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- PDB-5ky4: mouse POFUT1 in complex with mouse Notch1 EGF26 and GDP -

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Basic information

Entry
Database: PDB / ID: 5ky4
Titlemouse POFUT1 in complex with mouse Notch1 EGF26 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 / S-1,2-PROPANEDIOL / Neurogenic locus notch homolog protein 1 / GDP-fucose protein O-fucosyltransferase 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.472 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 20, 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)45,7768
Polymers44,6622
Non-polymers1,1146
Water7,314406
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-13 kcal/mol
Surface area17050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.920, 66.372, 110.910
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 / Sugars , 3 types, 4 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: 4204.566 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.: 2
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

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Non-polymers , 3 types, 410 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
#5: Chemical ChemComp-PGO / S-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 406 / 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: 2.14 Å3/Da / Density % sol: 42.51 %
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: Apr 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.47→50 Å / Num. obs: 65598 / % possible obs: 100 % / Redundancy: 7.2 % / CC1/2: 0.991 / Rmerge(I) obs: 0.134 / Net I/σ(I): 7.6
Reflection shellResolution: 1.47→1.53 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1.218 / Mean I/σ(I) obs: 1.3 / CC1/2: 0.537 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementResolution: 1.472→47.023 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1675 3126 5.03 %0
Rwork0.1533 59002 --
obs0.154 62128 94.52 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 126.29 Å2 / Biso mean: 29.5226 Å2 / Biso min: 9.47 Å2
Refinement stepCycle: final / Resolution: 1.472→47.023 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3045 0 70 406 3521
Biso mean--29.15 34.06 -
Num. residues----390
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073329
X-RAY DIFFRACTIONf_angle_d1.0144555
X-RAY DIFFRACTIONf_chiral_restr0.073483
X-RAY DIFFRACTIONf_plane_restr0.007589
X-RAY DIFFRACTIONf_dihedral_angle_d19.711225
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4718-1.49480.323660.33331173123942
1.4948-1.51940.29041040.31011867197167
1.5194-1.54560.29091190.28262316243583
1.5456-1.57370.24341350.252594272993
1.5737-1.60390.29151480.22362719286797
1.6039-1.63670.23341460.21372806295299
1.6367-1.67230.18411380.18428112949100
1.6723-1.71120.22321580.166727772935100
1.7112-1.7540.17471560.165728152971100
1.754-1.80140.19161420.15828282970100
1.8014-1.85440.23141430.160828262969100
1.8544-1.91420.17431590.153927822941100
1.9142-1.98270.1651270.145528422969100
1.9827-2.06210.16351460.141828272973100
2.0621-2.15590.14741390.137828442983100
2.1559-2.26960.15141370.137828562993100
2.2696-2.41170.14041640.131128162980100
2.4117-2.59790.17871670.135928242991100
2.5979-2.85940.13941620.143828563018100
2.8594-3.2730.15381550.145828723027100
3.273-4.12330.15231720.137928943066100
4.1233-47.04670.15191430.15393057320099
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)
11.64760.57842.13912.31333.6696.4081-0.0389-0.14430.15360.0691-0.22780.17560.0245-0.29640.21950.1575-0.0088-0.0050.1317-0.02990.165112.790443.514426.1458
20.8980.37540.47631.38520.82021.4526-0.0505-0.10550.1733-0.0042-0.17960.2391-0.0762-0.21630.12810.14240.0103-0.01410.1327-0.06030.160810.690139.913823.6682
34.33550.71991.08391.76571.04050.8303-0.2290.19920.6754-0.3428-0.09420.3054-0.4714-0.02140.21660.35360.0085-0.090.202-0.00410.279912.092552.630618.6661
40.4957-0.13820.07632.29091.27061.5913-0.0383-0.05840.06120.0616-0.00640.0209-0.0099-0.01580.02760.1049-0.0053-0.01250.11120.00350.115818.092933.144920.9885
52.8347-0.4328-0.25831.89291.39333.2616-0.01140.3634-0.0723-0.1302-0.07620.0001-0.0999-0.00210.06010.0851-0.00480.00370.1134-0.01370.088219.039120.23923.967
60.8418-0.48610.63796.2601-2.55453.7159-0.0850.31060.8122-0.6603-0.2714-0.6962-1.56050.85850.25680.6718-0.1519-0.03150.37980.02480.471914.169645.33683.7932
76.1617-1.36881.47163.4486-1.90284.7905-0.03430.61140.5714-0.9787-0.0290.7967-0.8379-0.43540.01810.64150.1435-0.1810.34910.00550.39343.296841.5360.1317
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 31 through 48 )A31 - 48
2X-RAY DIFFRACTION2chain 'A' and (resid 49 through 136 )A49 - 136
3X-RAY DIFFRACTION3chain 'A' and (resid 137 through 186 )A137 - 186
4X-RAY DIFFRACTION4chain 'A' and (resid 187 through 234 )A187 - 234
5X-RAY DIFFRACTION5chain 'A' and (resid 235 through 384 )A235 - 384
6X-RAY DIFFRACTION6chain 'B' and (resid 969 through 990 )B969 - 990
7X-RAY DIFFRACTION7chain 'B' and (resid 991 through 1004 )B991 - 1004

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