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- PDB-5l0r: human POGLUT1 in complex with Notch1 EGF12 and UDP -

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Basic information

Entry
Database: PDB / ID: 5l0r
Titlehuman POGLUT1 in complex with Notch1 EGF12 and UDP
Components
  • Neurogenic locus notch homolog protein 1
  • Protein O-glucosyltransferase 1
KeywordsTRANSFERASE / transferase glycosyltransferase GT-B glucosyltransferase
Function / homology
Function and homology information


EGF-domain serine glucosyltransferase / EGF-domain serine xylosyltransferase / protein O-linked glycosylation via xylose / EGF-domain serine glucosyltransferase activity / EGF-domain serine xylosyltransferase activity / muscle tissue development / regulation of gastrulation / protein O-linked glycosylation via glucose / UDP-xylosyltransferase activity / Defective LFNG causes SCDO3 ...EGF-domain serine glucosyltransferase / EGF-domain serine xylosyltransferase / protein O-linked glycosylation via xylose / EGF-domain serine glucosyltransferase activity / EGF-domain serine xylosyltransferase activity / muscle tissue development / regulation of gastrulation / protein O-linked glycosylation via glucose / UDP-xylosyltransferase activity / Defective LFNG causes SCDO3 / coronary sinus valve morphogenesis / cardiac right atrium morphogenesis / growth involved in heart morphogenesis / regulation of cardioblast proliferation / cell differentiation in spinal cord / venous endothelial cell differentiation / arterial endothelial cell differentiation / cell migration involved in endocardial cushion formation / negative regulation of pro-B cell differentiation / Pre-NOTCH Processing in the Endoplasmic Reticulum / mitral valve formation / : / endocardium morphogenesis / distal tubule development / MAML1-RBP-Jkappa- ICN1 complex / cardiac chamber formation / cardiac atrium morphogenesis / negative regulation of endothelial cell chemotaxis / atrioventricular node development / cardiac ventricle morphogenesis / positive regulation of transcription of Notch receptor target / pericardium morphogenesis / cellular response to tumor cell / positive regulation of smooth muscle cell differentiation / collecting duct development / glomerular mesangial cell development / vasculogenesis involved in coronary vascular morphogenesis / negative regulation of extracellular matrix constituent secretion / regulation of extracellular matrix assembly / positive regulation of apoptotic process involved in morphogenesis / chemical synaptic transmission, postsynaptic / endocardial cell differentiation / epithelial to mesenchymal transition involved in endocardial cushion formation / T-helper 17 type immune response / left/right axis specification / Constitutive Signaling by NOTCH1 t(7;9)(NOTCH1:M1580_K2555) Translocation Mutant / UDP-glucosyltransferase activity / cardiac left ventricle morphogenesis / mesenchymal cell development / coronary vein morphogenesis / negative regulation of myotube differentiation / cardiac vascular smooth muscle cell development / paraxial mesoderm development / negative regulation of catalytic activity / negative regulation of cell adhesion molecule production / cardiac muscle cell myoblast differentiation / endocardium development / positive regulation of cardiac epithelial to mesenchymal transition / neuronal stem cell population maintenance / positive regulation of endothelial cell differentiation / cardiac epithelial to mesenchymal transition / heart trabecula morphogenesis / interleukin-17-mediated signaling pathway / regulation of cell adhesion involved in heart morphogenesis / positive regulation of astrocyte differentiation / Pre-NOTCH Processing in Golgi / negative regulation of collagen biosynthetic process / negative regulation of cardiac muscle hypertrophy / cellular response to follicle-stimulating hormone stimulus / glucosyltransferase activity / negative regulation of oligodendrocyte differentiation / tissue regeneration / luteolysis / pulmonary valve morphogenesis / circulatory system development / negative regulation of myoblast differentiation / negative regulation of cell migration involved in sprouting angiogenesis / coronary artery morphogenesis / negative regulation of cell-cell adhesion mediated by cadherin / protein O-linked glycosylation / ventricular trabecula myocardium morphogenesis / negative regulation of biomineral tissue development / tube formation / astrocyte differentiation / negative regulation of stem cell differentiation / positive regulation of BMP signaling pathway / positive regulation of Ras protein signal transduction / cardiac muscle tissue morphogenesis / transcription regulator activator activity / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RUNX3 regulates NOTCH signaling / Notch binding / determination of left/right symmetry / negative regulation of ossification / NOTCH4 Intracellular Domain Regulates Transcription / atrioventricular valve morphogenesis / Regulation of NFE2L2 gene expression / aortic valve morphogenesis / axial mesoderm development
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 (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 / 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 repeat profile. / Ankyrin repeats (3 copies) / Ankyrin repeat region circular profile. / ankyrin repeats / Ribbon / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / 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 / SYNCHROTRON / Resolution: 1.5 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
DepositionJul 28, 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 1.2Jul 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 1.3Mar 24, 2021Group: Source and taxonomy / Structure summary / Category: chem_comp / entity_src_gen
Item: _chem_comp.pdbx_synonyms / _entity_src_gen.pdbx_host_org_cell_line ..._chem_comp.pdbx_synonyms / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.4Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _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: Protein O-glucosyltransferase 1
B: Neurogenic locus notch homolog protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6168
Polymers46,6022
Non-polymers1,0146
Water6,323351
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-36 kcal/mol
Surface area17870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.580, 73.560, 83.280
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 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
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: 4524.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NOTCH1, TAN1 / Plasmid: pMal / Production host: Escherichia coli BL21(DE3) (bacteria) / 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.: 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 , 5 types, 355 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 351 / 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: 2.33 Å3/Da / Density % sol: 47.14 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG5000 MME, 50 mM MES pH 6.5, 2mM CaCl2, 250mM NaCl, 5% glycerol

