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- PDB-2fo1: Crystal Structure of the CSL-Notch-Mastermind ternary complex bou... -

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Basic information

Entry
Database: PDB / ID: 2fo1
TitleCrystal Structure of the CSL-Notch-Mastermind ternary complex bound to DNA
Components
  • 5'-D(*AP*AP*TP*CP*TP*TP*TP*CP*CP*CP*AP*CP*AP*GP*T)-3'
  • 5'-D(*TP*TP*AP*CP*TP*GP*TP*GP*GP*GP*AP*AP*AP*GP*A)-3'
  • Lin-12 and glp-1 phenotype protein 1, isoform b
  • Lin-12 protein
  • Protein lag-3
KeywordsGENE REGULATION/SIGNALLING PROTEIN/DNA / beta-barrel / PROTEIN-DNA COMPLEX / DOUBLE HELIX / ankyrin repeat / GENE REGULATION-SIGNALLING PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


stem cell fate determination / Pre-NOTCH Processing in Golgi / NOTCH4 Activation and Transmission of Signal to the Nucleus / Negative regulation of NOTCH4 signaling / regulation of mesodermal cell fate specification / dauer exit / positive regulation of vulval development / CSL-Notch-Mastermind transcription factor complex / cell projection morphogenesis / positive regulation of mesodermal cell fate specification ...stem cell fate determination / Pre-NOTCH Processing in Golgi / NOTCH4 Activation and Transmission of Signal to the Nucleus / Negative regulation of NOTCH4 signaling / regulation of mesodermal cell fate specification / dauer exit / positive regulation of vulval development / CSL-Notch-Mastermind transcription factor complex / cell projection morphogenesis / positive regulation of mesodermal cell fate specification / vulval development / regulation of vulval development / oocyte growth / nematode larval development / germ-line stem cell division / regulation of basement membrane organization / egg-laying behavior / regulation of cell fate specification / cell fate determination / sleep / Notch binding / cell fate specification / positive regulation of stem cell proliferation / Notch signaling pathway / transcription coactivator binding / positive regulation of miRNA transcription / RNA polymerase II transcription regulator complex / transmembrane signaling receptor activity / double-stranded DNA binding / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / transcription coactivator activity / DNA-binding transcription factor activity, RNA polymerase II-specific / apical plasma membrane / RNA polymerase II cis-regulatory region sequence-specific DNA binding / calcium ion binding / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus / plasma membrane
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #990 / Transcription activator LAG-3 / Transcriptional activator LAG-3 / 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 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #990 / Transcription activator LAG-3 / Transcriptional activator LAG-3 / 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 / 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 / EGF-like domain, extracellular / EGF-like domain / Calcium-binding EGF domain / Ankyrin repeat-containing domain / 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) / Protein lin-12 / Protein lag-3 / Suppressor of hairless protein homolog
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS, MIRAS, molecular replacement / Resolution: 3.12 Å
AuthorsWilson, J.J. / Kovall, R.A.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2006
Title: Crystal structure of the CSL-Notch-Mastermind ternary complex bound to DNA.
Authors: Wilson, J.J. / Kovall, R.A.
History
DepositionJan 12, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 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_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: 5'-D(*TP*TP*AP*CP*TP*GP*TP*GP*GP*GP*AP*AP*AP*GP*A)-3'
C: 5'-D(*AP*AP*TP*CP*TP*TP*TP*CP*CP*CP*AP*CP*AP*GP*T)-3'
A: Lin-12 and glp-1 phenotype protein 1, isoform b
D: Protein lag-3
E: Lin-12 protein


Theoretical massNumber of molelcules
Total (without water)115,1525
Polymers115,1525
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.093, 96.785, 243.538
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 4673.059 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: THE SEQUENCE COMES FROM A REGION WITHIN THE MAMMALIAN HES-1 PROMOTER
#2: DNA chain 5'-D(*AP*AP*TP*CP*TP*TP*TP*CP*CP*CP*AP*CP*AP*GP*T)-3'


Mass: 4503.949 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: THE SEQUENCE COMES FROM A REGION WITHIN THE MAMMALIAN HES-1 PROMOTER
#3: Protein Lin-12 and glp-1 phenotype protein 1, isoform b / LAG-1


Mass: 53761.641 Da / Num. of mol.: 1 / Fragment: CORE (RESIDUES 192-663)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: LAG-1 / Plasmid: PGEX6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA2(DE3)PLYSS / References: GenBank: 22532887, UniProt: V6CLJ5*PLUS
#4: Protein Protein lag-3 / PROTEIN SEL-8 / Abnormal germ line proliferation protein 3 / Abnormal cell lineage protein 3


Mass: 9755.596 Da / Num. of mol.: 1 / Fragment: CONSERVED N-TERMINUS (49-132)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: sel-8, lag-3 / Plasmid: pET28A pSMT variant / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA2(DE3)PLYSS / References: UniProt: Q09260
#5: Protein Lin-12 protein


Mass: 42457.406 Da / Num. of mol.: 1 / Fragment: RAM AND ANK REPEAT DOMAINS (931-1303)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: lin-12 / Plasmid: pGEX4T-2 / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA2(DE3)PLYSS / References: UniProt: P14585

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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: 3.39 Å3/Da / Density % sol: 63.68 %
Crystal growTemperature: 277 K / Method: microbatch / pH: 5.5
Details: 10% PEG 10K, 0.15M Ammonium Acetate, 0.1M BisTris, 10% ethylene glycol, pH 5.5, MICROBATCH, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
110% PEG 10K11
20.15M Ammonium Acetate11
30.1M BisTris11
410% ethylene glycol11
510% PEG 10K12
60.15M Ammonium Acetate12
710% ethylene glycol12

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.9796 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 1, 2005
RadiationMonochromator: Si(111) double-crystal system / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 3.12→50 Å / Num. all: 52029 / Num. obs: 47404 / % possible obs: 98.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 3 / Redundancy: 13.5 % / Rsym value: 0.086 / Net I/σ(I): 25
Reflection shellResolution: 3.12→3.23 Å / Redundancy: 9.1 % / Mean I/σ(I) obs: 3.2 / Rsym value: 0.465 / % possible all: 88.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: SIRAS, MIRAS, molecular replacement
Starting model: PDB ENTRY 1TTU PDB ENTRY 1OT8

1ttu

1ot8


Resolution: 3.12→43.51 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 68268.33 / Data cutoff high rms absF: 68268.33 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.34 4706 9.9 %RANDOM
Rwork0.273 ---
obs0.273 47404 88.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.6717 Å2 / ksol: 0.201211 e/Å3
Displacement parametersBiso mean: 103.8 Å2
Baniso -1Baniso -2Baniso -3
1-42.09 Å20 Å20 Å2
2---16.09 Å20 Å2
3----26.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.62 Å0.52 Å
Luzzati d res low-5 Å
Luzzati sigma a0.7 Å0.78 Å
Refinement stepCycle: LAST / Resolution: 3.12→43.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6330 609 0 0 6939
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.1
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it14.641.5
X-RAY DIFFRACTIONc_mcangle_it22.732
X-RAY DIFFRACTIONc_scbond_it19.922
X-RAY DIFFRACTIONc_scangle_it28.182.5
LS refinement shellResolution: 3.12→3.32 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.478 585 10.3 %
Rwork0.436 5103 -
obs--63.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top

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