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- PDB-8q64: Crystal structure of hydroxylated HIF2alpha-CODD peptide (523-542... -

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Basic information

Entry
Database: PDB / ID: 8q64
TitleCrystal structure of hydroxylated HIF2alpha-CODD peptide (523-542) bound to apo-HIF prolyl hydroxylase 2 (PHD2 181-407)
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 / 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 / regulation protein catabolic process at postsynapse / regulation of protein neddylation / Transcriptional regulation of pluripotent stem cells ...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 / regulation protein catabolic process at postsynapse / regulation of protein neddylation / Transcriptional regulation of pluripotent stem cells / PTK6 Expression / intracellular oxygen homeostasis / labyrinthine layer development / cardiac muscle tissue morphogenesis / norepinephrine metabolic process / heart trabecula formation / regulation of modification of postsynaptic structure / 2-oxoglutarate-dependent dioxygenase activity / surfactant homeostasis / L-ascorbic acid binding / epithelial cell maturation / Regulation of gene expression by Hypoxia-inducible Factor / response to nitric oxide / ventricular septum morphogenesis / embryonic placenta development / blood vessel remodeling / regulation of angiogenesis / regulation of heart rate / visual perception / Pexophagy / erythrocyte differentiation / mitochondrion organization / RNA polymerase II transcription regulatory region sequence-specific DNA binding / lung development / mRNA transcription by RNA polymerase II / ferrous iron binding / negative regulation of DNA-binding transcription factor activity / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / transcription coactivator binding / multicellular organismal-level iron ion homeostasis / positive regulation of cold-induced thermogenesis / Neddylation / cellular response to hypoxia / DNA-binding transcription activator activity, RNA polymerase II-specific / angiogenesis / intracellular iron ion homeostasis / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / response to oxidative stress / postsynaptic density / response to hypoxia / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear speck / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / intracellular membrane-bounded organelle / glutamatergic synapse / chromatin / regulation of transcription by RNA polymerase II / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol / cytoplasm
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 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: 1.36 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 10, 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)28,5116
Polymers28,2752
Non-polymers2364
Water4,288238
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-13 kcal/mol
Surface area10840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.054, 42.467, 130.457
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 / 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: 25949.502 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: 2325.544 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Synthetic peptide substrate. Hydroxylated proline (HYP531) obtained from oxygen exposure of crystals containing the non hydroxylated equivalent (P531)
Source: (synth.) Homo sapiens (human) / References: UniProt: Q99814
#3: Chemical
ChemComp-ACT / ACETATE ION


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


Mass: 18.015 Da / Num. of mol.: 238 / 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: 1.87 Å3/Da / Density % sol: 34.05 %
Crystal growTemperature: 298 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: I24 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 30, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.36→43.49 Å / Num. obs: 46479 / % possible obs: 99.9 % / Redundancy: 13.1 % / CC1/2: 1 / Net I/σ(I): 8.6
Reflection shellResolution: 1.36→1.38 Å / Num. unique obs: 2240 / CC1/2: 0.4

