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- PDB-1ot8: Structure of the Ankyrin Domain of the Drosophila Notch Receptor -

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Basic information

Entry
Database: PDB / ID: 1ot8
TitleStructure of the Ankyrin Domain of the Drosophila Notch Receptor
ComponentsNeurogenic locus Notch protein
KeywordsSIGNALING PROTEIN / Ankyrin Repeat / membrane protein
Function / homology
Function and homology information


response to symbiont / neuroblast fate specification / epithelial cell type specification, open tracheal system / lamellocyte differentiation / regulation of cardioblast cell fate specification / positive regulation of crystal cell differentiation / negative regulation of compound eye photoreceptor development / R1/R6 cell differentiation / formation of a compartment boundary / compartment boundary maintenance ...response to symbiont / neuroblast fate specification / epithelial cell type specification, open tracheal system / lamellocyte differentiation / regulation of cardioblast cell fate specification / positive regulation of crystal cell differentiation / negative regulation of compound eye photoreceptor development / R1/R6 cell differentiation / formation of a compartment boundary / compartment boundary maintenance / follicle cell of egg chamber migration / muscle cell fate determination / imaginal disc-derived leg joint morphogenesis / eye-antennal disc development / crystal cell differentiation / R7 cell differentiation / R3/R4 cell differentiation / germ-line stem-cell niche homeostasis / oocyte localization involved in germarium-derived egg chamber formation / hemocyte proliferation / negative regulation of lamellocyte differentiation / compound eye retinal cell programmed cell death / myoblast development / imaginal disc-derived male genitalia morphogenesis / germarium-derived egg chamber formation / leg disc morphogenesis / epithelial cell proliferation involved in Malpighian tubule morphogenesis / CSL-Notch-Mastermind transcription factor complex / lateral inhibition / Malpighian tubule tip cell differentiation / eye-antennal disc morphogenesis / second mitotic wave involved in compound eye morphogenesis / imaginal disc-derived wing margin morphogenesis / imaginal disc-derived leg segmentation / sensory organ precursor cell fate determination / female germ-line stem cell population maintenance / ommatidial rotation / wing disc dorsal/ventral pattern formation / defense response to insect / wing disc pattern formation / follicle cell of egg chamber stalk formation / imaginal disc-derived leg morphogenesis / chaeta morphogenesis / dorsal closure / compound eye morphogenesis / follicle cell of egg chamber development / larval lymph gland hemopoiesis / neuroblast development / lymph gland development / cell dedifferentiation / neuroblast fate determination / imaginal disc-derived wing vein specification / dorsal appendage formation / border follicle cell migration / intestinal stem cell homeostasis / compound eye development / chaeta development / foregut morphogenesis / asymmetric cell division / regulation of stem cell division / imaginal disc-derived wing morphogenesis / glial cell fate determination / neuron fate specification / regulation of neuroblast proliferation / retinal cell programmed cell death / glial cell migration / sensory organ development / germ-line stem cell population maintenance / dorsal/ventral axis specification / neuron fate determination / WW domain binding / glial cell differentiation / neuronal stem cell population maintenance / regulation of filopodium assembly / negative regulation of cell-cell adhesion mediated by cadherin / peripheral nervous system development / motor neuron axon guidance / nervous system process / Notch binding / regulation of growth / regulation of glycolytic process / embryonic hemopoiesis / histone acetyltransferase binding / muscle cell cellular homeostasis / morphogenesis of an epithelial fold / positive regulation of neuroblast proliferation / oogenesis / negative regulation of Notch signaling pathway / regulation of cell differentiation / mesoderm development / regulation of neurogenesis / endocytic vesicle / neuroblast proliferation / positive regulation of G1/S transition of mitotic cell cycle / cell fate commitment / long-term memory / Notch signaling pathway / regulation of mitotic cell cycle / multivesicular body / determination of adult lifespan
Similarity search - Function
Ankyrin repeats (many copies) / Notch, C-terminal / Domain of unknown function / Notch / Notch, NOD domain / Notch, NODP domain / NOTCH protein / NOTCH protein / NOD / NODP ...Ankyrin repeats (many copies) / 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 / EGF-like domain / 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 2. / EGF-like domain signature 1. / EGF-like domain / 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 / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Neurogenic locus Notch protein
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsZweifel, M.E. / Leahy, D.J. / Hughson, F.M. / Barrick, D.
CitationJournal: Protein Sci. / Year: 2003
Title: Structure and stability of the ankyrin domain of the Drosophila Notch receptor
Authors: Zweifel, M.E. / Leahy, D.J. / Hughson, F.M. / Barrick, D.
History
DepositionMar 21, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Neurogenic locus Notch protein
B: Neurogenic locus Notch protein
C: Neurogenic locus Notch protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,1786
Polymers77,1053
Non-polymers733
Water8,431468
1
A: Neurogenic locus Notch protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7262
Polymers25,7021
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Neurogenic locus Notch protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7262
Polymers25,7021
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Neurogenic locus Notch protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7262
Polymers25,7021
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.629, 73.629, 341.056
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Neurogenic locus Notch protein


Mass: 25701.574 Da / Num. of mol.: 3 / Fragment: Ankyrin Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: N OR EG:140G11.1 OR EG:163A10.2 OR CG3936 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P07207
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 468 / 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

CrystalDensity Matthews: 3.28 Å3/Da / Density % sol: 62.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: MPD, Magnesium Acetate, Sodium Cacodylate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110-15 mg/mlprotein1drop
2150 mM1dropNaCl
325 mMTris-HCl1droppH8.0
415-20 %(v/v)MPD1reservoir
5200 mMmagnesium acetate1reservoir
6100 mMsodium cacodylate1reservoirpH6.5-7.0

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2→19.94 Å / Num. all: 62729 / Num. obs: 62729
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 60 Å / % possible obs: 96.9 % / Rmerge(I) obs: 0.048
Reflection shell
*PLUS
% possible obs: 93.2 % / Rmerge(I) obs: 0.138

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.934 / SU ML: 0.083 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.141 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.19759 6340 10.1 %RANDOM
Rwork0.17742 ---
obs0.17947 56389 96.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.519 Å2
Baniso -1Baniso -2Baniso -3
1--1.01 Å20 Å20 Å2
2---1.01 Å20 Å2
3---2.02 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4565 0 3 468 5036
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0214626
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4341.9386280
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.2665602
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.1020.2740
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023564
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2350.22511
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2383
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.310.258
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1830.228
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.1141.53011
X-RAY DIFFRACTIONr_mcangle_it1.90824763
X-RAY DIFFRACTIONr_scbond_it3.65631615
X-RAY DIFFRACTIONr_scangle_it5.654.51517
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.218 452
Rwork0.186 3840
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.9704-0.87120.3592.1073-0.36850.7785-0.066-0.0057-0.02440.05190.0510.0031-0.0135-0.05390.01490.1456-0.01770.00830.01390.00060.013327.889176.944627.9919
20.72450.4080.51471.621.12542.3921-0.0128-0.0251-0.01420.01050.0317-0.1897-0.0120.07-0.01890.1246-0.00150.00420.01190.02880.0739.026127.810332.6889
31.54710.8881-0.61833.0388-0.76641.32890.00110.14820.0469-0.42210.0433-0.19220.03660.0049-0.04440.19910.02880.02330.0347-0.00170.082137.432252.387120.5522
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA60 - 23060 - 230
2X-RAY DIFFRACTION2BB60 - 23060 - 230
3X-RAY DIFFRACTION3CC60 - 23060 - 230
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.201 / Rfactor Rwork: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.005
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.43

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