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- PDB-2f8x: Crystal structure of activated Notch, CSL and MAML on HES-1 promo... -

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Basic information

Entry
Database: PDB / ID: 2f8x
TitleCrystal structure of activated Notch, CSL and MAML on HES-1 promoter DNA sequence
Components
  • 5'-D(*GP*TP*TP*AP*CP*TP*GP*TP*GP*GP*GP*AP*AP*AP*GP*AP*AP*A)-3'
  • 5'-D(*TP*TP*TP*CP*TP*TP*TP*CP*CP*CP*AP*CP*AP*GP*TP*AP*AP*C)-3'
  • Mastermind-like protein 1
  • Neurogenic locus notch homolog protein 1
  • Recombining binding protein suppressor of hairless, isoform 4
KeywordsTRANSCRIPTION/DNA / Notch / CSL / Mastermind / Hes-1 / ankyrin repeats / Rel-Homology region / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


blood vessel endothelial cell fate specification / positive regulation of ERBB signaling pathway / club cell differentiation / arterial endothelial cell fate commitment / blood vessel lumenization / regulation of generation of precursor metabolites and energy / regulation of timing of cell differentiation / positive regulation of ephrin receptor signaling pathway / atrioventricular node cell development / pulmonary valve development ...blood vessel endothelial cell fate specification / positive regulation of ERBB signaling pathway / club cell differentiation / arterial endothelial cell fate commitment / blood vessel lumenization / regulation of generation of precursor metabolites and energy / regulation of timing of cell differentiation / positive regulation of ephrin receptor signaling pathway / atrioventricular node cell development / pulmonary valve development / Defective LFNG causes SCDO3 / dorsal aorta morphogenesis / sebaceous gland development / 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 / Pre-NOTCH Processing in the Endoplasmic Reticulum / negative regulation of inner ear auditory receptor cell differentiation / positive regulation of cell proliferation involved in heart morphogenesis / 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 / secondary heart field specification / 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 / aortic valve development / cellular response to tumor cell / negative regulation of extracellular matrix constituent secretion / 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 / epithelial to mesenchymal transition involved in endocardial cushion formation / T-helper 17 type immune response / cardiac ventricle morphogenesis / Constitutive Signaling by NOTCH1 t(7;9)(NOTCH1:M1580_K2555) Translocation Mutant / positive regulation of smooth muscle cell differentiation / epidermal cell fate specification / mesenchymal cell development / coronary vein morphogenesis / cardiac left ventricle morphogenesis / pituitary gland development / cardiac vascular smooth muscle cell development / negative regulation of myotube differentiation / left/right axis specification / NOTCH2 intracellular domain regulates transcription / negative regulation of catalytic activity / glomerular mesangial cell development / somatic stem cell division / negative regulation of cell adhesion molecule production / 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 / positive regulation of cardiac epithelial to mesenchymal transition / atrioventricular canal development / interleukin-17-mediated signaling pathway / cardiac epithelial to mesenchymal transition / Pre-NOTCH Processing in Golgi / pericardium morphogenesis / cardiac atrium morphogenesis / hair follicle maturation / secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development / negative regulation of collagen biosynthetic process / neuronal stem cell population maintenance / cardiac muscle cell myoblast differentiation / cellular response to follicle-stimulating hormone stimulus / 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
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #970 / Neurogenic mastermind-like, N-terminal / Mastermind-like 1-3 / Neurogenic mastermind-like, N-terminal domain superfamily / : / : / MamL-1 domain / Mastermind-like 1/3, transactivation domain 2 / Mastermind-like 1/3, transactivation domain 1 / MamL-1 domain ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #970 / Neurogenic mastermind-like, N-terminal / Mastermind-like 1-3 / Neurogenic mastermind-like, N-terminal domain superfamily / : / : / MamL-1 domain / Mastermind-like 1/3, transactivation domain 2 / Mastermind-like 1/3, transactivation domain 1 / MamL-1 domain / LAG1, DNA binding domain / Beta-trefoil DNA-binding domain / RBP-J/Cbf11/Cbf12, DNA binding / Beta-trefoil domain superfamily / RBP-J/Cbf11, DNA binding domain superfamily / RBP-Jkappa, IPT domain / Suppressor of hairless-like / Beta-trefoil DNA-binding domain / LAG1, DNA binding / TIG domain / LAG1, DNA binding / Beta-trefoil DNA-binding domain / 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 domain / LNR (Lin-12/Notch) repeat profile. / Notch domain / Domain found in Notch and Lin-12 / EGF-like, conserved site / Human growth factor-like EGF / Ankyrin repeats (many copies) / : / Calcium-binding EGF domain / Ankyrin repeat-containing domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / EGF-like domain / p53-like transcription factor, DNA-binding / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / 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 / Helix non-globular / Ankyrin repeats (3 copies) / Special / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Immunoglobulin E-set / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Neurogenic locus notch homolog protein 1 / Recombining binding protein suppressor of hairless / Mastermind-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 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 / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: 5'-D(*GP*TP*TP*AP*CP*TP*GP*TP*GP*GP*GP*AP*AP*AP*GP*AP*AP*A)-3'
Y: 5'-D(*TP*TP*TP*CP*TP*TP*TP*CP*CP*CP*AP*CP*AP*GP*TP*AP*AP*C)-3'
C: Recombining binding protein suppressor of hairless, isoform 4
K: Neurogenic locus notch homolog protein 1
M: Mastermind-like protein 1


