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- PDB-7ujv: Structure of PHD2 in complex with HIF2a-CODD -

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Basic information

Entry
Database: PDB / ID: 7ujv
TitleStructure of PHD2 in complex with HIF2a-CODD
Components
  • Egl nine homolog 1
  • Endothelial PAS domain-containing protein 1
KeywordsOXIDOREDUCTASE / HIF-Prolyl-Hydroxylase / Complex / Oxygen-sensing / psuedohypoxic-disease
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 / peptidyl-proline hydroxylation to 4-hydroxy-L-proline / negative regulation of cyclic-nucleotide phosphodiesterase activity / regulation protein catabolic process at postsynapse / Cellular response to hypoxia / regulation of protein neddylation ...myoblast fate commitment / hypoxia-inducible factor-proline dioxygenase activity / hypoxia-inducible factor-proline dioxygenase / peptidyl-proline 4-dioxygenase activity / peptidyl-proline dioxygenase activity / peptidyl-proline hydroxylation to 4-hydroxy-L-proline / 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 / cardiac muscle tissue morphogenesis / 2-oxoglutarate-dependent dioxygenase activity / 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 / response to nitric oxide / ventricular septum morphogenesis / embryonic placenta development / blood vessel remodeling / regulation of angiogenesis / visual perception / Pexophagy / regulation of heart rate / mitochondrion organization / erythrocyte differentiation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / lung development / mRNA transcription by RNA polymerase II / 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 / Neddylation / positive regulation of cold-induced thermogenesis / 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 / response to oxidative stress / transcription regulator complex / 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 / 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. / MYND finger ...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
: / N-OXALYLGLYCINE / Endothelial PAS domain-containing protein 1 / Egl nine homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsFerens, F.G. / Tarade, D. / Lee, J.E. / Ohh, M.
Funding support Canada, 3items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT-159773 Canada
Canada Research ChairsCRC-2017-00140 Canada
Canada Foundation for Innovation Canada
CitationJournal: Commun Biol / Year: 2024
Title: Deficiency in PHD2-mediated hydroxylation of HIF2 alpha underlies Pacak-Zhuang syndrome.
Authors: Ferens, F.G. / Taber, C.C. / Stuart, S. / Hubert, M. / Tarade, D. / Lee, J.E. / Ohh, M.
History
DepositionMar 31, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Mar 13, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Egl nine homolog 1
A: Endothelial PAS domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4165
Polymers30,1212
Non-polymers2953
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Microscale thermophoresis was used to support the interaction of HIF2a-CODD and PHD2
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-26 kcal/mol
Surface area10890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.078, 37.597, 42.148
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-670-

HOH

21B-690-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules BA

#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: 27813.574 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(DE3) (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: 2307.552 Da / Num. of mol.: 1 / Fragment: CODD Peptide / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q99814

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Non-polymers , 4 types, 111 molecules

#3: Chemical ChemComp-OGA / N-OXALYLGLYCINE


Mass: 147.086 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H5NO5 / Feature type: SUBJECT OF INVESTIGATION / Comment: inhibitor*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 1.7 Å3/Da / Density % sol: 27.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 32.5% (w/v) PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97933 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 1.8→129.08 Å / Num. obs: 19834 / % possible obs: 100 % / Redundancy: 7.1 % / Biso Wilson estimate: 20.58 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.047 / Rrim(I) all: 0.126 / Net I/σ(I): 8.4
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 967 / CC1/2: 0.695 / Rpim(I) all: 0.334 / Rrim(I) all: 0.86 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALS2.1data reduction
DIALS2.1data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5L9B

5l9b


Resolution: 1.8→42.183 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.946 / WRfactor Rfree: 0.188 / WRfactor Rwork: 0.149 / SU B: 4.058 / SU ML: 0.115 / Average fsc free: 0.8855 / Average fsc work: 0.8965 / Cross valid method: FREE R-VALUE / ESU R: 0.137 / ESU R Free: 0.128
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflectionSelection details
Rfree0.2134 946 4.787 %Random
Rwork0.173 18814 --
all0.175 ---
obs-19760 99.838 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 29.036 Å2
Baniso -1Baniso -2Baniso -3
1--0.715 Å2-0 Å2-0 Å2
2---0.482 Å20 Å2
3---1.198 Å2
Refinement stepCycle: LAST / Resolution: 1.8→42.183 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1888 0 18 108 2014
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0121944
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161816
X-RAY DIFFRACTIONr_angle_refined_deg1.3681.6392623
X-RAY DIFFRACTIONr_angle_other_deg0.4611.5764193
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1985237
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.08722.056107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.2415332
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.351513
X-RAY DIFFRACTIONr_chiral_restr0.0660.2243
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022201
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02445
X-RAY DIFFRACTIONr_nbd_refined0.2350.2401
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1970.21862
X-RAY DIFFRACTIONr_nbtor_refined0.1850.2957
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.21062
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2114
X-RAY DIFFRACTIONr_metal_ion_refined00.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2720.222
X-RAY DIFFRACTIONr_nbd_other0.2230.265
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2150.29
X-RAY DIFFRACTIONr_mcbond_it2.0372.662954
X-RAY DIFFRACTIONr_mcbond_other2.0372.662953
X-RAY DIFFRACTIONr_mcangle_it3.0783.9761189
X-RAY DIFFRACTIONr_mcangle_other3.0763.9761190
X-RAY DIFFRACTIONr_scbond_it3.0232.995989
X-RAY DIFFRACTIONr_scbond_other3.0222.995990
X-RAY DIFFRACTIONr_scangle_it4.8374.3361433
X-RAY DIFFRACTIONr_scangle_other4.8354.3361434
X-RAY DIFFRACTIONr_lrange_it6.24831.4922220
X-RAY DIFFRACTIONr_lrange_other6.2331.2812200
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8470.302710.2971362X-RAY DIFFRACTION100
1.847-1.8970.291710.2691313X-RAY DIFFRACTION99.5683
1.897-1.9520.278640.2481303X-RAY DIFFRACTION99.9269
1.952-2.0120.246560.231279X-RAY DIFFRACTION99.6269
2.012-2.0780.244690.2071202X-RAY DIFFRACTION100
2.078-2.1510.216750.21156X-RAY DIFFRACTION99.7569
2.151-2.2330.185640.1851153X-RAY DIFFRACTION99.9179
2.233-2.3240.226480.171100X-RAY DIFFRACTION100
2.324-2.4270.247530.1781058X-RAY DIFFRACTION99.7307
2.427-2.5450.212370.1571026X-RAY DIFFRACTION99.8122
2.545-2.6830.149520.148983X-RAY DIFFRACTION99.4236
2.683-2.8460.213460.136911X-RAY DIFFRACTION99.8956
2.846-3.0420.219410.142866X-RAY DIFFRACTION100
3.042-3.2860.178380.15822X-RAY DIFFRACTION99.8839
3.286-3.5990.198320.134760X-RAY DIFFRACTION100
3.599-4.0230.207290.153700X-RAY DIFFRACTION100
4.023-4.6450.159360.146615X-RAY DIFFRACTION100
4.645-5.6870.225300.167519X-RAY DIFFRACTION100
5.687-8.0350.276230.241423X-RAY DIFFRACTION99.5536
8.035-42.1830.254110.188263X-RAY DIFFRACTION99.6364

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