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- PDB-3v79: Structure of human Notch1 transcription complex including CSL, RA... -

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Basic information

Entry
Database: PDB / ID: 3v79
TitleStructure of human Notch1 transcription complex including CSL, RAM, ANK, and MAML-1 on HES-1 promoter DNA sequence
Components
  • DNA 5'-D(*GP*TP*TP*AP*CP*TP*GP*TP*GP*GP*GP*AP*AP*AP*GP*AP*AP*A)-3'
  • DNA 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
  • RAM
  • Recombining binding protein suppressor of hairless
Keywordstranscription/DNA / beta-trefoil / ankyrin / transcription activation / DNA Binding / transcription-DNA complex
Function / homology
Function and homology information


regulation of generation of precursor metabolites and energy / 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 timing of cell differentiation / regulation of reproductive process / atrioventricular node cell development / positive regulation of ephrin receptor signaling pathway ...regulation of generation of precursor metabolites and energy / 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 timing of cell differentiation / regulation of reproductive process / atrioventricular node cell development / positive regulation of ephrin receptor signaling pathway / secondary heart field specification / positive regulation of cell proliferation involved in heart morphogenesis / pulmonary valve development / Defective LFNG causes SCDO3 / dorsal aorta morphogenesis / 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 / sebaceous gland development / arterial endothelial cell differentiation / cardiac chamber formation / 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 / 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 / aortic valve development / auditory receptor cell fate commitment / positive regulation of aorta morphogenesis / negative regulation of endothelial cell chemotaxis / neuroendocrine cell differentiation / collecting duct development / negative regulation of extracellular matrix constituent secretion / positive regulation of transcription of Notch receptor target / cellular response to tumor cell / positive regulation of apoptotic process involved in morphogenesis / compartment pattern specification / vasculogenesis involved in coronary vascular morphogenesis / T-helper 17 type immune response / regulation of extracellular matrix assembly / endocardial cell differentiation / epithelial to mesenchymal transition involved in endocardial cushion formation / cardiac ventricle morphogenesis / Constitutive Signaling by NOTCH1 t(7;9)(NOTCH1:M1580_K2555) Translocation Mutant / positive regulation of smooth muscle cell differentiation / cardiac left ventricle morphogenesis / mesenchymal cell development / epidermal cell fate specification / coronary vein morphogenesis / negative regulation of collagen biosynthetic process / cardiac vascular smooth muscle cell development / pituitary gland development / negative regulation of myotube differentiation / somatic stem cell division / left/right axis specification / NOTCH2 intracellular domain regulates transcription / negative regulation of cardiac muscle hypertrophy / 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 / positive regulation of cardiac epithelial to mesenchymal transition / atrioventricular canal development / Pre-NOTCH Processing in Golgi / cardiac epithelial to mesenchymal transition / negative regulation of calcium ion-dependent exocytosis / cardiac muscle cell myoblast differentiation / cellular response to follicle-stimulating hormone stimulus / pericardium morphogenesis / cardiac atrium morphogenesis / negative regulation of catalytic activity / hair follicle maturation / neuronal stem cell population maintenance / tissue regeneration / regulation of stem cell proliferation / negative regulation of oligodendrocyte differentiation / myeloid dendritic cell differentiation / positive regulation of astrocyte differentiation / calcium-ion regulated exocytosis / pulmonary valve morphogenesis
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 (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 / Calcium-binding EGF domain / Ankyrin repeat-containing domain / Ankyrin repeats (many copies) / EGF-type aspartate/asparagine hydroxylation site / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / EGF-like domain / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / p53-like transcription factor, DNA-binding / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / 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 2. / EGF-like domain signature 1. / EGF-like domain / Helix non-globular / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Special / Alpha Horseshoe / Immunoglobulin E-set / Immunoglobulins / Immunoglobulin-like fold / 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: 3.85 Å
AuthorsNam, Y. / Sliz, P. / Blacklow, S.
CitationJournal: Structure / Year: 2012
Title: Conformational Locking upon Cooperative Assembly of Notch Transcription Complexes.
Authors: Choi, S.H. / Wales, T.E. / Nam, Y. / O'Donovan, D.J. / Sliz, P. / Engen, J.R. / Blacklow, S.C.
History
DepositionDec 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2012Group: Database references
Revision 1.2Mar 21, 2012Group: Database references
Revision 1.3Sep 13, 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
K: Neurogenic locus notch homolog protein 1
C: Recombining binding protein suppressor of hairless
M: Mastermind-like protein 1
X: DNA 5'-D(*GP*TP*TP*AP*CP*TP*GP*TP*GP*GP*GP*AP*AP*AP*GP*AP*AP*A)-3'
Y: DNA 5'-D(*TP*TP*TP*CP*TP*TP*TP*CP*CP*CP*AP*CP*AP*GP*TP*AP*AP*C)-3'
R: RAM