Theoretical massNumber of molelcules
Total (without water)95,7425
Polymers95,7425
Non-polymers00
Water18010
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)273.866, 273.866, 121.016
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

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DNA chain , 2 types, 2 molecules XY

#1: DNA chain 5'-D(*GP*TP*TP*AP*CP*TP*GP*TP*GP*GP*GP*AP*AP*AP*GP*AP*AP*A)-3'


Mass: 5628.679 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*TP*TP*TP*CP*TP*TP*TP*CP*CP*CP*AP*CP*AP*GP*TP*AP*AP*C)-3'


Mass: 5401.517 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Protein , 3 types, 3 molecules CKM

#3: Protein Recombining binding protein suppressor of hairless, isoform 4


Mass: 49294.230 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pRSETa / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q06330
#4: Protein Neurogenic locus notch homolog protein 1 / (Notch 1) (hN1) (Translocation-associated notch protein TAN-1)


Mass: 27885.004 Da / Num. of mol.: 1
Fragment: [Contains: Notch 1 extracellular truncation; Notch 1 intracellular domain]
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NOTCH1, TAN1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P46531
#5: Protein Mastermind-like protein 1 / Mam-1


Mass: 7532.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAML1, KIAA0200 / Plasmid: pDEST15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q92585

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Non-polymers , 1 types, 10 molecules

#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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

Crystal growTemperature: 298 K / Method: hanging drop / pH: 7.9
Details: 50mM HEPES, 6% PEG 3350, and 5% ethylene glycol, pH 7.9, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1HEPES11
2PEG 335011
3ethylene glycol11
4H2O11
5HEPES12
6PEG 335012
7ethylene glycol12

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 10, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 3.25→44.82 Å / Num. all: 79964 / Num. obs: 72848 / % possible obs: 91.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rsym value: 0.084 / Net I/σ(I): 19.7
Reflection shellResolution: 3.25→3.45 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 3.3 / Num. unique all: 11314 / Rsym value: 0.411 / % possible all: 89.3

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
PDB_EXTRACT1.701data extraction
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries: 1TTU and 2F8Y

1ttu

2f8y


Resolution: 3.25→44.82 Å / Isotropic thermal model: group / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.257 3688 4.6 %random
Rwork0.222 ---
all0.241 79964 --
obs0.241 72848 91.1 %-
Solvent computationBsol: 38.828 Å2
Displacement parametersBiso mean: 89.29 Å2
Baniso -1Baniso -2Baniso -3
1-12.481 Å24.194 Å20 Å2
2--12.481 Å20 Å2
3----24.963 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.68 Å0.65 Å
Refinement stepCycle: LAST / Resolution: 3.25→44.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5497 732 0 10 6239
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_improper_angle_d1.21
LS refinement shellResolution: 3.25→3.45 Å / Rfactor Rfree error: 0.015
RfactorNum. reflection% reflection
Rfree0.374 590 -
Rwork0.357 --
obs-11904 89.3 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param

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