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- PDB-3p3p: Factor inhibiting HIF-1 Alpha in complex with Notch 1 fragment mo... -

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Basic information

Entry
Database: PDB / ID: 3p3p
TitleFactor inhibiting HIF-1 Alpha in complex with Notch 1 fragment mouse notch (1997-2016) peptide
Components
  • Hypoxia-inducible factor 1-alpha inhibitor
  • Notch 1 protein
KeywordsOxidoreductase/TRANSCRIPTION / Double Stranded Beta-Helix / hydroxylase / Iron binding / 2-oxoglutarate binding / Hypoxia Inducible Factor binding / Ankyrin Repeat domain binding / Oxidoreductase-TRANSCRIPTION complex
Function / homology
Function and homology information


Pre-NOTCH Processing in Golgi / regulation of cardioblast proliferation / regulation of inner ear auditory receptor cell differentiation / positive regulation of ephrin receptor signaling pathway / positive regulation of glial cell differentiation / osteoblast fate commitment / venous blood vessel morphogenesis / Activated NOTCH1 Transmits Signal to the Nucleus / coronary sinus valve morphogenesis / cardiac right atrium morphogenesis ...Pre-NOTCH Processing in Golgi / regulation of cardioblast proliferation / regulation of inner ear auditory receptor cell differentiation / positive regulation of ephrin receptor signaling pathway / positive regulation of glial cell differentiation / osteoblast fate commitment / venous blood vessel morphogenesis / Activated NOTCH1 Transmits Signal to the Nucleus / coronary sinus valve morphogenesis / cardiac right atrium morphogenesis / cardiac right ventricle formation / growth involved in heart morphogenesis / Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation / cell differentiation in spinal cord / retinal cone cell differentiation / venous endothelial cell differentiation / arterial endothelial cell differentiation / cardiac chamber formation / epithelial cell fate commitment / negative regulation of pro-B cell differentiation / negative regulation of inner ear auditory receptor cell differentiation / mitral valve formation / cell migration involved in endocardial cushion formation / glomerular mesangial cell development / negative regulation of photoreceptor cell differentiation / negative regulation of cell proliferation involved in heart valve morphogenesis / regulation of somitogenesis / inhibition of neuroepithelial cell differentiation / endocardium morphogenesis / atrioventricular node development / foregut morphogenesis / regulation of cell adhesion involved in heart morphogenesis / distal tubule development / MAML1-RBP-Jkappa- ICN1 complex / regulation of epithelial cell proliferation involved in prostate gland development / auditory receptor cell fate commitment / positive regulation of aorta morphogenesis / negative regulation of endothelial cell chemotaxis / NOTCH1 Intracellular Domain Regulates Transcription / RUNX3 regulates NOTCH signaling / neuroendocrine cell differentiation / collecting duct development / negative regulation of extracellular matrix constituent secretion / positive regulation of transcription of Notch receptor target / hypoxia-inducible factor-asparagine dioxygenase / : / [protein]-asparagine 3-dioxygenase activity / cellular response to tumor cell / positive regulation of apoptotic process involved in morphogenesis / Notch-HLH transcription pathway / compartment pattern specification / vasculogenesis involved in coronary vascular morphogenesis / T-helper 17 type immune response / endocardial cushion development / regulation of extracellular matrix assembly / peptidyl-histidine dioxygenase activity / endocardial cell differentiation / epithelial to mesenchymal transition involved in endocardial cushion formation / cardiac ventricle morphogenesis / positive regulation of smooth muscle cell differentiation / cardiac left ventricle morphogenesis / mesenchymal cell development / peptidyl-aspartic acid 3-dioxygenase activity / epidermal cell fate specification / regulation of Notch signaling pathway / coronary vein morphogenesis / negative regulation of collagen biosynthetic process / cardiac vascular smooth muscle cell development / negative regulation of myotube differentiation / somatic stem cell division / left/right axis specification / negative regulation of cardiac muscle hypertrophy / Cellular response to hypoxia / negative regulation of cell adhesion molecule production / interleukin-17-mediated signaling pathway / positive regulation of endothelial cell differentiation / secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development / endocardium development / apoptotic process involved in embryonic digit morphogenesis / glial cell differentiation / positive regulation of cardiac epithelial to mesenchymal transition / cardiac epithelial to mesenchymal transition / negative regulation of calcium ion-dependent exocytosis / cardiac muscle cell myoblast differentiation / cellular response to follicle-stimulating hormone stimulus / neuron fate commitment / pericardium morphogenesis / cardiac atrium morphogenesis / negative regulation of catalytic activity / carboxylic acid binding / neuronal stem cell population maintenance / positive regulation of vasculogenesis / tissue regeneration / regulation of stem cell proliferation / negative regulation of oligodendrocyte differentiation / positive regulation of astrocyte differentiation / calcium-ion regulated exocytosis / pulmonary valve morphogenesis / heart trabecula morphogenesis / negative regulation of biomineral tissue development
Similarity search - Function
Neurogenic locus notch homolog protein 1 / Clavaminate synthase-like / Notch, C-terminal / Domain of unknown function / Notch / Notch, NOD domain / Notch, NODP domain / Hypoxia-inducible factor 1-alpha inhibitor, domain II / NOTCH protein / NOTCH protein ...Neurogenic locus notch homolog protein 1 / Clavaminate synthase-like / Notch, C-terminal / Domain of unknown function / Notch / Notch, NOD domain / Notch, NODP domain / Hypoxia-inducible factor 1-alpha inhibitor, domain II / NOTCH protein / NOTCH protein / NOD / NODP / Notch-like domain superfamily / LNR (Lin-12/Notch) repeat profile. / LNR domain / Notch domain / Domain found in Notch and Lin-12 / Cupin-like domain 8 / Cupin-like domain / EGF-like, conserved site / Human growth factor-like EGF / : / Calcium-binding EGF domain / EGF-type aspartate/asparagine hydroxylation site / EGF-like domain / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / A domain family that is part of the cupin metalloenzyme superfamily. / Jelly Rolls / JmjC domain / JmjC domain profile. / Epidermal growth factor-like domain. / Ankyrin repeat / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / RmlC-like jelly roll fold / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Helix Hairpins / Jelly Rolls / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / : / Neurogenic locus notch homolog protein 1 / Neurogenic locus notch homolog protein 1 / Hypoxia-inducible factor 1-alpha inhibitor
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.6 Å
AuthorsMcDonough, M.A. / Schofield, C.J.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Asparaginyl hydroxylation of the Notch ankyrin repeat domain by factor inhibiting hypoxia-inducible factor
Authors: Coleman, M.L. / Mcdonough, M.A. / Hewitson, K.S. / Coles, C. / Mecinovic, J. / Edelmann, M. / Cook, K.M. / Cockman, M.E. / Lancaster, D.E. / Kessler, B.M. / Oldham, N.J. / Ratcliffe, P.J. / Schofield, C.J.
History
DepositionOct 5, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypoxia-inducible factor 1-alpha inhibitor
B: Notch 1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9289
Polymers42,2572
Non-polymers6707
Water2,936163
1
A: Hypoxia-inducible factor 1-alpha inhibitor
B: Notch 1 protein
hetero molecules

