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

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Basic information

Entry
Database: PDB / ID: 6yjr
TitleCrystal structure of unliganded MGAT5 (alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase V) luminal domain.
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
Alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.198 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)122,2869
Polymers121,0822
Non-polymers1,2047
Water1,58588
1
AAA: Alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2535
Polymers60,5411
Non-polymers7134
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)61,0324
Polymers60,5411
Non-polymers4913
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.809, 100.415, 207.981
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain: (Details: Chains AAA BBB)

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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: 60540.785 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: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: 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


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
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.58 Å3/Da / Density % sol: 52.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Citrate pH 5.0 16% w/v PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.198→48.81 Å / Num. obs: 36979 / % possible obs: 93.4 % / Redundancy: 7.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.047 / Net I/σ(I): 12.3
Reflection shellResolution: 2.2→2.49 Å / Rmerge(I) obs: 1.223 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2041 / CC1/2: 0.615 / Rpim(I) all: 0.479

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Processing

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

5zic


Resolution: 2.198→48.81 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.919 / SU B: 20.917 / SU ML: 0.238 / Cross valid method: FREE R-VALUE / ESU R: 0.934 / ESU R Free: 0.339
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2625 1866 5.046 %
Rwork0.2081 --
all0.211 --
obs-35113 57.085 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 70.676 Å2
Baniso -1Baniso -2Baniso -3
1--2.517 Å20 Å20 Å2
2--10.152 Å2-0 Å2
3----7.636 Å2
Refinement stepCycle: LAST / Resolution: 2.198→48.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7886 0 78 88 8052
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0138178
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177410
X-RAY DIFFRACTIONr_angle_refined_deg1.5721.65111066
X-RAY DIFFRACTIONr_angle_other_deg1.2461.58617257
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2385980
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.42422.881420
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.643151393
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0341540
X-RAY DIFFRACTIONr_chiral_restr0.0680.21042
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029027
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021703
X-RAY DIFFRACTIONr_nbd_refined0.2140.21676
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1850.27204
X-RAY DIFFRACTIONr_nbtor_refined0.1720.23815
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.23971
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2211
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.2080.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1980.233
X-RAY DIFFRACTIONr_nbd_other0.2320.261
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3110.29
X-RAY DIFFRACTIONr_mcbond_it3.1816.1043944
X-RAY DIFFRACTIONr_mcbond_other3.186.1033943
X-RAY DIFFRACTIONr_mcangle_it4.7799.1564916
X-RAY DIFFRACTIONr_mcangle_other4.7799.1574917
X-RAY DIFFRACTIONr_scbond_it3.526.5234234
X-RAY DIFFRACTIONr_scbond_other3.526.5234235
X-RAY DIFFRACTIONr_scangle_it5.5489.6246150
X-RAY DIFFRACTIONr_scangle_other5.5479.6246151
X-RAY DIFFRACTIONr_lrange_it7.37171.2728898
X-RAY DIFFRACTIONr_lrange_other7.36971.2718897
X-RAY DIFFRACTIONr_ncsr_local_group_10.0890.0515625
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.198-2.2550.439100.307130X-RAY DIFFRACTION2.9699
2.255-2.3170.39170.311311X-RAY DIFFRACTION7.1026
2.317-2.3840.355180.272461X-RAY DIFFRACTION10.6492
2.384-2.4570.286320.271663X-RAY DIFFRACTION16.0508
2.457-2.5380.291600.277983X-RAY DIFFRACTION24.6689
2.538-2.6270.331800.2791289X-RAY DIFFRACTION33.5375
2.627-2.7260.397810.2931713X-RAY DIFFRACTION45.1434
2.726-2.8370.3351240.2832093X-RAY DIFFRACTION58.2654
2.837-2.9640.3471160.2692474X-RAY DIFFRACTION70.9978
2.964-3.1080.2791440.2562885X-RAY DIFFRACTION86.5676
3.108-3.2760.2761670.2313131X-RAY DIFFRACTION98.5949
3.276-3.4750.2681750.2253005X-RAY DIFFRACTION99.9371
3.475-3.7150.3051540.1992841X-RAY DIFFRACTION99.9666
3.715-4.0120.2481370.1852658X-RAY DIFFRACTION100
4.012-4.3950.2181290.1582420X-RAY DIFFRACTION100
4.395-4.9140.1841190.1592241X-RAY DIFFRACTION100
4.914-5.6730.261110.1981973X-RAY DIFFRACTION100
5.673-6.9470.294830.2291700X-RAY DIFFRACTION99.832
6.947-9.8190.216730.1861351X-RAY DIFFRACTION99.9298
9.819-48.810.3360.236791X-RAY DIFFRACTION98.4524
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)
10.9739-0.346-0.42630.65340.32031.1619-0.01890.0868-0.0308-0.0307-0.0240.0866-0.1141-0.05150.04290.0413-0.0038-0.02720.009-0.00330.0858-13.0549-14.375845.0139
20.65760.3496-0.33680.7084-0.5921.7794-0.04480.062-0.0903-0.0914-0.0448-0.04960.10920.06270.08960.1430.02020.01280.0229-0.02720.1418-28.8894-50.21665.7909
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA214 - 903
2X-RAY DIFFRACTION2ALLBBB214 - 901

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