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

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Basic information

Entry
Database: PDB / ID: 6yjt
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
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: 1.7 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)120,31720
Polymers117,9942
Non-polymers2,32418
Water5,945330
1
AAA: Alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9678
Polymers58,9971
Non-polymers9707
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)60,35112
Polymers58,9971
Non-polymers1,35411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.030, 69.590, 90.000
Angle α, β, γ (deg.)107.770, 91.810, 106.940
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 / Sugars , 2 types, 4 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
#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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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

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Non-polymers , 4 types, 346 molecules

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


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 330 / 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: 2.25 Å3/Da / Density % sol: 45.43 %
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: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.7→43.43 Å / Num. obs: 108811 / % possible obs: 96 % / Redundancy: 3.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.03 / Net I/σ(I): 9.9
Reflection shellResolution: 1.7→1.74 Å / Rmerge(I) obs: 1.346 / Mean I/σ(I) obs: 1 / Num. unique obs: 8076 / CC1/2: 0.562 / Rpim(I) all: 0.804

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Processing

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

5zic


Resolution: 1.7→43.43 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.645 / SU ML: 0.116 / Cross valid method: FREE R-VALUE / ESU R: 0.114 / ESU R Free: 0.112
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2228 3727 3.437 %
Rwork0.1845 --
all0.186 --
obs-104711 95.643 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 54.886 Å2
Baniso -1Baniso -2Baniso -3
1--3.17 Å21.476 Å21.511 Å2
2--1.744 Å23.277 Å2
3----2.346 Å2
Refinement stepCycle: LAST / Resolution: 1.7→43.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8218 0 140 330 8688
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0138573
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177891
X-RAY DIFFRACTIONr_angle_refined_deg1.5361.65411589
X-RAY DIFFRACTIONr_angle_other_deg1.2551.58218397
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.05551013
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.19423.063431
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.595151506
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0221538
X-RAY DIFFRACTIONr_chiral_restr0.0740.21070
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029338
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021760
X-RAY DIFFRACTIONr_nbd_refined0.1920.21653
X-RAY DIFFRACTIONr_symmetry_nbd_other0.180.27616
X-RAY DIFFRACTIONr_nbtor_refined0.1640.24070
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.23834
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2341
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1940.215
X-RAY DIFFRACTIONr_nbd_other0.2280.273
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2060.215
X-RAY DIFFRACTIONr_mcbond_it4.1875.5674070
X-RAY DIFFRACTIONr_mcbond_other4.1825.5664069
X-RAY DIFFRACTIONr_mcangle_it5.6078.3435077
X-RAY DIFFRACTIONr_mcangle_other5.6088.3435078
X-RAY DIFFRACTIONr_scbond_it5.1496.0934503
X-RAY DIFFRACTIONr_scbond_other5.1216.0884480
X-RAY DIFFRACTIONr_scangle_it7.5988.9136512
X-RAY DIFFRACTIONr_scangle_other7.5948.9056477
X-RAY DIFFRACTIONr_lrange_it9.33564.4479410
X-RAY DIFFRACTIONr_lrange_other9.34464.3859368
X-RAY DIFFRACTIONr_ncsr_local_group_10.0880.0516614
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.74400.267734X-RAY DIFFRACTION91.6785
1.744-1.79200.2887747X-RAY DIFFRACTION95.1019
1.792-1.84400.2887600X-RAY DIFFRACTION95.996
1.844-1.9010.277820.287326X-RAY DIFFRACTION96.083
1.901-1.9630.3062980.2626939X-RAY DIFFRACTION96.2239
1.963-2.0320.2833520.2466619X-RAY DIFFRACTION96.5646
2.032-2.1080.2653290.2356425X-RAY DIFFRACTION96.7068
2.108-2.1940.2443010.2286198X-RAY DIFFRACTION97
2.194-2.2920.2532850.2085944X-RAY DIFFRACTION96.6486
2.292-2.4040.2762730.1975713X-RAY DIFFRACTION97.0178
2.404-2.5340.2382630.2045441X-RAY DIFFRACTION97.2881
2.534-2.6870.2232440.2125152X-RAY DIFFRACTION97.348
2.687-2.8720.2682490.2234804X-RAY DIFFRACTION96.5603
2.872-3.1020.2472380.214389X-RAY DIFFRACTION95.5794
3.102-3.3980.2491930.1953982X-RAY DIFFRACTION93.6519
3.398-3.7980.2371680.1653607X-RAY DIFFRACTION93.8354
3.798-4.3840.1731530.1283223X-RAY DIFFRACTION95.0451
4.384-5.3660.1591420.1212649X-RAY DIFFRACTION92.4478
5.366-7.5740.1921050.1472058X-RAY DIFFRACTION93.4341
7.574-43.430.211520.1471163X-RAY DIFFRACTION94.6262

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