Theoretical massNumber of molelcules
Total (without water)98,1346
Polymers98,1346
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11370 Å2
ΔGint-61 kcal/mol
Surface area38170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)272.646, 272.646, 119.987
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
DetailsIntracellular Notch, CSL, and MAML can form a heterotrimeric complex on DNA duplex as shown in the asymmetric unit. In some instances when the CSL binding sites are located close to each other, a heterotrimer may interact with another heterotrimer.

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Components

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Protein , 3 types, 3 molecules KCM

#1: Protein Neurogenic locus notch homolog protein 1 / Notch 1 / hN1 / Translocation-associated notch protein TAN-1 / Notch 1 extracellular truncation / ...Notch 1 / hN1 / Translocation-associated notch protein TAN-1 / Notch 1 extracellular truncation / Notch 1 intracellular domain / NICD


Mass: 27885.004 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NOTCH1, TAN1 / Production host: Escherichia coli (E. coli) / References: UniProt: P46531
#2: Protein Recombining binding protein suppressor of hairless / CBF-1 / J kappa-recombination signal-binding protein / RBP-J kappa / RBP-J / RBP-JK / Renal ...CBF-1 / J kappa-recombination signal-binding protein / RBP-J kappa / RBP-J / RBP-JK / Renal carcinoma antigen NY-REN-30


Mass: 49294.230 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGKJRB, IGKJRB1, RBPJ, RBPJK, RBPSUH / Production host: Escherichia coli (E. coli) / References: UniProt: Q06330
#3: 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 / Production host: Escherichia coli (E. coli) / References: UniProt: Q92585

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DNA chain , 2 types, 2 molecules XY

#4: DNA chain DNA 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 / Details: Synthesized oligonucleotides
#5: DNA chain DNA 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 / Details: Synthesized oligonucleotides

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Protein/peptide , 1 types, 1 molecules R

#6: Protein/peptide RAM


Mass: 2391.730 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P46531*PLUS

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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: 6.56 Å3/Da / Density % sol: 81.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: 6% PEG 3350, 5% Ethylene glycol, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792899 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 4, 2005
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792899 Å / Relative weight: 1
ReflectionResolution: 3.85→50 Å / Num. all: 47298 / Num. obs: 40195 / % possible obs: 85 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1

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Processing

Software
NameClassification
HKL-2000data collection
PHASERphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2F8X

2f8x


Resolution: 3.85→50 Å / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2446 2049 From PDB Code 2F8X
Rwork0.2128 --
all0.2128 47298 -
obs0.2128 40195 -
Refine analyze
FreeObs
Luzzati coordinate error0.54 Å0.46 Å
Luzzati d res low-5 Å
Luzzati sigma a0.85 Å0.87 Å
Refinement stepCycle: LAST / Resolution: 3.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5689 732 0 0 6421
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.003
X-RAY DIFFRACTIONc_angle_d0.773
X-RAY DIFFRACTIONc_mcbond_it9.144
X-RAY DIFFRACTIONc_mcangle_it14.186
X-RAY DIFFRACTIONc_scbond_it12.798
X-RAY DIFFRACTIONc_scangle_it18.289
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_improper_angle_d0.63

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