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- PDB-5l0u: human POGLUT1 in complex with EGF(+) and UDP-phosphono-glucose -

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Basic information

Entry
Database: PDB / ID: 5l0u
Titlehuman POGLUT1 in complex with EGF(+) and UDP-phosphono-glucose
Components
  • EGF(+)
  • Protein O-glucosyltransferase 1
KeywordsTRANSFERASE / transferase 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 / regulation of gastrulation / protein O-linked glycosylation via serine / UDP-xylosyltransferase activity / Pre-NOTCH Processing in the Endoplasmic Reticulum / UDP-glucosyltransferase activity ...EGF-domain serine glucosyltransferase / EGF-domain serine xylosyltransferase / EGF-domain serine glucosyltransferase activity / EGF-domain serine xylosyltransferase activity / muscle tissue development / regulation of gastrulation / protein O-linked glycosylation via serine / UDP-xylosyltransferase activity / Pre-NOTCH Processing in the Endoplasmic Reticulum / UDP-glucosyltransferase activity / circulatory system development / glucosyltransferase activity / paraxial mesoderm development / axial mesoderm development / protein O-linked glycosylation / positive regulation of Notch signaling pathway / gastrulation / endomembrane system / somitogenesis / endoplasmic reticulum lumen / endoplasmic reticulum
Similarity search - Function
Glycosyl transferase CAP10 domain / Glycosyl transferase family 90 / Putative lipopolysaccharide-modifying enzyme. / Laminin / Laminin / Ribbon / Mainly Beta
Similarity search - Domain/homology
Chem-660 / Protein O-glucosyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 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 1.2Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
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 1.4Mar 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

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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: EGF(+)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6017
Polymers46,3332
Non-polymers1,2685
Water5,549308
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint2 kcal/mol
Surface area18340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.850, 74.390, 83.310
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
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 EGF(+)


Mass: 4255.569 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pMal / Production host: Escherichia coli BL21(DE3) (bacteria)
#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 / N-Acetylglucosamine


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, 310 molecules

#4: Chemical ChemComp-660 / [[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-[[(2~{S},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]methyl]phosphinic acid / UDP-glucose phosphonate


Mass: 564.329 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H26N2O16P2
#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 / Water


Mass: 18.015 Da / Num. of mol.: 308 / 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: 2.41 Å3/Da / Density % sol: 48.97 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG5000 MME, 50 mM MES pH 6.5, 10mM CaCl2, 250mM NaCl, 5% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 38243 / % possible obs: 91 % / Redundancy: 6.5 % / Biso Wilson estimate: 29.8 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Net I/σ(I): 20
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.5 / CC1/2: 0.849 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XSCALEdata scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→37.195 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.44
RfactorNum. reflection% reflectionSelection details
Rfree0.1942 1878 4.91 %0
Rwork0.1718 ---
obs0.1728 38231 90.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 134.24 Å2 / Biso mean: 44.2452 Å2 / Biso min: 19.66 Å2
Refinement stepCycle: final / Resolution: 1.8→37.195 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3238 0 121 308 3667
Biso mean--46.97 42.6 -
Num. residues----396
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043460
X-RAY DIFFRACTIONf_angle_d0.9994719
X-RAY DIFFRACTIONf_chiral_restr0.061494
X-RAY DIFFRACTIONf_plane_restr0.005603
X-RAY DIFFRACTIONf_dihedral_angle_d12.0642070
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.84870.251430.25230413184100
1.8487-1.90310.28681310.25222419255080
1.9031-1.96450.26461010.23631814191560
1.9645-2.03470.25951670.209730373204100
2.0347-2.11620.1901960.20372140223670
2.1162-2.21250.19951610.188130243185100
2.2125-2.32910.22551280.18152408253678
2.3291-2.4750.19271570.184130543211100
2.475-2.6660.19421750.187530463221100
2.666-2.93420.23351580.183430763234100
2.9342-3.35860.18781680.177230853253100
3.3586-4.23050.17081440.14762927307193
4.2305-37.20290.16731490.147432823431100
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)
12.8698-1.1410.77861.7866-0.44122.1599-0.21-0.30640.00790.13980.23440.1850.1088-0.6688-0.02310.3227-0.03490.04770.5146-0.02680.28593.680830.877234.5224
22.5269-1.28570.1443.1176-1.39532.95720.0608-0.1607-0.1523-0.1552-0.0811-0.28370.83960.6990.04120.56530.2807-0.06890.5451-0.00960.441832.127912.780531.6426
31.6634-0.90350.4722.5747-0.92733.73660.0673-0.0638-0.1028-0.02670.0425-0.13440.64240.4471-0.04890.32050.0816-0.02290.2584-0.0330.268223.597319.847126.7358
43.3487-0.61350.521.83110.49012.70350.10380.16020.2887-0.1038-0.07940.0081-0.0719-0.1028-0.00290.27630.00280.05470.2150.04940.234910.25633.979311.7063
54.90932.32750.4871.10470.25233.9320.34771.1593-0.7266-0.5288-0.28260.23360.3165-0.15450.00770.41230.005-0.03980.4204-0.07040.27948.656723.09552.2688
62.4098-0.3212-0.07161.51830.06053.2570.05620.1043-0.0108-0.06680.00730.16930.1325-0.4515-0.07450.1935-0.0299-0.0140.20610.00850.23524.992329.810817.2977
79.3249-1.77222.84662.4285-0.66355.9150.0079-0.3471.11530.1535-0.00080.1747-0.6099-0.3567-0.05920.35370.01660.07310.2201-0.03850.39954.662941.115125.6278
84.2638-2.76950.73693.3024-0.38172.0664-0.1142-0.37820.06280.2890.1887-0.49850.31990.71750.03210.31650.1218-0.0610.4857-0.05490.328530.223622.670635.2915
94.87882.5308-0.55178.1124-0.41434.08280.0889-0.3265-0.3665-0.276-0.3422-0.35680.86930.15040.32980.51270.1010.04410.3968-0.00930.381925.902415.92678.0785
106.1146-2.95363.29245.6124-0.2668.84730.5021-0.49491.202-0.59840.5577-1.6045-0.49771.8431-0.97630.52130.0010.21540.5824-0.17110.719235.745824.99245.0765
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 227 )A177 - 227
5X-RAY DIFFRACTION5chain 'A' and (resid 228 through 248 )A228 - 248
6X-RAY DIFFRACTION6chain 'A' and (resid 249 through 331 )A249 - 331
7X-RAY DIFFRACTION7chain 'A' and (resid 332 through 349 )A332 - 349
8X-RAY DIFFRACTION8chain 'A' and (resid 350 through 385 )A350 - 385
9X-RAY DIFFRACTION9chain 'B' and (resid 1 through 26 )B1 - 26
10X-RAY DIFFRACTION10chain 'B' and (resid 27 through 40 )B27 - 40

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