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

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Basic information

Entry
Database: PDB / ID: 6yjs
TitleCrystal structure of MGAT5 (alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase V) luminal domain with a Lys329-Ile345 loop truncation, in complex with 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 / 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: 1.6 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

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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)121,90127
Polymers117,9942
Non-polymers3,90725
Water8,395466
1
AAA: Alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,79511
Polymers58,9971
Non-polymers1,79910
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)61,10616
Polymers58,9971
Non-polymers2,10915
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.280, 67.370, 91.050
Angle α, β, γ (deg.)108.810, 92.200, 106.720
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, 4 molecules

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


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-3[DGlcpNAcb1-2DManpa1-6]DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,5,4/[a1122h-1a_1-5][a2122h-1b_1-5_2*NCC/3=O]/1-1-2-1-2/a3-b1_a6-d1_b2-c1_d2-e1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: 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.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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, 487 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 466 / 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: 2.16 Å3/Da / Density % sol: 43.01 %
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 wXHPcQHrME

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.6→42.52 Å / Num. obs: 125194 / % possible obs: 96.2 % / Redundancy: 3.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.034 / Net I/σ(I): 10.4
Reflection shellResolution: 1.6→1.64 Å / Rmerge(I) obs: 1.162 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 9094 / CC1/2: 0.524 / Rpim(I) all: 0.722

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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: 1.6→42.52 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.494 / SU ML: 0.104 / Cross valid method: FREE R-VALUE / ESU R: 0.094 / ESU R Free: 0.093
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2145 3770 3.011 %
Rwork0.1841 --
all0.185 --
obs-125193 96.191 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 34.716 Å2
Baniso -1Baniso -2Baniso -3
1--0.394 Å21.502 Å2-0.052 Å2
2--2.302 Å2-0.13 Å2
3----2.354 Å2
Refinement stepCycle: LAST / Resolution: 1.6→42.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7738 0 246 466 8450
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0138187
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177543
X-RAY DIFFRACTIONr_angle_refined_deg1.621.6711063
X-RAY DIFFRACTIONr_angle_other_deg1.2911.59717600
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7565946
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.23422.985412
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.646151416
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0911538
X-RAY DIFFRACTIONr_chiral_restr0.0810.21051
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028761
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021657
X-RAY DIFFRACTIONr_nbd_refined0.20.21535
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1860.27129
X-RAY DIFFRACTIONr_nbtor_refined0.1670.23871
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.23522
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2409
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2340.226
X-RAY DIFFRACTIONr_nbd_other0.2420.2101
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1970.230
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0820.21
X-RAY DIFFRACTIONr_mcbond_it2.8883.3533814
X-RAY DIFFRACTIONr_mcbond_other2.8883.3533813
X-RAY DIFFRACTIONr_mcangle_it4.2245.0154747
X-RAY DIFFRACTIONr_mcangle_other4.2245.0154748
X-RAY DIFFRACTIONr_scbond_it4.243.9094373
X-RAY DIFFRACTIONr_scbond_other4.2193.8974334
X-RAY DIFFRACTIONr_scangle_it6.6055.6626315
X-RAY DIFFRACTIONr_scangle_other6.6035.6416256
X-RAY DIFFRACTIONr_lrange_it8.28840.0328942
X-RAY DIFFRACTIONr_lrange_other8.25839.8558855
X-RAY DIFFRACTIONr_ncsr_local_group_10.0870.0515401
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.64200.3489092X-RAY DIFFRACTION94.9457
1.642-1.68700.3278936X-RAY DIFFRACTION95.1144
1.687-1.73500.3048695X-RAY DIFFRACTION95.4655
1.735-1.78900.2818528X-RAY DIFFRACTION95.7342
1.789-1.84700.268279X-RAY DIFFRACTION96.0441
1.847-1.9120.2432670.2397690X-RAY DIFFRACTION96.1455
1.912-1.9840.2533830.2247324X-RAY DIFFRACTION96.2172
1.984-2.0650.2533630.2077083X-RAY DIFFRACTION96.6887
2.065-2.1570.2163360.196826X-RAY DIFFRACTION96.6141
2.157-2.2620.2163250.1776505X-RAY DIFFRACTION96.5917
2.262-2.3850.2082920.1716200X-RAY DIFFRACTION96.7511
2.385-2.5290.2372830.1775913X-RAY DIFFRACTION97.0856
2.529-2.7040.2092710.1755591X-RAY DIFFRACTION97.4564
2.704-2.920.222740.185115X-RAY DIFFRACTION97.0292
2.92-3.1980.2382300.1724696X-RAY DIFFRACTION96.5882
3.198-3.5750.2172070.1594278X-RAY DIFFRACTION96.1621
3.575-4.1270.1951770.143719X-RAY DIFFRACTION96.0079
4.127-5.0520.1711780.1293148X-RAY DIFFRACTION96.322
5.052-7.1320.2491210.1742463X-RAY DIFFRACTION96.7428
7.132-42.520.19630.1731343X-RAY DIFFRACTION95.9072

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