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- PDB-5ggg: Crystal structure of human protein O-mannose beta-1,2-N-acetylglu... -

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Basic information

Entry
Database: PDB / ID: 5ggg
TitleCrystal structure of human protein O-mannose beta-1,2-N-acetylglucosaminyltransferase form I
ComponentsProtein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1
KeywordsTRANSFERASE / SUGAR BINDING PROTEIN / glycosyltransferase / O-mannosylation / alpha-dystroglycan
Function / homology
Function and homology information


beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,3-N-acetylglucosaminyltransferase activity / Defective POMGNT1 causes MDDGA3, MDDGB3 and MDDGC3 / O-linked glycosylation / localization of cell / protein O-linked glycosylation via N-acetyl-galactosamine / protein O-linked glycosylation via mannose / reactive gliosis / acetylglucosaminyltransferase activity / basement membrane organization / dentate gyrus development ...beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,3-N-acetylglucosaminyltransferase activity / Defective POMGNT1 causes MDDGA3, MDDGB3 and MDDGC3 / O-linked glycosylation / localization of cell / protein O-linked glycosylation via N-acetyl-galactosamine / protein O-linked glycosylation via mannose / reactive gliosis / acetylglucosaminyltransferase activity / basement membrane organization / dentate gyrus development / protein O-linked glycosylation / Transferases; Glycosyltransferases; Hexosyltransferases / myelination / sensory perception of sound / manganese ion binding / carbohydrate binding / gene expression / Golgi membrane / membrane
Similarity search - Function
Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1, PANDER-like domain / : / Glycosyl transferase, family 13 / ILEI/PANDER domain / GNT-I family / Interleukin-like EMT inducer / GG-type lectin domain profile. / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases ...Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1, PANDER-like domain / : / Glycosyl transferase, family 13 / ILEI/PANDER domain / GNT-I family / Interleukin-like EMT inducer / GG-type lectin domain profile. / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å
AuthorsKuwabara, N. / Senda, T. / Kato, R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Carbohydrate-binding domain of the POMGnT1 stem region modulates O-mannosylation sites of alpha-dystroglycan
Authors: Kuwabara, N. / Manya, H. / Yamada, T. / Tateno, H. / Kanagawa, M. / Kobayashi, K. / Akasaka-Manya, K. / Hirose, Y. / Mizuno, M. / Ikeguchi, M. / Toda, T. / Hirabayashi, J. / Senda, T. / Endo, T. / Kato, R.
History
DepositionJun 16, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2016Group: Database references
Revision 1.2Feb 26, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Oct 16, 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-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1


Theoretical massNumber of molelcules
Total (without water)65,5511
Polymers65,5511
Non-polymers00
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.917, 99.917, 236.104
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1 / POMGnT1 / UDP-GlcNAc:alpha-D-mannoside beta-1 / 2-N-acetylglucosaminyltransferase I.2 / GnT I.2


Mass: 65551.453 Da / Num. of mol.: 1 / Fragment: UNP residues 92-660
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POMGNT1, MGAT1.2, UNQ746/PRO1475 / Cell line (production host): HEK-293T / Production host: Homo sapiens (human)
References: UniProt: Q8WZA1, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
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: 4.49 Å3/Da / Density % sol: 72.64 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: Na malonate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jan 31, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→44.684 Å / Num. obs: 45699 / % possible obs: 99.9 % / Redundancy: 14.2 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 30.8
Reflection shellResolution: 3→3.18 Å / Redundancy: 14.8 % / Rmerge(I) obs: 0.657 / Mean I/σ(I) obs: 4.6 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 3→44.684 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.21
Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.2412 3000 6.56 %
Rwork0.2048 --
obs0.2072 45699 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3→44.684 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4210 0 0 3 4213
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054331
X-RAY DIFFRACTIONf_angle_d0.9475908
X-RAY DIFFRACTIONf_dihedral_angle_d18.0252579
X-RAY DIFFRACTIONf_chiral_restr0.054649
X-RAY DIFFRACTIONf_plane_restr0.008764
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.04920.39341400.35232031X-RAY DIFFRACTION100
3.0492-3.10170.30821420.30512060X-RAY DIFFRACTION100
3.1017-3.15810.34641480.27612026X-RAY DIFFRACTION100
3.1581-3.21890.36181470.26832044X-RAY DIFFRACTION100
3.2189-3.28450.29541480.25292042X-RAY DIFFRACTION100
3.2845-3.35590.28421350.23292021X-RAY DIFFRACTION100
3.3559-3.4340.27491430.22142046X-RAY DIFFRACTION100
3.434-3.51980.29411370.23192013X-RAY DIFFRACTION100
3.5198-3.6150.27561460.21982041X-RAY DIFFRACTION100
3.615-3.72130.24811410.22432038X-RAY DIFFRACTION100
3.7213-3.84130.2661420.19082042X-RAY DIFFRACTION100
3.8413-3.97850.20951460.19092020X-RAY DIFFRACTION100
3.9785-4.13770.21851410.18692044X-RAY DIFFRACTION100
4.1377-4.32590.24911420.17522015X-RAY DIFFRACTION100
4.3259-4.55370.20481440.1632054X-RAY DIFFRACTION100
4.5537-4.83870.18841460.16922021X-RAY DIFFRACTION100
4.8387-5.21180.21051420.18672042X-RAY DIFFRACTION100
5.2118-5.73530.22211390.19112033X-RAY DIFFRACTION100
5.7353-6.5630.24821510.22012023X-RAY DIFFRACTION100
6.563-8.26020.29411390.21622038X-RAY DIFFRACTION100
8.2602-44.68920.19561410.19742005X-RAY DIFFRACTION99
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)
16.44250.0392.44833.01490.11888.04410.8268-0.05620.18740.09990.09470.35390.8834-2.3986-0.85210.8423-0.06350.07971.70230.1710.7812-4.671725.33942.1191
23.0459-1.10552.01521.240.9924.90550.74960.08310.61710.12440.28850.45690.1849-2.3272-0.51980.71490.27810.37571.84990.32871.2609-8.917932.5848-6.5815
33.464-0.1769-0.94512.0197-0.16353.55840.29310.3040.33260.06610.07510.0228-0.2552-0.2822-0.33130.3290.13970.03881.14950.0830.62120.323829.4714-25.1307
44.1239-2.13911.05171.6421-0.60462.04260.2218-0.56070.48790.2818-0.17940.1754-0.28460.4260.00760.4752-0.1410.08471.3851-0.03150.68443.703731.8171-14.793
52.03730.4411-0.24480.4489-0.02370.34780.0675-0.64780.28980.1387-0.0202-0.22740.17190.27230.1162-0.2054-0.2016-0.02751.8737-0.02270.585353.099525.4201-12.9585
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 97 through 226 )
2X-RAY DIFFRACTION2chain 'A' and (resid 227 through 269 )
3X-RAY DIFFRACTION3chain 'A' and (resid 270 through 500 )
4X-RAY DIFFRACTION4chain 'A' and (resid 501 through 618 )
5X-RAY DIFFRACTION5chain 'A' and (resid 619 through 647 )

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