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- PDB-2qc9: Mouse Notch 1 Ankyrin Repeat Intracellular Domain -

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Basic information

Entry
Database: PDB / ID: 2qc9
TitleMouse Notch 1 Ankyrin Repeat Intracellular Domain
ComponentsNotch 1 protein
KeywordsTRANSCRIPTION / beta-hydroxy asparagine / ankyrin repeat / factor inhibiting HIF
Function / homology
Function and homology information


Pre-NOTCH Processing in Golgi / cardiac right ventricle formation / regulation of inner ear auditory receptor cell differentiation / osteoblast fate commitment / negative regulation of inner ear auditory receptor cell differentiation / positive regulation of aorta morphogenesis / negative regulation of photoreceptor cell differentiation / apoptotic process involved in embryonic digit morphogenesis / venous blood vessel morphogenesis / regulation of somitogenesis ...Pre-NOTCH Processing in Golgi / cardiac right ventricle formation / regulation of inner ear auditory receptor cell differentiation / osteoblast fate commitment / negative regulation of inner ear auditory receptor cell differentiation / positive regulation of aorta morphogenesis / negative regulation of photoreceptor cell differentiation / apoptotic process involved in embryonic digit morphogenesis / venous blood vessel morphogenesis / regulation of somitogenesis / foregut morphogenesis / regulation of epithelial cell proliferation involved in prostate gland development / positive regulation of ephrin receptor signaling pathway / positive regulation of glial cell differentiation / auditory receptor cell fate commitment / secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development / CSL-Notch-Mastermind transcription factor complex / compartment pattern specification / endocardial cushion development / somatic stem cell division / coronary sinus valve morphogenesis / cardiac right atrium morphogenesis / growth involved in heart morphogenesis / regulation of cardioblast proliferation / mesenchymal cell development / cell differentiation in spinal cord / venous endothelial cell differentiation / arterial endothelial cell differentiation / collecting duct development / cell migration involved in endocardial cushion formation / negative regulation of pro-B cell differentiation / prostate gland epithelium morphogenesis / mitral valve formation / : / endocardium morphogenesis / distal tubule development / MAML1-RBP-Jkappa- ICN1 complex / cardiac chamber formation / cardiac atrium morphogenesis / endoderm development / NOTCH1 Intracellular Domain Regulates Transcription / RUNX3 regulates NOTCH signaling / pericardium morphogenesis / atrioventricular node development / cardiac ventricle morphogenesis / positive regulation of transcription of Notch receptor target / negative regulation of endothelial cell chemotaxis / cardiac septum morphogenesis / glomerular mesangial cell development / cellular response to tumor cell / Notch-HLH transcription pathway / positive regulation of smooth muscle cell differentiation / Activated NOTCH1 Transmits Signal to the Nucleus / vasculogenesis involved in coronary vascular morphogenesis / negative regulation of extracellular matrix constituent secretion / regulation of extracellular matrix assembly / chemical synaptic transmission, postsynaptic / positive regulation of apoptotic process involved in morphogenesis / endocardial cell differentiation / left/right axis specification / epithelial to mesenchymal transition involved in endocardial cushion formation / positive regulation of endothelial cell differentiation / cardiac left ventricle morphogenesis / embryonic hindlimb morphogenesis / negative regulation of myotube differentiation / coronary vein morphogenesis / negative regulation of glial cell proliferation / cardiac vascular smooth muscle cell development / neuronal stem cell population maintenance / endocardium development / positive regulation of astrocyte differentiation / cardiac muscle cell myoblast differentiation / negative regulation of cell adhesion molecule production / negative regulation of stem cell differentiation / glial cell differentiation / tissue regeneration / T-helper 17 type immune response / negative regulation of calcium ion-dependent exocytosis / skeletal muscle cell differentiation / positive regulation of cardiac epithelial to mesenchymal transition / regulation of Notch signaling pathway / cardiac epithelial to mesenchymal transition / heart trabecula morphogenesis / embryonic limb morphogenesis / neuron fate commitment / negative regulation of oligodendrocyte differentiation / regulation of cell adhesion involved in heart morphogenesis / interleukin-17-mediated signaling pathway / negative regulation of catalytic activity / negative regulation of myoblast differentiation / camera-type eye morphogenesis / cellular response to follicle-stimulating hormone stimulus / neural tube development / negative regulation of collagen biosynthetic process / negative regulation of cardiac muscle hypertrophy / luteolysis / determination of left/right symmetry / pulmonary valve morphogenesis / tube formation / cardiac muscle tissue morphogenesis
Similarity search - Function
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 ...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 / Notch-like domain superfamily / LNR (Lin-12/Notch) repeat profile. / LNR domain / Notch domain / Domain found in Notch and Lin-12 / EGF-like, conserved site / Human growth factor-like EGF / Ankyrin repeat-containing domain / : / Calcium-binding EGF domain / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / 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 / 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 / Ankyrin repeat profile. / Ankyrin repeats (3 copies) / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Neurogenic locus notch homolog protein 1 / Neurogenic locus notch homolog protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 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
DepositionJun 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). THE AUTHOR REPORTS THE BIOLOGICAL ASSEMBLY TO BE UNKNOWN

