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- PDB-3p3n: Factor inhibiting HIF-1 Alpha in complex with Notch 1 fragment mo... -

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Basic information

Entry
Database: PDB / ID: 3p3n
TitleFactor inhibiting HIF-1 Alpha in complex with Notch 1 fragment mouse notch (1930-1949) 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 inner ear auditory receptor cell differentiation / positive regulation of ephrin receptor signaling pathway / 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 ...Pre-NOTCH Processing in Golgi / regulation of inner ear auditory receptor cell differentiation / positive regulation of ephrin receptor signaling pathway / 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 / venous endothelial cell differentiation / retinal cone cell differentiation / arterial endothelial cell differentiation / 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 / negative regulation of photoreceptor cell differentiation / negative regulation of cell proliferation involved in heart valve morphogenesis / regulation of somitogenesis / endocardium morphogenesis / foregut morphogenesis / distal tubule development / inhibition of neuroepithelial cell differentiation / MAML1-RBP-Jkappa- ICN1 complex / regulation of epithelial cell proliferation involved in prostate gland development / cardiac chamber formation / NOTCH1 Intracellular Domain Regulates Transcription / RUNX3 regulates NOTCH signaling / auditory receptor cell fate commitment / negative regulation of endothelial cell chemotaxis / atrioventricular node development / positive regulation of transcription of Notch receptor target / neuroendocrine cell differentiation / positive regulation of aorta morphogenesis / cellular response to tumor cell / Notch-HLH transcription pathway / hypoxia-inducible factor-asparagine dioxygenase / : / negative regulation of extracellular matrix constituent secretion / [protein]-asparagine 3-dioxygenase activity / collecting duct development / compartment pattern specification / positive regulation of apoptotic process involved in morphogenesis / vasculogenesis involved in coronary vascular morphogenesis / regulation of extracellular matrix assembly / endocardial cell differentiation / chemical synaptic transmission, postsynaptic / peptidyl-histidine dioxygenase activity / epithelial to mesenchymal transition involved in endocardial cushion formation / T-helper 17 type immune response / cardiac ventricle morphogenesis / endocardial cushion development / positive regulation of smooth muscle cell differentiation / epidermal cell fate specification / mesenchymal cell development / peptidyl-aspartic acid 3-dioxygenase activity / coronary vein morphogenesis / cardiac left ventricle morphogenesis / cardiac vascular smooth muscle cell development / negative regulation of myotube differentiation / left/right axis specification / regulation of vascular endothelial growth factor receptor signaling pathway / negative regulation of catalytic activity / glomerular mesangial cell development / somatic stem cell division / negative regulation of cell adhesion molecule production / Cellular response to hypoxia / endocardium development / apoptotic process involved in embryonic digit morphogenesis / regulation of cell adhesion involved in heart morphogenesis / negative regulation of cardiac muscle hypertrophy / positive regulation of endothelial cell differentiation / regulation of Notch signaling pathway / positive regulation of cardiac epithelial to mesenchymal transition / interleukin-17-mediated signaling pathway / cardiac epithelial to mesenchymal transition / pericardium morphogenesis / cardiac atrium morphogenesis / secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development / neuron fate commitment / negative regulation of collagen biosynthetic process / neuronal stem cell population maintenance / cardiac muscle cell myoblast differentiation / cellular response to follicle-stimulating hormone stimulus / positive regulation of vasculogenesis / carboxylic acid binding / negative regulation of calcium ion-dependent exocytosis / positive regulation of astrocyte differentiation / negative regulation of oligodendrocyte differentiation / tissue regeneration / regulation of stem cell proliferation / pulmonary valve morphogenesis / luteolysis / calcium-ion regulated exocytosis / glial cell differentiation / heart trabecula morphogenesis
Similarity search - Function
Clavaminate synthase-like / Neurogenic locus notch homolog protein 1 / Notch, C-terminal / Domain of unknown function / : / Notch / Notch, NOD domain / Notch, NODP domain / NOTCH protein / NOTCH protein ...Clavaminate synthase-like / Neurogenic locus notch homolog protein 1 / Notch, C-terminal / Domain of unknown function / : / Notch / Notch, NOD domain / Notch, NODP domain / NOTCH protein / NOTCH protein / NOD / NODP / Hypoxia-inducible factor 1-alpha inhibitor, domain II / Notch-like domain superfamily / LNR domain / LNR (Lin-12/Notch) repeat profile. / 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-like domain / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Jelly Rolls / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / Ankyrin repeat / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 1. / EGF-like domain signature 2. / 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: 2.4 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 1.2Sep 6, 2023Group: 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 / 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)43,25210
Polymers42,4902
Non-polymers7628
Water2,990166
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)86,50420
Polymers84,9794
Non-polymers1,52516
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area10190 Å2
ΔGint-130 kcal/mol
Surface area28690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.188, 86.188, 147.943
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: 2161.312 Da / Num. of mol.: 1 / Fragment: UNP residues 1930-1949 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q8K428, UniProt: Q01705*PLUS

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Non-polymers , 5 types, 174 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 61.96 %
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: PX10.1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 2, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.4→37.3 Å / Num. obs: 20888 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 11.8 % / Biso Wilson estimate: 37.2 Å2 / Rsym value: 0.155 / Net I/σ(I): 14.78
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 11.8 % / Mean I/σ(I) obs: 3.33 / Rsym value: 0.8 / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1H2N

1h2n


Resolution: 2.4→37.3 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 310707.97 / 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 U OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.244 2060 9.9 %RANDOM
Rwork0.204 ---
obs0.204 20888 92.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 75.8104 Å2 / ksol: 0.348475 e/Å3
Displacement parametersBiso mean: 58.9 Å2
Baniso -1Baniso -2Baniso -3
1--6.47 Å20 Å20 Å2
2---6.47 Å20 Å2
3---12.95 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.4→37.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2779 0 45 166 2990
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.02
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.651.5
X-RAY DIFFRACTIONc_mcangle_it2.682
X-RAY DIFFRACTIONc_scbond_it2.42
X-RAY DIFFRACTIONc_scangle_it3.462.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.4→2.49 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.352 157 8.8 %
Rwork0.289 1632 -
obs--81.6 %
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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