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- PDB-5ky8: mouse POFUT1 in complex with O-glucosylated mouse Notch1 EGF12 mu... -

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Basic information

Entry
Database: PDB / ID: 5ky8
Titlemouse POFUT1 in complex with O-glucosylated mouse Notch1 EGF12 mutant (D464G) and GDP
Components
  • GDP-fucose protein O-fucosyltransferase 1
  • Neurogenic locus notch homolog protein 1
KeywordsTRANSFERASE / glycosyltransferase
Function / homology
Function and homology information


Pre-NOTCH Processing in Golgi / regulation of inner ear auditory receptor cell differentiation / fucosyltransferase activity / positive regulation of ephrin receptor signaling pathway / peptide-O-fucosyltransferase / protein O-linked glycosylation via fucose / peptide-O-fucosyltransferase activity / osteoblast fate commitment / venous blood vessel morphogenesis / Activated NOTCH1 Transmits Signal to the Nucleus ...Pre-NOTCH Processing in Golgi / regulation of inner ear auditory receptor cell differentiation / fucosyltransferase activity / positive regulation of ephrin receptor signaling pathway / peptide-O-fucosyltransferase / protein O-linked glycosylation via fucose / peptide-O-fucosyltransferase activity / osteoblast fate commitment / venous blood vessel morphogenesis / Activated NOTCH1 Transmits Signal to the Nucleus / 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 / negative regulation of inner ear auditory receptor cell differentiation / 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 / NOTCH1 Intracellular Domain Regulates Transcription / RUNX3 regulates NOTCH signaling / 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 / cellular response to tumor cell / Notch-HLH transcription pathway / 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 / endocardial cushion development / 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 / negative regulation of myotube differentiation / left/right axis specification / fucose metabolic process / 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 / regulation of Notch signaling pathway / positive regulation of cardiac epithelial to mesenchymal transition / interleukin-17-mediated signaling pathway / cardiac epithelial to mesenchymal transition / pericardium morphogenesis / cardiac atrium morphogenesis / secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development / neuron fate commitment / 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 / glial cell differentiation / heart trabecula morphogenesis / prostate gland epithelium morphogenesis / endoderm development / negative regulation of biomineral tissue development / coronary artery morphogenesis
Similarity search - Function
GDP-fucose protein O-fucosyltransferase 1 / GDP-fucose protein O-fucosyltransferase / GDP-fucose protein O-fucosyltransferase / Rossmann fold - #11340 / Rossmann fold - #11350 / Neurogenic locus notch homolog protein 1 / Notch, C-terminal / Domain of unknown function / : / Notch ...GDP-fucose protein O-fucosyltransferase 1 / GDP-fucose protein O-fucosyltransferase / GDP-fucose protein O-fucosyltransferase / Rossmann fold - #11340 / Rossmann fold - #11350 / 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 / : / Calcium-binding EGF 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 1. / EGF-like domain signature 2. / EGF-like domain / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
beta-D-glucopyranose / GUANOSINE-5'-DIPHOSPHATE / Neurogenic locus notch homolog protein 1 / GDP-fucose protein O-fucosyltransferase 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsLi, Z. / Rini, J.M.
CitationJournal: Nat. Chem. Biol. / Year: 2017
Title: Recognition of EGF-like domains by the Notch-modifying O-fucosyltransferase POFUT1.
Authors: Li, Z. / Han, K. / Pak, J.E. / Satkunarajah, M. / Zhou, D. / Rini, J.M.
History
DepositionJul 21, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1May 31, 2017Group: Database references
Revision 1.2Jun 28, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GDP-fucose protein O-fucosyltransferase 1
B: Neurogenic locus notch homolog protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6785
Polymers44,8332
Non-polymers8453
Water4,882271
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-11 kcal/mol
Surface area16500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.540, 65.900, 106.830
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein GDP-fucose protein O-fucosyltransferase 1 / Peptide-O-fucosyltransferase 1 / O-FucT-1


Mass: 40457.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pofut1 / Plasmid: PB-T-PAF / Production host: Homo sapiens (human) / References: UniProt: Q91ZW2, peptide-O-fucosyltransferase
#2: Protein/peptide Neurogenic locus notch homolog protein 1 / Notch 1 / Motch A / mT14 / p300


