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- PDB-2de0: Crystal structure of human alpha 1,6-fucosyltransferase, FUT8 -

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Basic information

Entry
Database: PDB / ID: 2de0
TitleCrystal structure of human alpha 1,6-fucosyltransferase, FUT8
ComponentsAlpha-(1,6)-fucosyltransferase
KeywordsTRANSFERASE / FUT8 / Fucosyltransferase / Glycosyltransferase / N-glycan / Core fucose / SH3 domain
Function / homology
Function and homology information


glycoprotein 6-alpha-L-fucosyltransferase / glycoprotein 6-alpha-L-fucosyltransferase activity / receptor metabolic process / GDP-L-fucose metabolic process / alpha-(1->6)-fucosyltransferase activity / N-glycan fucosylation / Reactions specific to the complex N-glycan synthesis pathway / L-fucose catabolic process / oligosaccharide biosynthetic process / regulation of cellular response to oxidative stress ...glycoprotein 6-alpha-L-fucosyltransferase / glycoprotein 6-alpha-L-fucosyltransferase activity / receptor metabolic process / GDP-L-fucose metabolic process / alpha-(1->6)-fucosyltransferase activity / N-glycan fucosylation / Reactions specific to the complex N-glycan synthesis pathway / L-fucose catabolic process / oligosaccharide biosynthetic process / regulation of cellular response to oxidative stress / N-glycan processing / respiratory gaseous exchange by respiratory system / protein N-linked glycosylation via asparagine / fibroblast migration / protein N-linked glycosylation / Golgi cisterna membrane / transforming growth factor beta receptor signaling pathway / integrin-mediated signaling pathway / SH3 domain binding / regulation of gene expression / Maturation of spike protein / in utero embryonic development / viral protein processing / Golgi membrane / Golgi apparatus / extracellular exosome / membrane
Similarity search - Function
Alpha-(1,6)-fucosyltransferase / Alpha-(1,6)-fucosyltransferase, SH3 domain / Alpha-(1,6)-fucosyltransferase, N- and catalytic domain / Alpha-(1,6)-fucosyltransferase N- and catalytic domains / Glycosyltransferase family 23 (GT23) domain / Glycosyltransferase family 23 (GT23) domain profile. / ESAT-6-like / Variant SH3 domain / SH3 Domains / SH3 type barrels. ...Alpha-(1,6)-fucosyltransferase / Alpha-(1,6)-fucosyltransferase, SH3 domain / Alpha-(1,6)-fucosyltransferase, N- and catalytic domain / Alpha-(1,6)-fucosyltransferase N- and catalytic domains / Glycosyltransferase family 23 (GT23) domain / Glycosyltransferase family 23 (GT23) domain profile. / ESAT-6-like / Variant SH3 domain / SH3 Domains / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Helix Hairpins / Roll / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Alpha-(1,6)-fucosyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.61 Å
AuthorsTaniguchi, N. / Ihara, H. / Nakagawa, A.
Citation
Journal: Glycobiology / Year: 2007
Title: Crystal structure of mammalian {alpha}1,6-fucosyltransferase, FUT8
Authors: Ihara, H. / Ikeda, Y. / Toma, S. / Wang, X. / Suzuki, T. / Gu, J. / Miyoshi, E. / Tsukihara, T. / Honke, K. / Matsumoto, A. / Nakagawa, A. / Taniguchi, N.
#1: Journal: Biochim Biophys Acta Gen Subj / Year: 2020
Title: Involvement of the alpha-helical and Src homology 3 domains in the molecular assembly and enzymatic activity of human alpha 1,6-fucosyltransferase, FUT8.
Authors: Ihara, H. / Okada, T. / Taniguchi, N. / Ikeda, Y.
History
DepositionFeb 7, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 26, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 11, 2020Group: Advisory / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / struct_ref_seq_dif
Item: _pdbx_struct_assembly_prop.biol_id / _struct_ref_seq_dif.details
Revision 1.4Mar 25, 2020Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: Alpha-(1,6)-fucosyltransferase


Theoretical massNumber of molelcules
Total (without water)60,2731
Polymers60,2731
Non-polymers00
Water2,468137
1
X: Alpha-(1,6)-fucosyltransferase

X: Alpha-(1,6)-fucosyltransferase


Theoretical massNumber of molelcules
Total (without water)120,5462
Polymers120,5462
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area6390 Å2
ΔGint-30 kcal/mol
Surface area39790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.030, 90.030, 380.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Alpha-(1,6)-fucosyltransferase / Glycoprotein 6-alpha-L-fucosyltransferase / GDP-fucose--glycoprotein fucosyltransferase / GDP-L-Fuc: ...Glycoprotein 6-alpha-L-fucosyltransferase / GDP-fucose--glycoprotein fucosyltransferase / GDP-L-Fuc:N-acetyl-beta-D-glucosaminide alpha1 / 6-fucosyltransferase / alpha1-6FucT / Fucosyltransferase 8


Mass: 60273.137 Da / Num. of mol.: 1 / Fragment: Residues 68-575
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pAcGP67B / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf21
References: UniProt: Q9BYC5, glycoprotein 6-alpha-L-fucosyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 3.69 Å3/Da / Density % sol: 66.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Na-HEPES, 1.5M Lithium sulfate monohydrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: Apr 3, 2003 / Details: mirror
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 28706 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 65.6 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 14.8
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.476 / Mean I/σ(I) obs: 1.2 / Num. unique all: 2277 / % possible all: 80.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.61→50 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.905 / SU B: 11.334 / SU ML: 0.235 / Cross valid method: THROUGHOUT / ESU R: 0.344 / ESU R Free: 0.288 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28336 1447 5.1 %RANDOM
Rwork0.22032 ---
obs0.22345 26977 97.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.728 Å2
Baniso -1Baniso -2Baniso -3
1-2.12 Å21.06 Å20 Å2
2--2.12 Å20 Å2
3----3.18 Å2
Refinement stepCycle: LAST / Resolution: 2.61→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3752 0 0 137 3889
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0213855
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7491.9435228
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7855458
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.5423.557194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.19715660
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.8961528
X-RAY DIFFRACTIONr_chiral_restr0.1190.2553
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022963
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.250.21949
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3220.22583
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2020.2213
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2170.277
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1270.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8241.52351
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.45623706
X-RAY DIFFRACTIONr_scbond_it1.93731729
X-RAY DIFFRACTIONr_scangle_it3.0714.51522
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.61→2.678 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.421 86 -
Rwork0.337 1578 -
obs--80 %

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