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- PDB-3nbn: Crystal structure of a dimer of Notch Transcription Complex trime... -

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Basic information

Entry
Database: PDB / ID: 3nbn
TitleCrystal structure of a dimer of Notch Transcription Complex trimers on HES1 DNA
Components
  • (DNA, HES1 promoter) x 2
  • Mastermind-like protein 1
  • Neurogenic locus notch homolog protein 1
  • Recombining binding protein suppressor of hairless
KeywordsTRANSCRIPTION/DNA / Promoter Regions / Notch1 / CSL / RBPJ / Mastermind / Transcription Factors / Transcription / Transcriptional Activation / 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 / cardiac vascular smooth muscle cell development / pituitary gland 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 / atrioventricular canal development / positive regulation of cardiac epithelial to mesenchymal transition / 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 / cardiac muscle cell myoblast differentiation / neuronal stem cell population maintenance / 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: 3.45 Å
AuthorsArnett, K.L. / Blacklow, S.C.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Structural and mechanistic insights into cooperative assembly of dimeric Notch transcription complexes.
Authors: Arnett, K.L. / Hass, M. / McArthur, D.G. / Ilagan, M.X. / Aster, J.C. / Kopan, R. / Blacklow, S.C.
History
DepositionJun 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 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
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Recombining binding protein suppressor of hairless
B: Neurogenic locus notch homolog protein 1
C: Mastermind-like protein 1
D: Recombining binding protein suppressor of hairless
E: Neurogenic locus notch homolog protein 1
F: Mastermind-like protein 1
X: DNA, HES1 promoter
Y: DNA, HES1 promoter


Theoretical massNumber of molelcules
Total (without water)192,0488
Polymers192,0488
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20020 Å2
ΔGint-83 kcal/mol
Surface area69420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)295.112, 108.059, 87.239
Angle α, β, γ (deg.)90.00, 102.52, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12B
22E
13C
23F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A12 - 434
2111D12 - 434
1121B1921 - 2119
2121E1921 - 2119
1131C16 - 70
2131F16 - 70

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Recombining binding protein suppressor of hairless / J kappa-recombination signal-binding protein / RBP-J kappa / RBP-JK / RBP-J / CBF-1 / Renal ...J kappa-recombination signal-binding protein / RBP-J kappa / RBP-JK / RBP-J / CBF-1 / Renal carcinoma antigen NY-REN-30


Mass: 49237.180 Da / Num. of mol.: 2 / Fragment: residues 23-448
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGKJRB, IGKJRB1, RBPJ, RBPJK, RBPSUH / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta II pLysS / References: UniProt: Q06330
#2: 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


Mass: 27885.004 Da / Num. of mol.: 2 / Fragment: residues 1872-2126
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NOTCH1, TAN1 / Plasmid: PDEST15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P46531
#3: Protein Mastermind-like protein 1 / Mam-1


Mass: 7532.758 Da / Num. of mol.: 2 / Fragment: residues 13-74
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIAA0200, MAML1 / Plasmid: pRSET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q92585
#4: DNA chain DNA, HES1 promoter


Mass: 11526.458 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Sequence from mouse and human HES1 promoter region
#5: DNA chain DNA, HES1 promoter


Mass: 11211.222 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Sequence from mouse and human HES1 promoter region
Has protein modificationY

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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: 3.87 Å3/Da / Density % sol: 68.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 3% PEG3350, 10% ethylene glycol, 0.15M NaCl, 0.1M magnesium chloride, 0.1M BIS-TRIS, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 27, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 3.45→50 Å / Num. obs: 35389 / % possible obs: 99.9 % / Redundancy: 9.5 % / Rmerge(I) obs: 0.063 / Χ2: 1.069 / Net I/σ(I): 12.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
3.45-3.517.20.39617331.17299.9
3.51-3.577.70.36517771.112100
3.57-3.648.10.3217671.118100
3.64-3.728.80.27917521.099100
3.72-3.89.10.24917791.08100
3.8-3.899.50.21817481.085100
3.89-3.989.70.16817791.04100
3.98-4.099.90.13217361.065100
4.09-4.21100.11117771.095100
4.21-4.3510.10.09317741.038100
4.35-4.510.20.08417521.06199.9
4.5-4.6810.10.0717661.034100
4.68-4.8910.10.0717611.013100
4.89-5.1510.20.0717981.08100
5.15-5.47100.07317491.067100
5.47-5.910.10.07517771.025100
5.9-6.49100.06117731.066100
6.49-7.439.80.04717841.199.8
7.43-9.359.90.03117871.04599.4
9.35-509.90.02918201.04598.8

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation3.63 Å47.77 Å
Translation3.63 Å47.77 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 37527
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
14.26-10044.90.56507
11-14.2636.40.707606
9.28-1132.40.754751
8.18-9.2839.80.72848
7.4-8.1842.80.716953
6.8-7.445.30.6691038
6.33-6.846.20.6441121
5.94-6.3345.40.6491233
5.62-5.9447.90.6471258
5.35-5.6246.90.6731340
5.11-5.3543.50.6781385
4.9-5.1141.60.7091477
4.71-4.941.10.7171538
4.55-4.7139.60.7251578
4.4-4.5541.30.6871613
4.26-4.441.50.7021700
4.14-4.2644.50.6781699
4.02-4.1444.50.6711764
3.92-4.0246.30.631770
3.82-3.92490.6151767
3.73-3.8250.90.6211772
3.65-3.7351.50.5971756
3.57-3.6552.10.5751671
3.5-3.5749.90.5841552
3.43-3.5550.5591381
3.36-3.4357.70.4961239
3.3-3.3658.30.4961002
3.19-3.362.60.4611208

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
DM6phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: protein components of 2F8X

2f8x


Resolution: 3.45→45.02 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.896 / WRfactor Rfree: 0.299 / WRfactor Rwork: 0.252 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.763 / SU B: 32.278 / SU ML: 0.523 / SU Rfree: 0.631 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.631 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.298 1802 5.1 %RANDOM
Rwork0.254 ---
obs0.256 35361 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 221.64 Å2 / Biso mean: 126.54 Å2 / Biso min: 63.23 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20.02 Å2
2---0.11 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 3.45→45.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10686 1512 0 0 12198
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02112593
X-RAY DIFFRACTIONr_bond_other_d0.0020.028203
X-RAY DIFFRACTIONr_angle_refined_deg1.6092.11317339
X-RAY DIFFRACTIONr_angle_other_deg1.049319991
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.69351342
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.41123.684532
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.912151938
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7061598
X-RAY DIFFRACTIONr_chiral_restr0.0810.21917
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02112933
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022362
X-RAY DIFFRACTIONr_mcbond_it0.6811.56722
X-RAY DIFFRACTIONr_mcbond_other0.0731.52714
X-RAY DIFFRACTIONr_mcangle_it1.266210826
X-RAY DIFFRACTIONr_scbond_it1.03935871
X-RAY DIFFRACTIONr_scangle_it1.8734.56513
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A5757TIGHT POSITIONAL0.030.05
1A5757TIGHT THERMAL0.050.5
2B2524TIGHT POSITIONAL0.030.05
2B2524TIGHT THERMAL0.20.5
3C833TIGHT POSITIONAL0.020.05
3C833TIGHT THERMAL0.570.5
LS refinement shellResolution: 3.448→3.537 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 109 -
Rwork0.342 2394 -
all-2503 -
obs--96.01 %

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