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- PDB-6yjq: Crystal structure of unliganded MGAT5 (alpha-1,6-mannosylglycopro... -

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Basic information

Entry
Database: PDB / ID: 6yjq
TitleCrystal structure of unliganded MGAT5 (alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase V) luminal domain with a Lys329-Ile345 loop truncation
ComponentsAlpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A,Alpha-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: 1.9 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,Alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A
BBB: Alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A,Alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,67221
Polymers117,9942
Non-polymers1,67819
Water5,170287
1
AAA: Alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A,Alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5678
Polymers58,9971
Non-polymers5707
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A,Alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,10513
Polymers58,9971
Non-polymers1,10812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.000, 68.170, 90.990
Angle α, β, γ (deg.)108.360, 92.280, 106.860
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain: (Details: Chains AAA BBB) / NCS ensembles : (Details: AAA BBB)

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Components

#1: Protein Alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A,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.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#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.: 1
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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 287 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.55 Å3/Da / Density % sol: 20.52 %
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: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→43.31 Å / Num. obs: 77533 / % possible obs: 97 % / Redundancy: 3.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.042 / Net I/σ(I): 9.9
Reflection shellResolution: 1.9→1.95 Å / Rmerge(I) obs: 1.159 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 5611 / CC1/2: 0.422 / Rpim(I) all: 0.721

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Processing

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

5zic


Resolution: 1.9→43.31 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.518 / SU ML: 0.128 / Cross valid method: FREE R-VALUE / ESU R: 0.172 / ESU R Free: 0.156
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2371 3684 4.752 %
Rwork0.1941 --
all0.196 --
obs-77533 96.94 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 46.468 Å2
Baniso -1Baniso -2Baniso -3
1--0.211 Å20.557 Å20.304 Å2
2--1.185 Å21.592 Å2
3----2.33 Å2
Refinement stepCycle: LAST / Resolution: 1.9→43.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7989 0 96 287 8372
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0138283
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177680
X-RAY DIFFRACTIONr_angle_refined_deg1.4571.64311183
X-RAY DIFFRACTIONr_angle_other_deg1.2521.57717892
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8345977
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.2223.017421
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.703151477
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0181538
X-RAY DIFFRACTIONr_chiral_restr0.0710.21029
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029000
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021700
X-RAY DIFFRACTIONr_nbd_refined0.1990.21495
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1720.27126
X-RAY DIFFRACTIONr_nbtor_refined0.1640.23872
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.23882
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2328
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0840.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2060.221
X-RAY DIFFRACTIONr_nbd_other0.1950.272
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1150.214
X-RAY DIFFRACTIONr_mcbond_it3.5994.6873935
X-RAY DIFFRACTIONr_mcbond_other3.5984.6873934
X-RAY DIFFRACTIONr_mcangle_it4.7957.0094903
X-RAY DIFFRACTIONr_mcangle_other4.7947.0094904
X-RAY DIFFRACTIONr_scbond_it4.1635.1574348
X-RAY DIFFRACTIONr_scbond_other4.1325.1454309
X-RAY DIFFRACTIONr_scangle_it6.1327.5376280
X-RAY DIFFRACTIONr_scangle_other6.1137.5176221
X-RAY DIFFRACTIONr_lrange_it7.64653.7738975
X-RAY DIFFRACTIONr_lrange_other7.62453.6958937
X-RAY DIFFRACTIONr_ncsr_local_group_10.0880.0515776
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.9490.342580.3245345X-RAY DIFFRACTION95.5003
1.949-2.0030.3252680.295217X-RAY DIFFRACTION95.5076
2.003-2.0610.2762460.265126X-RAY DIFFRACTION95.2651
2.061-2.1240.2852720.2394942X-RAY DIFFRACTION95.5996
2.124-2.1940.2672380.2294833X-RAY DIFFRACTION96.3885
2.194-2.2710.2782410.2024764X-RAY DIFFRACTION97.2033
2.271-2.3560.2392100.1944565X-RAY DIFFRACTION97.3298
2.356-2.4520.2462010.1974431X-RAY DIFFRACTION97.4953
2.452-2.5610.222210.1774174X-RAY DIFFRACTION97.645
2.561-2.6860.261960.1824055X-RAY DIFFRACTION97.9042
2.686-2.8310.2341950.1813902X-RAY DIFFRACTION98.1317
2.831-3.0030.2592000.1953613X-RAY DIFFRACTION98.1215
3.003-3.210.2471740.1933459X-RAY DIFFRACTION98.402
3.21-3.4670.2511600.1983178X-RAY DIFFRACTION98.0611
3.467-3.7970.2111230.1812969X-RAY DIFFRACTION97.7244
3.797-4.2440.2121280.1682660X-RAY DIFFRACTION97.8246
4.244-4.8990.1941480.162285X-RAY DIFFRACTION97.6716
4.899-5.9950.224950.1951993X-RAY DIFFRACTION97.8444
5.995-8.4570.236680.2091519X-RAY DIFFRACTION97.4217
8.457-43.310.248420.197819X-RAY DIFFRACTION94.0984

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