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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: Sep 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 68848 / % possible obs: 98 % / Redundancy: 5.7 % / Biso Wilson estimate: 17.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Net I/σ(I): 19.19
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.864 / Mean I/σ(I) obs: 1.64 / CC1/2: 0.661 / % possible all: 91

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementResolution: 1.5→43.448 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.7
RfactorNum. reflection% reflectionSelection details
Rfree0.1707 3442 5 %0
Rwork0.1489 ---
obs0.15 68829 98.29 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 156.43 Å2 / Biso mean: 32.5202 Å2 / Biso min: 12.15 Å2
Refinement stepCycle: final / Resolution: 1.5→43.448 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3249 0 89 351 3689
Biso mean--25.35 37.46 -
Num. residues----396
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133467
X-RAY DIFFRACTIONf_angle_d1.2994716
X-RAY DIFFRACTIONf_chiral_restr0.072488
X-RAY DIFFRACTIONf_plane_restr0.01601
X-RAY DIFFRACTIONf_dihedral_angle_d14.8932080
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.52060.27091180.30452248236686
1.5206-1.54230.28711280.28042416254491
1.5423-1.56530.30381360.25532594273099
1.5653-1.58980.25591370.237325992736100
1.5898-1.61580.24421380.218126232761100
1.6158-1.64370.21931410.206826602801100
1.6437-1.67360.18411370.196826172754100
1.6736-1.70580.19861390.188626412780100
1.7058-1.74060.18541380.172426142752100
1.7406-1.77840.2091380.168426412779100
1.7784-1.81980.17021390.158826442783100
1.8198-1.86530.18361380.151526192757100
1.8653-1.91580.16471400.141426492789100
1.9158-1.97210.18881380.140726282766100
1.9721-2.03580.16251390.137626482787100
2.0358-2.10850.13521380.136626182756100
2.1085-2.1930.15651410.131826792820100
2.193-2.29280.16581370.13172606274399
2.2928-2.41360.1441400.12752658279899
2.4136-2.56480.15161390.13372642278199
2.5648-2.76280.17341400.1392643278399
2.7628-3.04080.18221390.13972652279198
3.0408-3.48070.14131390.13632646278597
3.4807-4.38460.15371400.12372660280097
4.3846-43.46640.17021450.15682742288796
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)
13.6322-0.92270.7210.9968-0.27621.7436-0.1191-0.35540.020.08860.14570.17290.0628-0.6882-0.05020.1923-0.02380.02240.4228-0.00230.15783.585729.799534.6921
22.1412-0.6658-0.35292.9602-0.80194.2746-0.0006-0.2222-0.2451-0.0102-0.0418-0.13520.5580.51480.02060.26010.129-0.05930.3141-0.00890.258732.185412.643231.973