Mass: 4375.868 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Notch1, Motch / Production host: Escherichia coli (E. coli) / References: UniProt: Q01705

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Sugars , 2 types, 2 molecules

#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 272 molecules

#4: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.02 Å3/Da / Density % sol: 39.21 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 20% PEG2000 MME, 50 mM Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Dec 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 44218 / % possible obs: 99 % / Redundancy: 5.7 % / Biso Wilson estimate: 27.6 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Net I/σ(I): 13.3
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 5.5 % / Rmerge(I) obs: 1.127 / Mean I/σ(I) obs: 1.33 / CC1/2: 0.567 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→46.42 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2106 2225 5.03 %0
Rwork0.1895 41986 --
obs0.1906 44211 99.25 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 127.21 Å2 / Biso mean: 43.1469 Å2 / Biso min: 18.15 Å2
Refinement stepCycle: final / Resolution: 1.65→46.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3068 0 87 271 3426
Biso mean--54.32 41.02 -
Num. residues----391
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043224
X-RAY DIFFRACTIONf_angle_d0.7764402
X-RAY DIFFRACTIONf_chiral_restr0.046471
X-RAY DIFFRACTIONf_plane_restr0.005565
X-RAY DIFFRACTIONf_dihedral_angle_d15.7141904
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.65-1.68590.36541430.3362545268899
1.6859-1.72510.3361380.312826302768100
1.7251-1.76820.28341360.286726002736100
1.7682-1.81610.3261270.273426052732100
1.8161-1.86950.29731430.252626022745100
1.8695-1.92980.26421310.238926362767100
1.9298-1.99880.25591230.229426382761100
1.9988-2.07880.22951380.21626072745100
2.0788-2.17350.23381160.206926282744100
2.1735-2.2880.22711450.19926282773100
2.288-2.43140.23191540.19862616277099
2.4314-2.61910.2221480.19272629277799
2.6191-2.88260.20271520.19222606275899
2.8826-3.29970.22141390.18372637277698
3.2997-4.15680.16821590.1582622278198
4.1568-46.43840.18221330.1632757289097
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)
11.4151-0.1159-0.26742.70630.81731.94330.0145-0.5020.03330.2274-0.14090.22310.08770.11710.14630.2576-0.02350.02870.3462-0.07570.194310.982839.197822.5978
22.2677-0.2719-0.45093.10620.78161.367-0.0069-0.31240.26680.06140.0050.002-0.20720.14470.02850.2547-0.04330.0050.2634-0.08010.168513.42445.845418.7842
34.3843-0.7265-1.66733.26581.22152.32-0.22550.1538-0.7375-0.0402-0.10050.11930.08880.00520.07410.1969-0.00050.03590.1643-0.05510.309719.762321.12683.8743
47.06432.9135-5.05431.2404-2.40646.42460.3589-0.26250.7923-1.1214-0.1862-1.7609-1.21851.1264-0.13060.5588-0.11610.1340.3704-0.04480.805118.71350.49265.6616
55.3417-2.5545-1.87161.94550.62475.51550.53670.1690.9318-0.8126-0.5386-0.2289-0.62360.032-0.03750.50170.06310.04860.33210.02210.485814.28444.92781.7021
64.5726-0.7536-0.76592.7036-1.99027.1139-0.42581.01440.4953-1.38690.10071.5207-0.4185-1.24590.20320.61260.0618-0.28360.6035-0.03880.57753.857641.6919-1.6326
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 33 through 121 )A33 - 121
2X-RAY DIFFRACTION2chain 'A' and (resid 122 through 234 )A122 - 234
3X-RAY DIFFRACTION3chain 'A' and (resid 235 through 384 )A235 - 384
4X-RAY DIFFRACTION4chain 'B' and (resid 453 through 458 )B453 - 458
5X-RAY DIFFRACTION5chain 'B' and (resid 459 through 477 )B459 - 477
6X-RAY DIFFRACTION6chain 'B' and (resid 478 through 491 )B478 - 491

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