[English] 日本語
Yorodumi
- PDB-3nbn: Crystal structure of a dimer of Notch Transcription Complex trime... -

+
Open data


ID or keywords:

Loading...

-
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


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 / positive regulation of smooth muscle cell differentiation / 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 / Constitutive Signaling by NOTCH1 t(7;9)(NOTCH1:M1580_K2555) Translocation Mutant / epithelial to mesenchymal transition involved in endocardial cushion formation / regulation of extracellular matrix assembly / endocardial cell differentiation / cardiac ventricle morphogenesis / cardiac left ventricle morphogenesis / mesenchymal cell development / epidermal cell fate specification / negative regulation of collagen biosynthetic process / coronary vein morphogenesis / cardiac vascular smooth muscle cell development / pituitary gland development / negative regulation of myotube differentiation / somatic stem cell division / left/right axis specification / negative regulation of cell adhesion molecule production / NOTCH2 intracellular domain regulates transcription / negative regulation of cardiac muscle hypertrophy / positive regulation of endothelial cell differentiation / secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development / interleukin-17-mediated signaling pathway / apoptotic process involved in embryonic digit morphogenesis / endocardium development / positive regulation of cardiac epithelial to mesenchymal transition / atrioventricular canal development / cardiac epithelial to mesenchymal transition / Pre-NOTCH Processing in Golgi / 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 / tissue regeneration / neuronal stem cell population maintenance / tube formation / positive regulation of astrocyte differentiation / negative regulation of oligodendrocyte differentiation / myeloid dendritic cell differentiation / endoderm development / regulation of stem cell proliferation
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: 3.45 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water0
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more