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- PDB-5ky9: mouse POFUT1 in complex with mouse Notch1 EGF12 mutant (D464G/A46... -

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Basic information

Entry
Database: PDB / ID: 5ky9
Titlemouse POFUT1 in complex with mouse Notch1 EGF12 mutant (D464G/A465G) 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
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: 1.83 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 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._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 1.4Nov 6, 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

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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)45,4844
Polymers44,8192
Non-polymers6642
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-16 kcal/mol
Surface area16290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.100, 66.520, 109.960
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#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: 4361.842 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
#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
#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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O
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: 2.13 Å3/Da / Density % sol: 42.14 %
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: 1.83→50 Å / Num. obs: 34467 / % possible obs: 100 % / Redundancy: 6.9 % / Biso Wilson estimate: 37.6 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Net I/σ(I): 16.4
Reflection shellResolution: 1.83→1.9 Å / Redundancy: 7 % / Rmerge(I) obs: 1.272 / Mean I/σ(I) obs: 1.31 / CC1/2: 0.636 / % 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: 1.83→47.082 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2112 1736 5.04 %0
Rwork0.1893 32729 --
obs0.1904 34465 99.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 182.01 Å2 / Biso mean: 57.1009 Å2 / Biso min: 23.25 Å2
Refinement stepCycle: final / Resolution: 1.83→47.082 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2968 0 66 152 3186
Biso mean--54.04 46.53 -
Num. residues----384
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063110
X-RAY DIFFRACTIONf_angle_d0.9594253
X-RAY DIFFRACTIONf_chiral_restr0.053458
X-RAY DIFFRACTIONf_plane_restr0.008544
X-RAY DIFFRACTIONf_dihedral_angle_d12.9581823
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.83-1.88390.30761530.315626872840
1.8839-1.94470.33131280.274326932821
1.9447-2.01420.25371350.243727172852
2.0142-2.09480.22511410.234626692810
2.0948-2.19010.22561210.218126992820
2.1901-2.30560.24581390.214127192858
2.3056-2.45010.23691540.20426932847
2.4501-2.63920.25931590.207727102869
2.6392-2.90480.21691550.205427282883
2.9048-3.3250.20831470.188327392886
3.325-4.18880.1811660.167127472913
4.1888-47.0980.19661380.168229283066
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)
10.85090.16080.35352.72551.63572.1651-0.0834-0.25030.295-0.0735-0.32750.3572-0.3268-0.26780.29770.43630.0335-0.03940.3949-0.14150.469812.966141.759521.661
23.76390.4522-1.72151.22070.97734.4745-0.05530.6367-0.1475-0.0378-0.06530.4527-0.3475-0.7446-0.02030.32680.044-0.06880.3662-0.03040.293415.611123.23571.446
30.9436-0.39660.0612.6977-2.08972.30960.0130.60780.7099-0.5113-0.14020.0354-0.83840.3274-0.0010.4998-0.02940.00990.51290.05330.373424.79531.7377-1.315
43.73420.5264-0.75063.15221.95014.7127-0.16090.3587-0.44210.1608-0.17070.14530.3214-0.18450.29770.2707-0.0060.04270.3016-0.04570.294317.976416.29886.1355
52.9851.5262-3.00093.8024-2.04235.33370.66390.23781.8071-0.5838-0.59080.1949-1.686-0.1898-0.30160.95020.1094-0.04010.4038-0.00440.7813.085344.66564.2834
62.92491.0698-3.60423.256-1.62194.47430.04171.87130.7157-0.4718-0.46770.8028-0.6382-0.60570.05580.94640.2566-0.39830.95150.05120.74893.175741.75770.4496
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 32 through 234 )A32 - 234
2X-RAY DIFFRACTION2chain 'A' and (resid 235 through 259 )A235 - 259
3X-RAY DIFFRACTION3chain 'A' and (resid 260 through 291 )A260 - 291
4X-RAY DIFFRACTION4chain 'A' and (resid 292 through 384 )A292 - 384
5X-RAY DIFFRACTION5chain 'B' and (resid 455 through 477 )B455 - 477
6X-RAY DIFFRACTION6chain 'B' and (resid 478 through 491 )B478 - 491

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