A: Hypoxia-inducible factor 1-alpha inhibitor
B: Notch 1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,85518
Polymers84,5154
Non-polymers1,34114
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area10030 Å2
ΔGint-137 kcal/mol
Surface area28500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.336, 86.336, 146.450
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Hypoxia-inducible factor 1-alpha inhibitor / Hypoxia-inducible factor asparagine hydroxylase / Factor inhibiting HIF-1 / FIH-1


Mass: 40328.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FIH1, HIF1AN / Plasmid: PET28A(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9NWT6, peptide-aspartate beta-dioxygenase
#2: Protein/peptide Notch 1 protein


Mass: 1929.049 Da / Num. of mol.: 1 / Fragment: UNP residues 1999-2016 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q8K428, UniProt: Q01705*PLUS

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Non-polymers , 5 types, 170 molecules

#3: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O

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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: 3.23 Å3/Da / Density % sol: 61.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.6M AMMONIUM SULFATE, 4% PEG400, 0.1M HEPES PH7.5, NITROGEN ATMOSPHERE, 20MG/ML PROTEIN WITH 1MM FE(II), 2.0MM 2OG AND 10MM PEPTIDE , VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 2, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→40 Å / Num. obs: 16449 / % possible obs: 99.3 % / Observed criterion σ(I): 1 / Redundancy: 3.4 % / Biso Wilson estimate: 47.8 Å2 / Rsym value: 0.078 / Net I/σ(I): 14.75
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 1739 / Rsym value: 0.59 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
CNS1.1refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.6→34.15 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8274 / Data cutoff high absF: 268336 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: RESOLUTION-DEPENDENT WEIGHTING SCHEME USED OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1617 9.8 %RANDOM
Rwork0.208 ---
obs-16449 92.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 80.6721 Å2 / ksol: 0.3665 e/Å3
Displacement parametersBiso max: 161.13 Å2 / Biso mean: 60.8028 Å2 / Biso min: 22.74 Å2
Baniso -1Baniso -2Baniso -3
1--6.17 Å20 Å20 Å2
2---6.17 Å20 Å2
3---12.35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.6→34.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2795 0 39 163 2997
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_mcbond_it1.41.5
X-RAY DIFFRACTIONc_mcangle_it2.42
X-RAY DIFFRACTIONc_scbond_it1.912
X-RAY DIFFRACTIONc_scangle_it2.922.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 32

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.6-2.630.3887410.315378419
2.63-2.660.3754410.3374419460
2.66-2.690.4048460.3165406452
2.69-2.720.362460.2919419465
2.72-2.750.3207390.3044408447
2.75-2.790.3994430.2604435478
2.79-2.820.3081330.274432465
2.82-2.860.2893440.2759440484
2.86-2.90.3823410.2648462503
2.9-2.950.2511450.2224440485
2.95-2.990.314610.2551464525
2.99-3.040.2862480.2308431479
3.04-3.090.3391510.2629455506
3.09-3.150.2736460.2231458504
3.15-3.210.3271500.2204473523
3.21-3.280.3241460.2208460506
3.28-3.350.2613640.2224459523
3.35-3.420.321530.2206467520
3.42-3.510.247480.1787489537
3.51-3.610.2179390.1786490529
3.61-3.710.2306610.1871472533
3.71-3.830.2261650.1966459524
3.83-3.970.2534530.1832486539
3.97-4.130.1887600.1557486546
4.13-4.320.1963530.1605488541
4.32-4.540.233430.1625507550
4.54-4.830.232540.1657497551
4.83-5.20.2246710.1638473544
5.2-5.720.2435550.2107510565
5.72-6.550.2675590.2236509568
6.55-8.250.2449600.2238515575
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4gol.pargol.top
X-RAY DIFFRACTION52og.par2og.top

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