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- PDB-5ub5: human POGLUT1 in complex with human Notch1 EGF12 S458T mutant and UDP -

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Basic information

Entry
Database: PDB / ID: 5ub5
Titlehuman POGLUT1 in complex with human Notch1 EGF12 S458T mutant and UDP
Components
  • Neurogenic locus notch homolog protein 1
  • Protein O-glucosyltransferase 1
KeywordsTRANSFERASE / glycosyltransferase / GT-B glucosyltransferase
Function / homology
Function and homology information


EGF-domain serine glucosyltransferase / EGF-domain serine xylosyltransferase / EGF-domain serine glucosyltransferase activity / EGF-domain serine xylosyltransferase activity / muscle tissue development / protein O-linked glycosylation via serine / UDP-xylosyltransferase activity / regulation of gastrulation / Defective LFNG causes SCDO3 / coronary sinus valve morphogenesis ...EGF-domain serine glucosyltransferase / EGF-domain serine xylosyltransferase / EGF-domain serine glucosyltransferase activity / EGF-domain serine xylosyltransferase activity / muscle tissue development / protein O-linked glycosylation via serine / UDP-xylosyltransferase activity / regulation of gastrulation / Defective LFNG causes SCDO3 / 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 / Pre-NOTCH Processing in the Endoplasmic Reticulum / 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 / regulation of cell adhesion involved in heart 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 / auditory receptor cell fate commitment / positive regulation of aorta morphogenesis / negative regulation of endothelial cell chemotaxis / atrioventricular node development / positive regulation of transcription of Notch receptor target / neuroendocrine cell differentiation / negative regulation of extracellular matrix constituent secretion / cellular response to tumor cell / 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 / UDP-glucosyltransferase activity / T-helper 17 type immune response / endocardial cell differentiation / chemical synaptic transmission, postsynaptic / epithelial to mesenchymal transition involved in endocardial cushion formation / Constitutive Signaling by NOTCH1 t(7;9)(NOTCH1:M1580_K2555) Translocation Mutant / cardiac ventricle morphogenesis / positive regulation of smooth muscle cell differentiation / mesenchymal cell development / epidermal cell fate specification / glomerular mesangial cell development / negative regulation of myotube differentiation / coronary vein morphogenesis / cardiac left ventricle morphogenesis / cardiac vascular smooth muscle cell development / left/right axis specification / somatic stem cell division / negative regulation of cell adhesion molecule production / tissue regeneration / negative regulation of catalytic activity / interleukin-17-mediated signaling pathway / endocardium development / apoptotic process involved in embryonic digit morphogenesis / positive regulation of endothelial cell differentiation / positive regulation of cardiac epithelial to mesenchymal transition / Pre-NOTCH Processing in Golgi / cardiac epithelial to mesenchymal transition / negative regulation of collagen biosynthetic process / pericardium morphogenesis / cardiac atrium morphogenesis / secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development / negative regulation of cardiac muscle hypertrophy / glucosyltransferase activity / cellular response to follicle-stimulating hormone stimulus / negative regulation of calcium ion-dependent exocytosis / circulatory system development / cardiac muscle cell myoblast differentiation / neuronal stem cell population maintenance / calcium-ion regulated exocytosis / paraxial mesoderm development / negative regulation of oligodendrocyte differentiation / positive regulation of astrocyte differentiation / pulmonary valve morphogenesis / heart trabecula morphogenesis / regulation of stem cell proliferation / coronary artery morphogenesis / luteolysis / prostate gland epithelium morphogenesis / negative regulation of biomineral tissue development / endoderm development / negative regulation of myoblast differentiation / negative regulation of cell migration involved in sprouting angiogenesis
Similarity search - Function
Glycosyl transferase CAP10 domain / : / Glycosyl transferase family 90 / Putative lipopolysaccharide-modifying enzyme. / Neurogenic locus notch homolog protein 1 / Notch, C-terminal / Domain of unknown function / : / Notch / Notch, NOD domain ...Glycosyl transferase CAP10 domain / : / Glycosyl transferase family 90 / Putative lipopolysaccharide-modifying enzyme. / 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 / Laminin / Laminin / 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 / Ribbon / Mainly Beta
Similarity search - Domain/homology
URIDINE-5'-DIPHOSPHATE / Neurogenic locus notch homolog protein 1 / Protein O-glucosyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.089 Å
AuthorsLi, Z. / Rini, J.M.
CitationJournal: Nat Commun / Year: 2017
Title: Structural basis of Notch O-glucosylation and O-xylosylation by mammalian protein-O-glucosyltransferase 1 (POGLUT1).
Authors: Li, Z. / Fischer, M. / Satkunarajah, M. / Zhou, D. / Withers, S.G. / Rini, J.M.
History
DepositionDec 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 4, 2018Group: Data collection / Source and taxonomy / Category: diffrn_source / entity_src_gen
Item: _diffrn_source.type / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / diffrn_radiation_wavelength ...chem_comp / diffrn_radiation_wavelength / 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 1.4Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein O-glucosyltransferase 1
B: Neurogenic locus notch homolog protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7247
Polymers46,6162
Non-polymers1,1085
Water6,071337
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-9 kcal/mol
Surface area18150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.951, 74.072, 83.583
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, 5 molecules AB

#1: Protein Protein O-glucosyltransferase 1 / CAP10-like 46 kDa protein / hCLP46 / KTEL motif-containing protein 1 / Myelodysplastic syndromes ...CAP10-like 46 kDa protein / hCLP46 / KTEL motif-containing protein 1 / Myelodysplastic syndromes relative protein / O-glucosyltransferase Rumi homolog / hRumi / Protein O-xylosyltransferase