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
PHASERphasing
DIALSdata reduction
xia2data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.36→42.47 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2117 2274 4.9 %
Rwork0.1901 --
obs0.1912 46380 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.36→42.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1845 0 16 238 2099
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051991
X-RAY DIFFRACTIONf_angle_d0.872709
X-RAY DIFFRACTIONf_dihedral_angle_d6.073287
X-RAY DIFFRACTIONf_chiral_restr0.073290
X-RAY DIFFRACTIONf_plane_restr0.008359
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.36-1.390.3821160.40052689X-RAY DIFFRACTION99
1.39-1.420.38561350.36842736X-RAY DIFFRACTION100
1.42-1.460.37521400.35322708X-RAY DIFFRACTION100
1.46-1.50.28661540.31622692X-RAY DIFFRACTION100
1.5-1.540.32281380.31182721X-RAY DIFFRACTION100
1.54-1.590.26341370.26322738X-RAY DIFFRACTION100
1.59-1.650.2611530.25472693X-RAY DIFFRACTION100
1.65-1.710.28351400.23122729X-RAY DIFFRACTION100
1.71-1.790.23391340.2062756X-RAY DIFFRACTION100
1.79-1.890.22431400.19222737X-RAY DIFFRACTION100
1.89-20.22691510.19232766X-RAY DIFFRACTION100
2-2.160.19851390.16572740X-RAY DIFFRACTION100
2.16-2.380.18141460.16172812X-RAY DIFFRACTION100
2.38-2.720.17821580.16232778X-RAY DIFFRACTION100
2.72-3.430.18891420.15572816X-RAY DIFFRACTION100
3.43-42.470.17711510.15582995X-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)
13.32452.3419-1.03363.7929-0.86521.25560.0870.09610.21060.2310.06890.1815-0.1274-0.1605-0.15430.13550.04420.0060.17030.02030.1326-5.786-9.3352-14.1734
23.3736-3.72230.09034.73230.58590.894-0.06260.20320.57840.21170.06110.1121-0.11860.0378-0.04240.2068-0.02110.02560.14930.07390.290212.21516.0469-18.4137
32.5318-0.1701-1.49291.21760.23891.97850.04530.03980.08120.0364-0.039-0.0875-0.10860.0801-0.04160.13010.0024-0.0130.12890.03470.118515.1973-8.1183-14.8501
45.97133.2406-2.60942.6922-2.21053.78340.0958-0.202-0.10050.0248-0.179-0.1141-0.06940.03450.06080.10250.05360.01290.0375-0.01460.10467.9315-13.4386-11.1959
52.52651.4582-2.30686.615-3.88935.9485-0.0450.3539-0.0359-0.3705-0.1345-0.20050.14540.26460.06560.12290.02330.00010.22350.0120.119714.3568-15.0377-29.142
61.2366-0.02250.24743.7026-2.2953.6322-0.00440.26730.121-0.080.03180.0092-0.0471-0.02930.04290.08330.00280.00760.14920.03260.1167.9082-9.8051-22.8738
78.91956.04122.69524.37582.49225.95120.01010.2597-0.4513-0.09310.10230.05540.2715-0.6211-0.1320.13170.012-0.01590.2819-0.00290.16310.0119-19.596-28.5118
81.35740.7252-0.53413.8542-0.29741.86830.04950.1960.15970.0162-0.03260.041-0.2013-0.0794-0.02820.1020.02540.00830.14880.02530.12762.3163-9.7778-21.6687
94.20214.1751-3.397.0057-5.1856.6387-0.1450.5357-0.1913-0.2962-0.0032-0.19290.1813-0.10570.12550.10890.03660.01230.19960.00310.11828.5765-15.8405-28.0446
101.1799-1.31581.25245.7844-4.5485.17920.0495-0.0241-0.08140.08550.02430.01290.12230.0531-0.03950.1133-0.0059-0.01160.11390.00510.10513.5959-18.1591-10.3685
116.75335.41720.15345.3768-2.33365.8598-0.06960.5028-1.3302-0.58310.3285-0.66541.31270.1129-0.38220.29180.018-0.01340.19-0.0320.288116.6775-28.1768-23.7917
122.8316-3.646-3.60764.7074.73545.0121-0.3043-0.5040.18690.47640.4739-0.25010.48950.8516-0.23010.19820.0076-0.01430.2478-0.03430.17715.9639-15.0015-7.5674
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 188 through 215 )
2X-RAY DIFFRACTION2chain 'A' and (resid 216 through 231 )
3X-RAY DIFFRACTION3chain 'A' and (resid 232 through 283 )
4X-RAY DIFFRACTION4chain 'A' and (resid 284 through 304 )
5X-RAY DIFFRACTION5chain 'A' and (resid 305 through 314 )
6X-RAY DIFFRACTION6chain 'A' and (resid 315 through 342 )
7X-RAY DIFFRACTION7chain 'A' and (resid 343 through 353 )
8X-RAY DIFFRACTION8chain 'A' and (resid 354 through 369 )
9X-RAY DIFFRACTION9chain 'A' and (resid 370 through 381 )
10X-RAY DIFFRACTION10chain 'A' and (resid 382 through 406 )
11X-RAY DIFFRACTION11chain 'B' and (resid 523 through 529 )
12X-RAY DIFFRACTION12chain 'B' and (resid 530 through 542 )

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