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- PDB-8ce3: Crystal structure of MGAT5 (alpha-1,6-mannosylglycoprotein 6-beta... -

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Basic information

Entry
Database: PDB / ID: 8ce3
TitleCrystal structure of MGAT5 (alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase V) luminal domain with a Lys329-Ile345 loop truncation, in complex with 3D fragment 2548
ComponentsAlpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A
KeywordsCARBOHYDRATE / Glycosyltransferase / fragment
Function / homology
Function and homology information


alpha-1,6-mannosyl-glycoprotein 6-beta-N-acetylglucosaminyltransferase / alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase activity / N-Glycan antennae elongation / positive regulation of receptor signaling pathway via STAT / protein N-linked glycosylation via asparagine / negative regulation of protein tyrosine phosphatase activity / protein N-linked glycosylation / protein phosphatase inhibitor activity / manganese ion binding / Maturation of spike protein ...alpha-1,6-mannosyl-glycoprotein 6-beta-N-acetylglucosaminyltransferase / alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase activity / N-Glycan antennae elongation / positive regulation of receptor signaling pathway via STAT / protein N-linked glycosylation via asparagine / negative regulation of protein tyrosine phosphatase activity / protein N-linked glycosylation / protein phosphatase inhibitor activity / manganese ion binding / Maturation of spike protein / viral protein processing / positive regulation of cell migration / Golgi membrane / Golgi apparatus / extracellular exosome / membrane
Similarity search - Function
Glycosyltransferase family 18 / Domain of unknown function DUF4525 / Glycosyltransferase family 18 / Domain of unknown function (DUF4525)
Similarity search - Domain/homology
: / Alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsGilio, A.K. / Darby, J.F. / Wu, L. / Davies, G.J.
Funding support United Kingdom, European Union, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/N008332/1 United Kingdom
Marie Sklodowska-Curie Actions, FragNET ITN675899European Union
Royal SocietyINF/R1/191028 United Kingdom
CitationJournal: To Be Published
Title: A Modular 3-D Fragment Collection: Design, Synthesis and Screening
Authors: Downes, T.D. / Jones, S.P. / Firth, J.D. / Darby, J.F. / Gilio, A.K. / Klein, H.F. / Blakemore, D.C. / de Fusco, C. / Roughley, S.D. / Vidler, L.R. / Whatton, M.A. / Woolford, A.J.A. / ...Authors: Downes, T.D. / Jones, S.P. / Firth, J.D. / Darby, J.F. / Gilio, A.K. / Klein, H.F. / Blakemore, D.C. / de Fusco, C. / Roughley, S.D. / Vidler, L.R. / Whatton, M.A. / Woolford, A.J.A. / Wrigley, G.L. / Hubbard, R.E. / Wu, L. / Davies, G.J. / O'Brien, P.
History
DepositionFeb 1, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 21, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A
B: Alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,93823
Polymers117,9942
Non-polymers1,94521
Water6,287349
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, elutes as a single peak at expected retention time for a monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5390 Å2
ΔGint-100 kcal/mol
Surface area41820 Å2
Unit cell
Length a, b, c (Å)46.860, 68.540, 91.310
Angle α, β, γ (deg.)107.300, 92.160, 107.050
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 1 / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 214 - 728 / Label seq-ID: 1 - 515

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A / Alpha-mannoside beta-1 / 6-N-acetylglucosaminyltransferase V / GlcNAc-T V / GNT-V / Mannoside ...Alpha-mannoside beta-1 / 6-N-acetylglucosaminyltransferase V / GlcNAc-T V / GNT-V / Mannoside acetylglucosaminyltransferase 5 / N-acetylglucosaminyl-transferase V


Mass: 58996.906 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MGAT5, GGNT5 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q09328, alpha-1,6-mannosyl-glycoprotein 6-beta-N-acetylglucosaminyltransferase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-UE0 / (3~{S})-1-ethanoyl-3-(4-methylphenyl)piperidine-3-carboxylic acid


Mass: 261.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H19NO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 349 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.25 Å3/Da / Density % sol: 45.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES pH 8.0, 0.3 M Li2SO4, 30 % (w/v) PEG 3350, 10 % (v/v) ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.95 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.89→60.47 Å / Num. obs: 80017 / % possible obs: 97.26 % / Redundancy: 3.5 % / CC1/2: 1 / Rrim(I) all: 0.047 / Net I/σ(I): 13.6
Reflection shellResolution: 1.89→1.92 Å / Num. unique obs: 5618 / CC1/2: 0.6 / Rrim(I) all: 1.297