Mass: 42077.117 Da / Num. of mol.: 1 / Fragment: UNP residues 29-385
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: POGLUT1, C3orf9, CLP46, KTELC1, MDSRP, MDS010, UNQ490/PRO1006
Plasmid: PB-T-PAF / Cell line (production host): HEK293S GnTI- / Production host: Homo sapiens (human)
References: UniProt: Q8NBL1, Transferases; Glycosyltransferases; Hexosyltransferases, protein xylosyltransferase
#2: Protein/peptide Neurogenic locus notch homolog protein 1 / hN1 / Translocation-associated notch protein TAN-1


Mass: 4538.979 Da / Num. of mol.: 1 / Fragment: UNP residues 452-491
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NOTCH1, TAN1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P46531
#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.: 3
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, 339 molecules

#4: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / 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: 2.36 Å3/Da / Density % sol: 47.79 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% (v/v) PEG5000 MME, 50 mM MES pH 6.5, 2mM CaCl2, 250mM NaCl, 5% (v/v) 2-methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER TURBO X-RAY SOURCE / Wavelength: 1.5418 Å
DetectorType: BRUKER PHOTON 100 / Detector: PIXEL / Date: Nov 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.089→20.9 Å / Num. obs: 26486 / % possible obs: 98.96 % / Redundancy: 11 % / Biso Wilson estimate: 21.44 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.09068 / Net I/σ(I): 18.74
Reflection shellResolution: 2.089→2.164 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.5486 / Mean I/σ(I) obs: 3.16 / Num. unique obs: 2401 / CC1/2: 0.826 / % possible all: 91.49

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
SAINTdata scaling
PDB_EXTRACT3.22data extraction
SAINTdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5L0R

5l0r


Resolution: 2.089→20.896 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1931 1365 5.16 %0
Rwork0.1526 25114 --
obs0.1547 26479 99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 130.98 Å2 / Biso mean: 32.9548 Å2 / Biso min: 6.44 Å2
Refinement stepCycle: final / Resolution: 2.089→20.896 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3246 0 121 337 3704
Biso mean--39.69 35 -
Num. residues----396
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123483
X-RAY DIFFRACTIONf_angle_d1.2354752
X-RAY DIFFRACTIONf_chiral_restr0.071496
X-RAY DIFFRACTIONf_plane_restr0.01609
X-RAY DIFFRACTIONf_dihedral_angle_d12.2872072
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0887-2.16330.27871160.23692258237490
2.1633-2.24980.24841330.193425042637100
2.2498-2.35210.21291390.164124822621100
2.3521-2.47590.19531360.154425142650100
2.4759-2.63070.22291520.155325102662100
2.6307-2.83340.21430.150425082651100
2.8334-3.11770.19011320.158725382670100
3.1177-3.56690.18771390.141325482687100
3.5669-4.48660.16441450.126925652710100
4.4866-20.89680.16721300.14612687281799
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)
10.9881-0.49570.03790.77560.04940.0547-0.1598-0.18570.04350.25140.06590.0150.2015-0.5032-0.21840.191-0.02530.06030.4234-0.01090.12094.096130.397734.9009
20.188-0.0092-0.20680.0197-0.010.2499-0.0749-0.333-0.2480.09120.0338-0.14720.32840.36950.00280.33530.208-0.01590.39330.06380.283232.241112.924531.9428
30.1284-0.024-0.00930.74540.29750.5596-0.0572-0.1373-0.1560.12240.1213-0.1970.31980.38520.03850.23530.0637-0.02090.21710.00050.186727.854120.812328.9275
40.6668-0.35360.08310.40380.30750.52220.0207-0.0441-0.00590.04260.0334-0.02140.07790.10760.19060.14690.01980.01050.07610.00230.148719.83426.107821.8291
50.71060.0271-0.15840.11030.07560.8080.0550.3539-0.0685-0.0284-0.03380.04160.0996-0.34620.08170.1207-0.0063-0.00930.1948-0.04560.13055.547727.11146.2448
60.7324-0.149-0.1960.3367-0.06910.8549-0.01510.00870.07130.01280.00070.06730.0168-0.31230.00630.0922-0.01050.00380.1281-0.00680.10694.878131.532318.8246
70.5383-0.35370.27330.3539-0.34740.8362-0.157-0.44430.07810.14910.178-0.32030.11530.48940.1390.21950.1379-0.01440.33790.01590.176730.084922.903135.4433
80.2486-0.14410.20730.0822-0.11570.1809-0.00980.1402-0.2956-0.0033-0.08060.04340.43420.1862-0.0860.34710.08320.04570.1542-0.08780.268826.221815.55078.1296
90.1014-0.07370.12890.0559-0.09560.16840.17190.15140.0471-0.14540.3893-0.28280.04960.10430.03280.311-0.04860.09050.355-0.08210.30336.266524.49295.5307
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 30 through 68 )A30 - 68
2X-RAY DIFFRACTION2chain 'A' and (resid 69 through 104 )A69 - 104
3X-RAY DIFFRACTION3chain 'A' and (resid 105 through 139 )A105 - 139
4X-RAY DIFFRACTION4chain 'A' and (resid 140 through 197 )A140 - 197
5X-RAY DIFFRACTION5chain 'A' and (resid 198 through 248 )A198 - 248
6X-RAY DIFFRACTION6chain 'A' and (resid 249 through 349 )A249 - 349
7X-RAY DIFFRACTION7chain 'A' and (resid 350 through 385 )A350 - 385
8X-RAY DIFFRACTION8chain 'B' and (resid 452 through 477 )B452 - 477
9X-RAY DIFFRACTION9chain 'B' and (resid 478 through 491 )B478 - 491

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