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Notch 1 protein
B: Notch 1 protein


Theoretical massNumber of molelcules
Total (without water)46,2662
Polymers46,2662
Non-polymers00
Water7,963442
1
A: Notch 1 protein


Theoretical massNumber of molelcules
Total (without water)23,1331
Polymers23,1331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Notch 1 protein


Theoretical massNumber of molelcules
Total (without water)23,1331
Polymers23,1331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)98.203, 98.203, 108.703
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
DetailsTHE AUTHOR REPORTS THE BIOLOGICAL ASSEMBLY TO BE UNKNOWN

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Components

#1: Protein Notch 1 protein


Mass: 23132.811 Da / Num. of mol.: 2 / Fragment: Ankyrin Repeat Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Notch1 / Plasmid: pGEX-4T1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q8K428, UniProt: Q01705*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 442 / 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: 3.47 Å3/Da / Density % sol: 64.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 30% PEG 6000, 100mM HEPES, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Dec 15, 2005 / Details: Montel 200
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection twinType: hemihedral / Operator: h,-h-k,-l / Fraction: 0.19
ReflectionResolution: 2.35→67 Å / Num. obs: 48746 / % possible obs: 100 % / Redundancy: 11.1 % / Rsym value: 0.1423 / Net I/σ(I): 7.43
Reflection shellResolution: 2.35→2.4 Å / Redundancy: 9.27 % / Mean I/σ(I) obs: 2.56 / Num. unique all: 1534 / Rsym value: 0.4344 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
SAINTdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACT2data extraction
PROTEUM PLUSPLUSdata collection
SAINTdata reduction
SADABSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YYH

1yyh


Resolution: 2.35→67 Å / σ(F): 2205
RfactorNum. reflection% reflection
Rfree0.228 3699 7.6 %
Rwork0.173 --
obs-43554 89.2 %
Solvent computationBsol: 63.82 Å2
Displacement parametersBiso mean: 21.372 Å2
Baniso -1Baniso -2Baniso -3
1--4.241 Å20.137 Å20 Å2
2---4.241 Å20 Å2
3---8.482 Å2
Refinement stepCycle: LAST / Resolution: 2.35→67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3022 0 0 442 3464
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.2881.5
X-RAY DIFFRACTIONc_scbond_it2.0042
X-RAY DIFFRACTIONc_mcangle_it2.0922
X-RAY DIFFRACTIONc_scangle_it2.9672.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.35-2.460.2763840.24146325016
2.46-2.590.2664400.21650635503
2.59-2.750.2634960.20850115507
2.75-2.960.2425460.19248945440
2.96-3.260.254620.17847445206
3.26-3.730.2343870.1647755162
3.73-4.70.185240.12752395763
4.7-500.010.2034600.15254975957
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param

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