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
xia2data reduction
xia2data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→60.465 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.952 / WRfactor Rfree: 0.241 / WRfactor Rwork: 0.197 / SU B: 4.945 / SU ML: 0.137 / Average fsc free: 0.9498 / Average fsc work: 0.9652 / Cross valid method: FREE R-VALUE / ESU R: 0.165 / ESU R Free: 0.151
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2327 3795 4.743 %
Rwork0.1897 76222 -
all0.192 --
obs-80017 97.259 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 54.819 Å2
Baniso -1Baniso -2Baniso -3
1--0.258 Å21.025 Å20.567 Å2
2---0.062 Å21.78 Å2
3----1.538 Å2
Refinement stepCycle: LAST / Resolution: 1.89→60.465 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8033 0 112 349 8494
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0128332
X-RAY DIFFRACTIONr_bond_other_d0.0010.0167912
X-RAY DIFFRACTIONr_angle_refined_deg1.511.65111245
X-RAY DIFFRACTIONr_angle_other_deg0.4871.57718271
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8985983
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.242539
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.187101482
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.50110384
X-RAY DIFFRACTIONr_chiral_restr0.0740.21203
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.029438
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021911
X-RAY DIFFRACTIONr_nbd_refined0.2180.21625
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1970.27374
X-RAY DIFFRACTIONr_nbtor_refined0.1840.23944
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.24354
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2650.2355
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1370.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1760.215
X-RAY DIFFRACTIONr_nbd_other0.190.266
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2010.215
X-RAY DIFFRACTIONr_mcbond_it5.4565.3583959
X-RAY DIFFRACTIONr_mcbond_other5.4565.3583959
X-RAY DIFFRACTIONr_mcangle_it6.8399.6094933
X-RAY DIFFRACTIONr_mcangle_other6.8399.6094934
X-RAY DIFFRACTIONr_scbond_it6.4595.9624373
X-RAY DIFFRACTIONr_scbond_other6.4595.9634374
X-RAY DIFFRACTIONr_scangle_it9.08710.676312
X-RAY DIFFRACTIONr_scangle_other9.08710.6716313
X-RAY DIFFRACTIONr_lrange_it10.51354.6039233
X-RAY DIFFRACTIONr_lrange_other10.51254.6029233
X-RAY DIFFRACTIONr_ncsr_local_group_10.1020.0515860
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.101790.05008
12AX-RAY DIFFRACTIONLocal ncs0.101790.05008
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.89-1.9390.3422590.33356180.33360810.9020.9196.64530.33
1.939-1.9920.3042880.29454410.29559230.9340.93796.72460.288
1.992-2.050.3222730.27553410.27757990.9290.94896.80980.263
2.05-2.1130.2872670.25851340.2655860.940.95396.68810.243
2.113-2.1820.3362530.24449610.24853770.9330.96196.96860.224
2.182-2.2590.2962470.2248560.22452700.9490.96996.83110.201
2.259-2.3440.2642130.20447950.20651490.9560.97497.26160.186
2.344-2.4390.2592140.20644790.20948110.9540.97497.54730.188
2.439-2.5470.2542100.20143690.20346920.9620.97697.59160.183
2.547-2.6720.2631990.18641570.1944620.960.97997.62440.174
2.672-2.8160.262070.19139260.19442390.9580.97897.49940.181
2.816-2.9860.2722050.20737600.2140490.9530.97497.92540.201
2.986-3.1920.2541810.19534570.19837290.9620.97897.55970.195
3.192-3.4470.2141550.20633030.20635420.9670.97897.62850.21
3.447-3.7750.251340.18630240.18932300.9640.98297.77090.198
3.775-4.2180.1871330.15927390.1629430.9780.98797.58750.178
4.218-4.8670.1661450.13123710.13325720.9830.9997.82270.155
4.867-5.9510.191990.16120460.16221810.9810.98798.34940.19
5.951-8.3750.222710.18715850.18916880.9730.98398.10430.222
8.375-60.4650.225420.1828600.1849470.9660.97995.24820.25

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