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- PDB-5l9v: HIF prolyl hydroxylase 2 (PHD2-R281C/P317C) cross-linked to HIF-1... -

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Basic information

Entry
Database: PDB / ID: 5l9v
TitleHIF prolyl hydroxylase 2 (PHD2-R281C/P317C) cross-linked to HIF-1alpha NODD-L397C/D412C and N-oxalylglycine (NOG) (complex-1)
Components
  • Egl nine homolog 1
  • Hypoxia-inducible factor 1-alpha
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 / 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 ...epithelial cell differentiation involved in mammary gland alveolus development / neural fold elevation formation / iris morphogenesis / 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 / peptidyl-proline dioxygenase activity / negative regulation of mesenchymal cell apoptotic process / hemoglobin biosynthetic process / connective tissue replacement involved in inflammatory response wound healing / cardiac ventricle morphogenesis / negative regulation of cyclic-nucleotide phosphodiesterase activity / positive regulation of hormone biosynthetic process / intestinal epithelial cell maturation / Cellular response to hypoxia / retina vasculature development in camera-type eye / negative regulation of growth / positive regulation of mitophagy / mesenchymal cell apoptotic process / regulation of protein neddylation / PTK6 Expression / negative regulation of bone mineralization / intracellular oxygen homeostasis / collagen metabolic process / B-1 B cell homeostasis / vascular endothelial growth factor production / labyrinthine layer development / regulation protein catabolic process at postsynapse / dopaminergic neuron differentiation / cardiac muscle tissue morphogenesis / 2-oxoglutarate-dependent dioxygenase activity / transcription regulator activator activity / heart trabecula formation / regulation of modification of postsynaptic structure / STAT3 nuclear events downstream of ALK signaling / negative regulation of thymocyte apoptotic process / lactate metabolic process / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / positive regulation of cytokine production involved in inflammatory response / positive regulation of signaling receptor activity / negative regulation of TOR signaling / L-ascorbic acid binding / positive regulation of vascular endothelial growth factor receptor signaling pathway / insulin secretion involved in cellular response to glucose stimulus / response to iron ion / neural crest cell migration / Regulation of gene expression by Hypoxia-inducible Factor / embryonic hemopoiesis / motile cilium / regulation of glycolytic process / muscle cell cellular homeostasis / DNA-binding transcription repressor activity / DNA-binding transcription activator activity / digestive tract morphogenesis / response to nitric oxide / regulation of aerobic respiration / PTK6 promotes HIF1A stabilization / ventricular septum morphogenesis / response to muscle activity / positive regulation of neuroblast proliferation / axonal transport of mitochondrion / bone mineralization / heart looping / E-box binding / intracellular glucose homeostasis / TOR signaling / outflow tract morphogenesis / positive regulation of insulin secretion involved in cellular response to glucose stimulus / cellular response to interleukin-1 / positive regulation of epithelial cell migration / positive regulation of vascular endothelial growth factor production / neuroblast proliferation / positive regulation of blood vessel endothelial cell migration / negative regulation of reactive oxygen species metabolic process / embryonic placenta development / epithelial to mesenchymal transition / chondrocyte differentiation / regulation of angiogenesis / cis-regulatory region sequence-specific DNA binding / positive regulation of chemokine production / axon cytoplasm / regulation of neuron apoptotic process / positive regulation of endothelial cell proliferation / lactation / negative regulation of miRNA transcription / positive regulation of nitric-oxide synthase activity / positive regulation of erythrocyte differentiation / positive regulation of glycolytic process / nuclear receptor binding / response to reactive oxygen species / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Hsp90 protein binding / transcription coactivator binding / negative regulation of DNA-binding transcription factor activity / euchromatin
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, 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 ...Hypoxia-inducible factor-1 alpha / : / HIF-1 alpha, transactivation domain, C-terminal / HIF-1 alpha C terminal transactivation 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. / q2cbj1_9rhob like domain / 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 / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / N-OXALYLGLYCINE / Hypoxia-inducible factor 1-alpha / Egl nine homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.829 Å
AuthorsChowdhury, R. / Schofield, C.J.
Citation
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.
#1: Journal: Structure / Year: 2009
Title: Structural basis for binding of hypoxia-inducible factor to the oxygen-sensing prolyl hydroxylases.
Authors: Chowdhury, R. / McDonough, M.A. / Mecinovic, J. / Loenarz, C. / Flashman, E. / Hewitson, K.S. / Domene, C. / Schofield, C.J.
History
DepositionJun 11, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2016Group: Database references
Revision 1.2Nov 29, 2017Group: Database references / Category: pdbx_database_related
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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: Egl nine homolog 1
C: Hypoxia-inducible factor 1-alpha
D: Hypoxia-inducible factor 1-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0568
Polymers59,6524
Non-polymers4044
Water4,035224
1
A: Egl nine homolog 1
C: Hypoxia-inducible factor 1-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0284
Polymers29,8262
Non-polymers2022
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-29 kcal/mol
Surface area10500 Å2
MethodPISA
2
B: Egl nine homolog 1
D: Hypoxia-inducible factor 1-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0284
Polymers29,8262
Non-polymers2022
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-29 kcal/mol
Surface area10480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.807, 73.088, 70.407
Angle α, β, γ (deg.)90.00, 91.17, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#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: 27930.738 Da / Num. of mol.: 2 / Fragment: Catalytic domain, UNP RESIDUES 181-426 / Mutation: C201A, R281C, P317C, R398A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EGLN1, C1orf12, PNAS-118, PNAS-137 / Plasmid: PET28A(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9GZT9, hypoxia-inducible factor-proline dioxygenase
#2: 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: 1895.203 Da / Num. of mol.: 2
Fragment: N-TERMINAL OXYGEN DEPENDENT DEGRADATION DOMAIN (NODD), UNP RESIDUES 395-413
Mutation: L397C, D412C / Source method: obtained synthetically / Details: Synthetic peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: Q16665
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-OGA / N-OXALYLGLYCINE


