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- PDB-5ky0: mouse POFUT1 in complex with mouse Notch1 EGF12(D464G) and GDP -

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Basic information

Entry
Database: PDB / ID: 5ky0
Titlemouse POFUT1 in complex with mouse Notch1 EGF12(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 cardioblast proliferation / regulation of inner ear auditory receptor cell differentiation / positive regulation of ephrin receptor signaling pathway / positive regulation of glial cell differentiation / peptide-O-fucosyltransferase / protein O-linked fucosylation / peptide-O-fucosyltransferase activity / fucosyltransferase activity / osteoblast fate commitment ...Pre-NOTCH Processing in Golgi / regulation of cardioblast proliferation / regulation of inner ear auditory receptor cell differentiation / positive regulation of ephrin receptor signaling pathway / positive regulation of glial cell differentiation / peptide-O-fucosyltransferase / protein O-linked fucosylation / peptide-O-fucosyltransferase activity / 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 / retinal cone cell differentiation / venous endothelial cell differentiation / arterial endothelial cell differentiation / cardiac chamber formation / 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 / glomerular mesangial cell development / negative regulation of photoreceptor cell differentiation / negative regulation of cell proliferation involved in heart valve morphogenesis / regulation of somitogenesis / NOTCH1 Intracellular Domain Regulates Transcription / RUNX3 regulates NOTCH signaling / inhibition of neuroepithelial cell differentiation / endocardium morphogenesis / atrioventricular node development / foregut morphogenesis / regulation of cell adhesion involved in heart morphogenesis / distal tubule development / Notch-HLH transcription pathway / MAML1-RBP-Jkappa- ICN1 complex / regulation of epithelial cell proliferation involved in prostate gland development / auditory receptor cell fate commitment / positive regulation of aorta morphogenesis / negative regulation of endothelial cell chemotaxis / neuroendocrine cell differentiation / collecting duct development / negative regulation of extracellular matrix constituent secretion / positive regulation of transcription of Notch receptor target / positive regulation of smooth muscle cell differentiation / cellular response to tumor cell / positive regulation of apoptotic process involved in morphogenesis / compartment pattern specification / vasculogenesis involved in coronary vascular morphogenesis / T-helper 17 type immune response / endocardial cushion development / epithelial to mesenchymal transition involved in endocardial cushion formation / regulation of extracellular matrix assembly / endocardial cell differentiation / cardiac ventricle morphogenesis / fucose metabolic process / cardiac left ventricle morphogenesis / mesenchymal cell development / epidermal cell fate specification / regulation of Notch signaling pathway / negative regulation of collagen biosynthetic process / coronary vein morphogenesis / cardiac vascular smooth muscle cell development / negative regulation of myotube differentiation / somatic stem cell division / left/right axis specification / negative regulation of cell adhesion molecule production / negative regulation of cardiac muscle hypertrophy / positive regulation of endothelial cell differentiation / secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development / interleukin-17-mediated signaling pathway / apoptotic process involved in embryonic digit morphogenesis / endocardium development / glial cell differentiation / positive regulation of cardiac epithelial to mesenchymal transition / cardiac epithelial to mesenchymal transition / negative regulation of calcium ion-dependent exocytosis / neuron fate commitment / cardiac muscle cell myoblast differentiation / cellular response to follicle-stimulating hormone stimulus / pericardium morphogenesis / cardiac atrium morphogenesis / negative regulation of catalytic activity / tissue regeneration / neuronal stem cell population maintenance / tube formation / positive regulation of astrocyte differentiation / negative regulation of oligodendrocyte differentiation / endoderm development / regulation of stem cell proliferation / pulmonary valve morphogenesis / calcium-ion regulated exocytosis / heart trabecula morphogenesis / negative regulation of biomineral tissue development / negative regulation of cell-cell adhesion mediated by cadherin
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 / Notch, NOD domain ...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 (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 / EGF-type aspartate/asparagine hydroxylation site / EGF-like domain / 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 / 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 / molecular replacement / Resolution: 1.53 Å
AuthorsLi, Z. / Rini, J.M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
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 20, 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 1.3Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Jul 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

