-2.8286.0257-9.7309
50.02090.0018-0.00170.04740.06210.11080.14210.0505-0.6063-0.0251-0.06360.32130.2862-0.22670.00030.2403-0.0235-0.03260.2732-0.01720.334-21.28071.1099-8.5589
60.01820.0140.02850.0060.01860.0304-0.10950.33910.0871-0.0139-0.0262-0.0048-0.0469-0.30130.00020.32730.0241-0.06650.3703-0.01010.2804-28.286613.2003-16.2276
71.69890.84671.3551.16610.41121.52510.0974-0.0084-0.2553-0.11010.1506-0.2440.21480.2424-0.13150.07810.0412-0.01880.3599-0.12420.2647-6.69318.5494-7.426
80.08630.0728-0.07420.0606-0.05780.0589-0.03470.28430.0548-0.14980.1145-0.1735-0.13550.4370.00090.2124-0.0405-0.00680.2934-0.01140.1943-8.787621.1045-10.7187
90.20470.25790.05730.3120.08060.02630.06970.008-0.14810.10360.105-0.0977-0.11720.04230.00010.16290.0128-0.0370.23820.00010.1973-13.300910.1977-1.2299
100.07670.0801-0.02230.17260.07890.0879-0.0488-0.14210.14790.0936-0.0065-0.0599-0.32530.1184-0.00220.20990.0398-0.02470.2586-0.04990.1814-12.576722.33852.396
110.25320.043-0.03260.25980.07350.0955-0.0475-0.57160.11160.250.13990.0079-0.0976-0.1284-0.06260.24730.07-0.01540.3118-0.04580.2437-15.30116.78784.4651
120.0420.03150.01290.07850.00760.0009-0.0522-0.15470.0803-0.10060.12320.2064-0.0714-0.21560.0010.17240.0358-0.0150.2324-0.00940.1767-19.045418.7072-8.0929
130.14820.07940.18540.12120.08780.2410.128-0.0493-0.1419-0.0710.02520.1046-0.11830.11340.03960.1668-0.0118-0.01560.2744-0.05710.2218-7.216220.1802-0.0134
140.84750.12950.38841.2551-0.18690.58550.0607-0.0043-0.0824-0.16770.2856-0.32730.14720.03670.12550.11240.0371-0.03050.2856-0.08290.2274-12.49259.6643-8.4581
150.1871-0.1610.17390.1433-0.15610.1873-0.1781-0.15750.1134-0.37140.2319-0.1772-0.0339-0.28640.00520.3992-0.10440.02950.3596-0.02070.244-15.217716.4338-26.1929
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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