Mass: 147.086 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H5NO5 / Comment: inhibitor*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.18 Å3/Da / Density % sol: 43.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M ammonium chloride, 20 % w/v polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 4, 2011 / 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: 1.829→43.798 Å / Num. obs: 38965 / % possible obs: 99.7 % / Redundancy: 3.6 % / Biso Wilson estimate: 24.5 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.101 / Net I/σ(I): 11.3375
Reflection shellResolution: 1.829→1.9 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.908 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-2000706Edata reduction
HKL-2000706Edata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HQR

3hqr


Resolution: 1.829→43.798 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1904 1960 5.03 %
Rwork0.1694 --
obs0.1705 38938 99.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT MODEL / Bsol: 60.7256 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 40 Å2
Baniso -1Baniso -2Baniso -3
1--8.31 Å20 Å2-0.16 Å2
2--18.62 Å20 Å2
3----10.31 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a-0.33 Å
Refinement stepCycle: LAST / Resolution: 1.829→43.798 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3563 0 22 224 3809
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053726
X-RAY DIFFRACTIONf_angle_d0.7115059
X-RAY DIFFRACTIONf_dihedral_angle_d13.8772219
X-RAY DIFFRACTIONf_chiral_restr0.047545
X-RAY DIFFRACTIONf_plane_restr0.003664
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8294-1.87520.31941300.28692455X-RAY DIFFRACTION93
1.8752-1.92590.2671360.26692670X-RAY DIFFRACTION100
1.9259-1.98250.23541270.24812674X-RAY DIFFRACTION100
1.9825-2.04650.26141380.21392616X-RAY DIFFRACTION100
2.0465-2.11970.22731250.19652678X-RAY DIFFRACTION100
2.1197-2.20450.22161620.18292650X-RAY DIFFRACTION100
2.2045-2.30490.21791210.17732669X-RAY DIFFRACTION100
2.3049-2.42640.19461350.17662670X-RAY DIFFRACTION100
2.4264-2.57840.19621690.17242613X-RAY DIFFRACTION100
2.5784-2.77740.18871680.17412602X-RAY DIFFRACTION100
2.7774-3.05690.18921280.15772692X-RAY DIFFRACTION100
3.0569-3.49910.17181420.16212635X-RAY DIFFRACTION99
3.4991-4.40780.16151270.1392678X-RAY DIFFRACTION99
4.4078-43.81040.16231520.14842676X-RAY DIFFRACTION99

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