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- PDB-2f8y: Crystal structure of human Notch1 ankyrin repeats to 1.55A resolution. -

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Basic information

Entry
Database: PDB / ID: 2f8y
TitleCrystal structure of human Notch1 ankyrin repeats to 1.55A resolution.
ComponentsNotch homolog 1, translocation-associated (Drosophila)
KeywordsTRANSCRIPTION / Notch / Ankyrin repeats
Function / homology
Function and homology information


Defective LFNG causes SCDO3 / 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 ...Defective LFNG causes SCDO3 / 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 / Pre-NOTCH Processing in the Endoplasmic Reticulum / mitral valve formation / : / endocardium morphogenesis / distal tubule development / MAML1-RBP-Jkappa- ICN1 complex / cardiac chamber formation / cardiac atrium morphogenesis / 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 / positive regulation of smooth muscle cell differentiation / 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 / Constitutive Signaling by NOTCH1 t(7;9)(NOTCH1:M1580_K2555) Translocation Mutant / positive regulation of endothelial cell differentiation / cardiac left ventricle 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 / tissue regeneration / T-helper 17 type immune response / positive regulation of cardiac epithelial to mesenchymal transition / cardiac epithelial to mesenchymal transition / heart trabecula morphogenesis / negative regulation of oligodendrocyte differentiation / regulation of cell adhesion involved in heart morphogenesis / interleukin-17-mediated signaling pathway / Pre-NOTCH Processing in Golgi / negative regulation of catalytic activity / negative regulation of myoblast differentiation / cellular response to follicle-stimulating hormone stimulus / 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 / oligodendrocyte differentiation / atrioventricular valve morphogenesis / ventricular trabecula myocardium morphogenesis / coronary artery morphogenesis / negative regulation of cell migration involved in sprouting angiogenesis / negative regulation of cell-cell adhesion mediated by cadherin / negative regulation of ossification / negative regulation of biomineral tissue development / response to muramyl dipeptide / astrocyte differentiation / positive regulation of BMP signaling pathway / endocardial cushion morphogenesis / transcription regulator activator activity / homeostasis of number of cells within a tissue / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RUNX3 regulates NOTCH signaling / Notch binding / Regulation of NFE2L2 gene expression / NOTCH4 Intracellular Domain Regulates Transcription / positive regulation of neuroblast proliferation / aortic valve morphogenesis / negative regulation of cold-induced thermogenesis / negative regulation of neuron differentiation / NOTCH3 Intracellular Domain Regulates Transcription / NFE2L2 regulating tumorigenic genes / heart looping / ventricular septum morphogenesis / Notch-HLH transcription pathway / Formation of paraxial mesoderm / Somitogenesis
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 / Ankyrin repeats (many copies) / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsNam, Y. / Sliz, P. / Blacklow, S.C.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2006
Title: Structural basis for cooperativity in recruitment of MAML coactivators to Notch transcription complexes.
Authors: Nam, Y. / Sliz, P. / Song, L. / Aster, J.C. / Blacklow, S.C.
History
DepositionDec 4, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Notch homolog 1, translocation-associated (Drosophila)
B: Notch homolog 1, translocation-associated (Drosophila)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1974
Polymers49,0052
Non-polymers1922
Water7,278404
1
A: Notch homolog 1, translocation-associated (Drosophila)


Theoretical massNumber of molelcules
Total (without water)24,5021
Polymers24,5021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Notch homolog 1, translocation-associated (Drosophila)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6943
Polymers24,5021
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.933, 97.933, 109.068
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Notch homolog 1, translocation-associated (Drosophila)


Mass: 24502.348 Da / Num. of mol.: 2 / Fragment: ankyrin repeat domain, repeats 1-7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Notch1 / Plasmid: pDEST15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P46531
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 404 / 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: 3.18 Å3/Da / Density % sol: 61.34 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 28, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.55→30 Å / Num. all: 85821 / Num. obs: 70977 / % possible obs: 82.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Rsym value: 0.068 / Net I/σ(I): 11.9
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2 / Num. unique all: 3220 / Rsym value: 0.375 / % possible all: 45.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OT8

1ot8


Resolution: 1.55→30 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1901493.44 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.187 4762 6.7 %RANDOM
Rwork0.15 ---
all0.152 85821 --
obs0.152 70977 82.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 71.4968 Å2 / ksol: 0.406579 e/Å3
Displacement parametersBiso mean: 26.6 Å2
Baniso -1Baniso -2Baniso -3
1-2.79 Å22.24 Å20 Å2
2--2.79 Å20 Å2
3----5.58 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.55→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3282 0 10 404 3696
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.181.5
X-RAY DIFFRACTIONc_mcangle_it1.942
X-RAY DIFFRACTIONc_scbond_it1.962
X-RAY DIFFRACTIONc_scangle_it3.092.5
LS refinement shellResolution: 1.55→1.61 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.279 247 7.1 %
Rwork0.283 4981 -
obs-3220 45.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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