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

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Basic information

Entry
Database: PDB / ID: 6yju
TitleCrystal structure of MGAT5 (alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase V) luminal domain with a Lys329-Ile345 loop truncation, in complex with UDP and biantennary pentasaccharide M592
ComponentsAlpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A
KeywordsTRANSFERASE / Carbohydrate / Enzyme / N-glycosylation / GlcNAc
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 / negative regulation of protein tyrosine phosphatase activity / protein N-linked glycosylation via asparagine / 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 / negative regulation of protein tyrosine phosphatase activity / protein N-linked glycosylation via asparagine / 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
URIDINE-5'-DIPHOSPHATE / Alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsWu, L. / Darby, J.F. / Gilio, A.K. / Davies, G.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
European Research Council (ERC)ErC-2012-AdG-322942 United Kingdom
CitationJournal: Acs Catalysis / Year: 2020
Title: Substrate Engagement and Catalytic Mechanisms of N-Acetylglucosaminyltransferase V
Authors: Darby, J.F. / Gilio, A.K. / Piniello, B. / Roth, C. / Blagova, E. / Rovira, C. / Hubbard, R.E. / Davies, G.J. / Wu, L.
History
DepositionApr 4, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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
AAA: Alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A
BBB: Alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,49813
Polymers117,9942
Non-polymers2,50411
Water4,342241
1
AAA: Alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4597
Polymers58,9971
Non-polymers1,4626
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0396
Polymers58,9971
Non-polymers1,0425
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.600, 69.550, 90.940
Angle α, β, γ (deg.)107.480, 92.260, 106.220
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain: (Details: Chains AAA BBB)

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Components

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Protein , 1 types, 2 molecules AAABBB

#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

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Sugars , 2 types, 2 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose


Type: oligosaccharide / Mass: 707.630 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-6[DManpa1-3]DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a1122h-1a_1-5][a2122h-1b_1-5_2*NCC/3=O]/1-1-1-2/a3-b1_a6-c1_c2-d1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose


Type: oligosaccharide / Mass: 383.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a1122h-1a_1-5][a2122h-1b_1-5_2*NCC/3=O]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 250 molecules

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


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C2H6O2
#6: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 241 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.27 Å3/Da / Density % sol: 45.74 %
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: 0.95004 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95004 Å / Relative weight: 1
ReflectionResolution: 1.96→85.95 Å / Num. obs: 71053 / % possible obs: 95.5 % / Redundancy: 3.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.035 / Net I/σ(I): 12.8
Reflection shellResolution: 1.96→2.01 Å / Rmerge(I) obs: 1.244 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 5324 / CC1/2: 0.581 / Rpim(I) all: 0.791

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
xia2data reduction
xia2data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5zic

5zic


Resolution: 1.96→85.95 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.936 / WRfactor Rfree: 0.237 / WRfactor Rwork: 0.187 / SU B: 7.758 / SU ML: 0.196 / Average fsc free: 0.7544 / Average fsc work: 0.7822 / Cross valid method: FREE R-VALUE / ESU R: 0.203 / ESU R Free: 0.181
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2523 3368 4.74 %
Rwork0.1999 67685 -
all0.202 --
obs-71053 95.437 %
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: 51.702 Å2
Baniso -1Baniso -2Baniso -3
1--2.859 Å20.183 Å20.84 Å2
2--2.288 Å23.094 Å2
3----2.145 Å2
Refinement stepCycle: LAST / Resolution: 1.96→85.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8103 0 157 241 8501
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0138480
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177803
X-RAY DIFFRACTIONr_angle_refined_deg1.5971.66311477
X-RAY DIFFRACTIONr_angle_other_deg1.2611.58918210
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1395996
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.37723.019424
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.991151491
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2741538
X-RAY DIFFRACTIONr_chiral_restr0.0770.21075
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029176
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021740
X-RAY DIFFRACTIONr_nbd_refined0.2040.21624
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1790.27483
X-RAY DIFFRACTIONr_nbtor_refined0.1650.24056
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.23707
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2336
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0040.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2240.215
X-RAY DIFFRACTIONr_nbd_other0.2140.252
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1380.212
X-RAY DIFFRACTIONr_mcbond_it4.4895.2864005
X-RAY DIFFRACTIONr_mcbond_other4.4895.2864004
X-RAY DIFFRACTIONr_mcangle_it5.9657.9194994
X-RAY DIFFRACTIONr_mcangle_other5.9647.9194995
X-RAY DIFFRACTIONr_scbond_it5.145.7134475
X-RAY DIFFRACTIONr_scbond_other5.0925.74456
X-RAY DIFFRACTIONr_scangle_it7.2358.3596483
X-RAY DIFFRACTIONr_scangle_other7.1998.346454
X-RAY DIFFRACTIONr_lrange_it8.79660.6989310
X-RAY DIFFRACTIONr_lrange_other8.79660.6799286
X-RAY DIFFRACTIONr_ncsr_local_group_10.0840.0516454
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
1.96-2.0110.3832670.34550490.34755190.5220.55796.32180.344
2.011-2.0660.3742450.35547930.35653590.5080.54194.01010.349
2.066-2.1260.3712270.34746100.34852480.5130.52492.16840.336
2.126-2.1910.3422280.28746450.2950250.6780.7196.97510.271
2.191-2.2630.4732150.38640970.39149080.290.38187.85660.366
2.263-2.3420.2841890.25443930.25647840.7570.75595.77760.231
2.342-2.4310.2482210.19942310.20245620.8880.89797.58880.175
2.431-2.530.2951880.20441220.20944210.8860.89697.48930.18
2.53-2.6420.2831820.21939220.22242180.8480.87497.29730.192
2.642-2.7710.2991940.21236860.21640730.8520.995.26150.187
2.771-2.9210.2482030.19135580.19438510.9020.92397.66290.173
2.921-3.0980.2591600.19133420.19436130.8980.92696.92780.176
3.098-3.3110.2441520.19231640.19434220.920.93296.90240.182
3.311-3.5760.2561420.18928460.19231830.9160.93993.87370.182
3.576-3.9170.2311050.17525920.17729120.9030.94592.61680.173
3.917-4.3780.1951230.15324310.15526420.9330.94496.66920.16
4.378-5.0530.1691310.13821390.1423370.9670.97197.13310.151
5.053-6.1830.188920.15518410.15719730.9520.96197.97260.17
6.183-8.7220.24670.16114320.16515260.9330.9598.23070.184
8.722-85.950.207370.1657920.1678480.9450.96597.75940.204

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