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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)45,9037
Polymers44,8332
Non-polymers1,0705
Water8,629479
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-16 kcal/mol
Surface area16750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.101, 66.476, 110.277
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 / 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
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


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, 482 molecules

#4: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 479 / 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: 2.13 Å3/Da / Density % sol: 42.25 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 25% PEG 2000 MME 50mM Tris pH8.5

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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: 1.53→50 Å / Num. obs: 58604 / % possible obs: 100 % / Redundancy: 7.3 % / Biso Wilson estimate: 17.4 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.052 / Net I/σ(I): 20
Reflection shellResolution: 1.53→1.59 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.626 / Mean I/σ(I) obs: 2.79 / CC1/2: 0.842 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXdev_1405refinement
XSCALEdata scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.53→47.108 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 15.77
RfactorNum. reflection% reflectionSelection details
Rfree0.1641 2931 5.01 %0
Rwork0.1438 ---
obs0.1448 58453 99.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 131.56 Å2 / Biso mean: 29.68 Å2 / Biso min: 11.42 Å2
Refinement stepCycle: final / Resolution: 1.53→47.108 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3067 0 122 487 3676
Biso mean--33.82 36.14 -
Num. residues----387
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013447
X-RAY DIFFRACTIONf_angle_d1.3924709
X-RAY DIFFRACTIONf_chiral_restr0.078500
X-RAY DIFFRACTIONf_plane_restr0.008607
X-RAY DIFFRACTIONf_dihedral_angle_d15.7821303
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.53-1.55510.27151370.23132507264497
1.5551-1.58190.21651270.199326492776100
1.5819-1.61070.19751420.180625772719100
1.6107-1.64170.22561280.18326302758100
1.6417-1.67520.21621370.16926152752100
1.6752-1.71160.2091480.164325972745100
1.7116-1.75150.19191450.161526252770100
1.7515-1.79530.17941260.151926432769100
1.7953-1.84380.19751380.148826272765100
1.8438-1.89810.16331500.145626192769100
1.8981-1.95930.16681260.14526362762100
1.9593-2.02930.15421260.140426232749100
2.0293-2.11060.15381410.136726572798100
2.1106-2.20670.15461150.13626652780100
2.2067-2.3230.15651440.132126222766100
2.323-2.46850.15071570.133526592816100
2.4685-2.65910.17121480.137226582806100
2.6591-2.92670.17341570.139626542811100
2.9267-3.35010.18161400.143226842824100
3.3501-4.22030.12951660.128327232889100
4.2203-47.13030.15571330.147528522985100
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)
10.70730.05450.12281.4351.11431.5321-0.0547-0.01040.122-0.1101-0.13150.1793-0.1923-0.09520.14660.13830.0088-0.0210.1388-0.02330.154513.117740.18620.1299
23.4249-0.98572.11211.1756-0.27371.4333-0.14681.07760.8428-0.85920.0108-0.0182-0.66250.4620.12150.7343-0.0719-0.02730.61670.16750.607723.56434.4646-2.169
31.8031-0.5719-0.23881.39630.75842.4568-0.02240.2862-0.1536-0.0715-0.08550.04480.0770.05340.11380.12870.0090.01440.1815-0.02110.144719.291617.66284.6155
42.03790.10852.56513.3113-0.04423.2880.03070.56830.6874-0.4722-0.0307-0.8543-0.49780.8742-0.00170.621-0.1292-0.01260.5476-0.00810.609518.517849.20837.4716
53.4675-1.90520.81573.27531.15632.4997-0.05040.23670.6492-0.59160.062-0.4374-0.7990.3188-0.01750.5009-0.0118-0.02920.3468-0.02520.395313.848444.50823.0779
60.9309-0.1517-1.05894.56-0.64581.4498-0.02060.49780.2935-0.3995-0.19350.3627-0.3947-0.47520.20990.69450.1563-0.27150.4553-0.06540.44853.182542.30220.506
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 31 through 254 )A31 - 254
2X-RAY DIFFRACTION2chain 'A' and (resid 255 through 274 )A255 - 274
3X-RAY DIFFRACTION3chain 'A' and (resid 275 through 384 )A275 - 384
4X-RAY DIFFRACTION4chain 'B' and (resid 454 through 458 )B454 - 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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