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- PDB-6vlf: Crystal structure of mouse alpha 1,6-fucosyltransferase, FUT8 in ... -

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Basic information

Entry
Database: PDB / ID: 6vlf
TitleCrystal structure of mouse alpha 1,6-fucosyltransferase, FUT8 in its Apo-form
ComponentsAlpha-(1,6)-fucosyltransferase
KeywordsTRANSFERASE / FUT8 / Fucosyltransferase / Glycosyltransferase / N-glycan / Core fucose / SH3 domain
Function / homology
Function and homology information


Reactions specific to the complex N-glycan synthesis pathway / 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 / regulation of cellular response to oxidative stress / N-glycan processing / respiratory gaseous exchange by respiratory system ...Reactions specific to the complex N-glycan synthesis pathway / 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 / 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 / glycosyltransferase activity / transforming growth factor beta receptor signaling pathway / integrin-mediated signaling pathway / SH3 domain binding / cell migration / regulation of gene expression
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 speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsJarva, M.A. / Dramicanin, M. / Lingford, J.P. / Mao, R. / John, A. / Goddard-Borger, E.
Funding support Australia, 1items
OrganizationGrant numberCountry
Other governmentGNT1139546 Australia
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Structural basis of substrate recognition and catalysis by fucosyltransferase 8.
Authors: Jarva, M.A. / Dramicanin, M. / Lingford, J.P. / Mao, R. / John, A. / Jarman, K.E. / Grinter, R. / Goddard-Borger, E.D.
History
DepositionJan 23, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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
A: Alpha-(1,6)-fucosyltransferase
B: Alpha-(1,6)-fucosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,15015
Polymers125,2082
Non-polymers94313
Water11,277626
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9010 Å2
ΔGint-60 kcal/mol
Surface area39410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.874, 71.353, 126.951
Angle α, β, γ (deg.)90.000, 126.080, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Alpha-(1,6)-fucosyltransferase / Alpha1-6FucT / Fucosyltransferase 8 / GDP-L-Fuc:N-acetyl-beta-D-glucosaminide alpha1 / 6- ...Alpha1-6FucT / Fucosyltransferase 8 / GDP-L-Fuc:N-acetyl-beta-D-glucosaminide alpha1 / 6-fucosyltransferase / GDP-fucose--glycoprotein fucosyltransferase / Glycoprotein 6-alpha-L-fucosyltransferase


Mass: 62603.777 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Fut8 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9WTS2, glycoprotein 6-alpha-L-fucosyltransferase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 626 / 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: 2.7 Å3/Da / Density % sol: 54.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 12% PEG 3350, 0.25 M NH4SO4, 0.1M Tris, pH 7.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.8→49.2 Å / Num. obs: 123197 / % possible obs: 99.6 % / Redundancy: 3.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.033 / Rrim(I) all: 0.062 / Net I/σ(I): 10.6 / Num. measured all: 422751 / Scaling rejects: 3
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 3.5 % / Rmerge(I) obs: 1.268 / Num. measured all: 21511 / Num. unique obs: 6122 / CC1/2: 0.463 / Rpim(I) all: 0.788 / Rrim(I) all: 1.496 / Net I/σ(I) obs: 0.9 / % possible all: 99.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.16_3549refinement
XDSdata reduction
Aimless0.7.2data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DE0

2de0


Resolution: 1.8→44.527 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.72
RfactorNum. reflection% reflection
Rfree0.2082 6054 4.92 %
Rwork0.1842 --
obs0.1854 123157 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 221.65 Å2 / Biso mean: 43.9381 Å2 / Biso min: 21.29 Å2
Refinement stepCycle: final / Resolution: 1.8→44.527 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7330 0 56 626 8012
Biso mean--72.27 47.86 -
Num. residues----898
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8-1.82050.39292030.34733880100
1.8205-1.84190.37281940.33033890100
1.8419-1.86430.31421950.30773923100
1.8643-1.88790.32782190.29883867100
1.8879-1.91280.30772160.27993885100
1.9128-1.9390.28331990.26323878100
1.939-1.96670.27612100.25523891100
1.9667-1.9960.2952150.24913859100
1.996-2.02720.28062090.2471386199
2.0272-2.06050.25431770.216389499
2.0605-2.0960.25331950.20613898100
2.096-2.13410.212050.20443859100
2.1341-2.17520.22471830.19183941100
2.1752-2.21950.22091780.1911392299
2.2195-2.26780.22391890.1954388199
2.2678-2.32060.22281950.1884389899
2.3206-2.37860.2381990.191391699
2.3786-2.44290.23441870.1938391299
2.4429-2.51480.20892110.19383867100
2.5148-2.59590.2082280.1919389599
2.5959-2.68870.22231980.1869391199
2.6887-2.79630.20921990.19613866100
2.7963-2.92360.21492080.1922390599
2.9236-3.07770.20561940.1863949100
3.0777-3.27050.22152130.1834389599
3.2705-3.52290.17162020.1763922100
3.5229-3.87720.20322030.1674391699
3.8772-4.43780.18092020.1502395999
4.4378-5.58950.15932150.1507393799
5.5895-44.5270.19072130.1708402699
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)
10.3895-0.15240.01790.5861-0.37640.8385-0.011-0.06560.01470.0525-0.03360.0042-0.02030.0077-0.14660.2273-0.00250.0010.2113-0.00430.245226.5764.84338.6385
20.3254-0.068-0.29810.33970.16851.60680.02990.11170.078-0.05430.0112-0.0018-0.1539-0.210.0280.20960.0199-0.00680.23490.04570.256428.158623.8319-3.2796
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 106 through 575)A106 - 575
2X-RAY DIFFRACTION2(chain 'B' and resid 106 through 575)B106 - 575

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