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- PDB-7z0b: Solution NMR structure of N-acetylglucosaminyltransferase V (GnTV... -

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Basic information

Entry
Database: PDB / ID: 7z0b
TitleSolution NMR structure of N-acetylglucosaminyltransferase V (GnTV) G22L and G26L double mutant TMD
ComponentsAlpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A
KeywordsMEMBRANE PROTEIN / GnTV / TMD / Golgi / Glycosyltransferase / intramembrane / SPPL3
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)
MethodSOLUTION NMR / simulated annealing
AuthorsSilber, M. / Muhle-Goll, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)FOR2290 Germany
CitationJournal: Sci Rep / Year: 2022
Title: Helical stability of the GnTV transmembrane domain impacts on SPPL3 dependent cleavage.
Authors: Papadopoulou, A.A. / Stelzer, W. / Silber, M. / Schlosser, C. / Spitz, C. / Haug-Kroper, M. / Straub, T. / Muller, S.A. / Lichtenthaler, S.F. / Muhle-Goll, C. / Langosch, D. / Fluhrer, R.
History
DepositionFeb 22, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A


Theoretical massNumber of molelcules
Total (without water)3,6641
Polymers3,6641
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)50 / 400structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide 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: 3663.636 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: Q09328, alpha-1,6-mannosyl-glycoprotein 6-beta-N-acetylglucosaminyltransferase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H TOCSY
121isotropic12D 1H-1H NOESY
131isotropic12D 1H-13C HSQC
141isotropic12D 1H-15N HSQC

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Sample preparation

DetailsType: solution / Contents: 500 uM GNTV_G22LG26L, trifluoroethanol/water / Details: 80% TFE, 20% H2O / Label: GNTV_G22LG26L / Solvent system: trifluoroethanol/water
SampleConc.: 500 uM / Component: GNTV_G22LG26L / Isotopic labeling: none
Sample conditionsIonic strength: 1 Not defined / Label: GNTV_G22LG26L / pH: 7.0 / Pressure: 1 atm / Temperature: 300 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz / Details: cryo probe

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Processing

NMR software
NameDeveloperClassification
CNSBrunger A. T. et.al.refinement
ARIALinge, O'Donoghue and Nilgesstructure calculation
CcpNmr AnalysisVranken WF, Boucher W, Stevens TJ, Fogh RH, Pajon A, Llinas M, Ulrich EL, Markley JL, Ionides J, Laue EDchemical shift assignment
CcpNmr AnalysisVranken WF, Boucher W, Stevens TJ, Fogh RH, Pajon A, Llinas M, Ulrich EL, Markley JL, Ionides J, Laue EDpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 400 / Conformers submitted total number: 50

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