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- PDB-5zib: Crystal structure of human GnT-V luminal domain in apo form -

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Basic information

Entry
Database: PDB / ID: 5zib
TitleCrystal structure of human GnT-V luminal domain in apo form
ComponentsAlpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A
KeywordsSUGAR BINDING PROTEIN / Glycosyltransferase Cancer metastasis Luminal protein
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 / SAD / Resolution: 1.9 Å
AuthorsNagae, M. / Yamaguchi, Y.
Funding support Japan, 1items
OrganizationGrant numberCountry
MEXT17K07303 Japan
CitationJournal: Nat Commun / Year: 2018
Title: Structure and mechanism of cancer-associated N-acetylglucosaminyltransferase-V.
Authors: Nagae, M. / Kizuka, Y. / Mihara, E. / Kitago, Y. / Hanashima, S. / Ito, Y. / Takagi, J. / Taniguchi, N. / Yamaguchi, Y.
History
DepositionMar 14, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,8072
Polymers71,5861
Non-polymers2211
Water5,296294
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint4 kcal/mol
Surface area27320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.671, 97.671, 268.856
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-1394-

HOH

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Components

#1: Protein Alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A / Alpha-mannoside beta-1 / 6-N-acetylglucosaminyltransferase / GlcNAc-T V / GNT-V / Mannoside ...Alpha-mannoside beta-1 / 6-N-acetylglucosaminyltransferase / GlcNAc-T V / GNT-V / Mannoside acetylglucosaminyltransferase 5 / N-acetylglucosaminyl-transferase V


Mass: 71586.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MGAT5, GGNT5 / Plasmid: pSec-nPA / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
References: UniProt: Q09328, alpha-1,6-mannosyl-glycoprotein 6-beta-N-acetylglucosaminyltransferase
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / Source method: isolated from a natural source / Formula: H2O

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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: 2.59 Å3/Da / Density % sol: 52.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.15M DL-malic acid (pH 7.0), 20% (w/v) polyethylene glycol (PEG) 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.9→48.82 Å / Num. obs: 60787 / % possible obs: 100 % / Redundancy: 14.6 % / CC1/2: 0.995 / Rpim(I) all: 0.066 / Rrim(I) all: 0.253 / Net I/σ(I): 8.8
Reflection shellResolution: 1.9→2 Å / Redundancy: 14.8 % / Mean I/σ(I) obs: 2.5 / CC1/2: 0.718 / Rpim(I) all: 0.494 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→48.049 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.68
RfactorNum. reflection% reflection
Rfree0.2243 3093 5.1 %
Rwork0.1893 --
obs0.1911 60666 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→48.049 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4703 0 14 294 5011
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074863
X-RAY DIFFRACTIONf_angle_d0.8756585
X-RAY DIFFRACTIONf_dihedral_angle_d13.1052938
X-RAY DIFFRACTIONf_chiral_restr0.053699
X-RAY DIFFRACTIONf_plane_restr0.006839
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.92970.33481300.26442557X-RAY DIFFRACTION100
1.9297-1.96130.26911240.24732595X-RAY DIFFRACTION100
1.9613-1.99520.27441630.23282541X-RAY DIFFRACTION100
1.9952-2.03140.26241420.22612554X-RAY DIFFRACTION100
2.0314-2.07050.26421520.22632559X-RAY DIFFRACTION100
2.0705-2.11280.25271370.21122550X-RAY DIFFRACTION100
2.1128-2.15870.231260.2042593X-RAY DIFFRACTION100
2.1587-2.20890.28631560.19522557X-RAY DIFFRACTION100
2.2089-2.26420.21551290.18812582X-RAY DIFFRACTION100
2.2642-2.32540.23771220.19292628X-RAY DIFFRACTION100
2.3254-2.39380.20471440.18812565X-RAY DIFFRACTION100
2.3938-2.47110.24951540.1922567X-RAY DIFFRACTION100
2.4711-2.55940.24871380.19452624X-RAY DIFFRACTION100
2.5594-2.66190.24651340.19052594X-RAY DIFFRACTION100
2.6619-2.7830.21741510.20052608X-RAY DIFFRACTION100
2.783-2.92970.24251440.1992602X-RAY DIFFRACTION100
2.9297-3.11320.2591410.2012637X-RAY DIFFRACTION100
3.1132-3.35350.22331520.19932632X-RAY DIFFRACTION100
3.3535-3.69090.211340.17462662X-RAY DIFFRACTION100
3.6909-4.22470.19211400.15712693X-RAY DIFFRACTION100
4.2247-5.32160.16921520.15522721X-RAY DIFFRACTION100
5.3216-48.06460.2061280.18822952X-RAY DIFFRACTION100

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