31.7689-0.59710.27721.5173-0.70143.34390.0377-0.1566-0.15110.0740.0978-0.02480.26670.1864-0.08090.15110.0299-0.02260.1351-0.01490.142423.759719.74926.658
43.1272-1.2184-0.24181.05210.71971.3376-0.03250.16020.4674-0.1660.0611-0.1042-0.4290.1191-0.02340.2319-0.03590.01450.10870.01270.212819.81838.810316.0966
53.06030.16940.50272.47461.19572.78660.11030.29150.0245-0.0332-0.13630.1945-0.077-0.30810.00950.12060.0060.00820.1890.01580.10583.318929.73418.8107
64.17981.0965-0.09080.57980.83092.69780.19060.8387-0.4308-0.1122-0.0926-0.01780.1197-0.0999-0.10130.16410.0082-0.0290.2532-0.05720.12958.792622.0782.6479
71.7601-0.0857-0.02890.83810.12172.61740.0390.04080.01960.00120.02280.0291-0.0553-0.1597-0.06580.12170.0038-0.00390.10760.00310.12318.218929.364317.4971
83.7809-1.67260.11857.8451.07694.17180.02780.3092-0.11920.0182-0.06850.41120.0506-0.60120.03220.1267-0.0120.00880.28010.00620.1672-6.472828.25816.8414
95.5025-1.27866.08122.6455-1.20327.0694-0.2318-0.44040.72750.25480.09080.1753-0.4529-0.47570.1960.24020.06230.03520.1735-0.02220.22814.111840.421525.5226
103.4555-1.59420.52072.6553-0.91472.3621-0.1081-0.3908-0.04850.24950.1054-0.26380.07140.44990.04960.19970.0351-0.0480.3209-0.03660.175530.306722.738335.2708
119.27121.2831-1.96875.65022.33566.6112-0.0276-0.013-0.61990.2361-0.05280.08180.72150.16240.14840.23940.0422-0.01560.1722-0.03140.164224.93217.25747.9705
127.67121.70443.61073.68552.35452.4337-0.0491-0.1759-1.59160.65740.0246-0.81921.85160.09210.30180.59350.07780.02170.2497-0.02290.433329.475112.11148.9572
137.0509-1.4967-1.79365.96481.62731.99920.24380.04610.4785-0.26130.4209-0.4611-0.25121.13-0.60590.2352-0.02070.04170.38-0.06930.275636.016224.0255.3921
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 176 )A105 - 176
4X-RAY DIFFRACTION4chain 'A' and (resid 177 through 197 )A177 - 197
5X-RAY DIFFRACTION5chain 'A' and (resid 198 through 227 )A198 - 227
6X-RAY DIFFRACTION6chain 'A' and (resid 228 through 248 )A228 - 248
7X-RAY DIFFRACTION7chain 'A' and (resid 249 through 311 )A249 - 311
8X-RAY DIFFRACTION8chain 'A' and (resid 312 through 331 )A312 - 331
9X-RAY DIFFRACTION9chain 'A' and (resid 332 through 349 )A332 - 349
10X-RAY DIFFRACTION10chain 'A' and (resid 350 through 385 )A350 - 385
11X-RAY DIFFRACTION11chain 'B' and (resid 452 through 470 )B452 - 470
12X-RAY DIFFRACTION12chain 'B' and (resid 471 through 477 )B471 - 477
13X-RAY DIFFRACTION13chain 'B' and (resid 478 through 491 )B478 - 491

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