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- PDB-8d0q: Human FUT9 bound to GDP-CF3-Fucose and H-Type 2 -

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Basic information

Entry
Database: PDB / ID: 8d0q
TitleHuman FUT9 bound to GDP-CF3-Fucose and H-Type 2
Components4-galactosyl-N-acetylglucosaminide 3-alpha-L-fucosyltransferase 9
KeywordsTRANSFERASE / Glycosyltransferase / Alpha-(1 / 3)-fucosyltransferase / GT 10 / GT-B fold / Inverting mechanism
Function / homology
Function and homology information


neuronal stem cell division / alpha-(1->3)-fucosyltransferase activity / Lewis x epitope biosynthetic process / regulation of leukocyte cell-cell adhesion / regulation of leukocyte tethering or rolling / Lewis blood group biosynthesis / 4-galactosyl-N-acetylglucosaminide 3-alpha-L-fucosyltransferase / 4-galactosyl-N-acetylglucosaminide 3-alpha-L-fucosyltransferase activity / fucosylation / N-glycan fucosylation ...neuronal stem cell division / alpha-(1->3)-fucosyltransferase activity / Lewis x epitope biosynthetic process / regulation of leukocyte cell-cell adhesion / regulation of leukocyte tethering or rolling / Lewis blood group biosynthesis / 4-galactosyl-N-acetylglucosaminide 3-alpha-L-fucosyltransferase / 4-galactosyl-N-acetylglucosaminide 3-alpha-L-fucosyltransferase activity / fucosylation / N-glycan fucosylation / fucosyltransferase activity / glycosphingolipid biosynthetic process / L-fucose catabolic process / oligosaccharide biosynthetic process / polysaccharide biosynthetic process / protein O-linked glycosylation / protein N-linked glycosylation / protein glycosylation / trans-Golgi network membrane / trans-Golgi network / neuron differentiation / positive regulation of neuron projection development / carbohydrate metabolic process / Golgi membrane / Golgi apparatus / protein homodimerization activity
Similarity search - Function
Fucosyltransferase, N-terminal / Fucosyltransferase, N-terminal / Glycosyl transferase family 10 / GT10-like, C-terminal domain superfamily / Glycosyltransferase family 10 (fucosyltransferase) C-term
Similarity search - Domain/homology
Chem-6CK / GUANOSINE-5'-DIPHOSPHATE / 4-galactosyl-N-acetylglucosaminide 3-alpha-L-fucosyltransferase 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 Å
AuthorsKadirvelraj, R. / Wood, Z.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Alcohol Abuse and Alcoholism (NIH/NIAAA)GM130915, GM103390 and P01GM107012 United States
CitationJournal: Nat.Chem.Biol. / Year: 2023
Title: Structural basis for Lewis antigen synthesis by the alpha 1,3-fucosyltransferase FUT9.
Authors: Kadirvelraj, R. / Boruah, B.M. / Wang, S. / Chapla, D. / Huang, C. / Ramiah, A. / Hudson, K.L. / Prudden, A.R. / Boons, G.J. / Withers, S.G. / Wood, Z.A. / Moremen, K.W.
History
DepositionMay 26, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4-galactosyl-N-acetylglucosaminide 3-alpha-L-fucosyltransferase 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6158
Polymers37,8531
Non-polymers2,7627
Water5,441302
1
A: 4-galactosyl-N-acetylglucosaminide 3-alpha-L-fucosyltransferase 9
hetero molecules

A: 4-galactosyl-N-acetylglucosaminide 3-alpha-L-fucosyltransferase 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,22916
Polymers75,7052
Non-polymers5,52414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation14_665-x+1,-y+3/2,z1
Buried area9050 Å2
ΔGint-19 kcal/mol
Surface area26030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.810, 127.810, 127.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11A-759-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein 4-galactosyl-N-acetylglucosaminide 3-alpha-L-fucosyltransferase 9 / / Fucosyltransferase 9 / Fucosyltransferase IX / Fuc-TIX / FucT-IX / Galactoside 3-L-fucosyltransferase


Mass: 37852.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FUT9 / Cell line (production host): HEK293S / Production host: Homo sapiens (human)
References: UniProt: Q9Y231, 4-galactosyl-N-acetylglucosaminide 3-alpha-L-fucosyltransferase

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Sugars , 3 types, 3 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 529.490 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
LFucpa1-2DGalpb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5][a1221m-1a_1-5]/1-2-3/a4-b1_b2-c1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(2+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 529.490 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
LFucpa1-2DGalpb1-4DGlcpNAca1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1a_1-5_2*NCC/3=O][a2112h-1b_1-5][a1221m-1a_1-5]/1-2-3/a4-b1_b2-c1WURCSPDB2Glycan 1.1.0

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Non-polymers , 4 types, 306 molecules

#5: Chemical ChemComp-6CK / [(2R,3S,4R,5R)-5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4R,5S,6R)-3,4,5-trihydroxy-6-(trifluoromethyl)tetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name)


Mass: 643.313 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H22F3N5O15P2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#7: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 302 / 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: 2.4 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 1.6 M Ammonium sulfate, 100 mM Tris pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 15, 2018
RadiationMonochromator: Si (111) Rosenbaum-Rock double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.39→40.4 Å / Num. obs: 69390 / % possible obs: 99.9 % / Redundancy: 17 % / Biso Wilson estimate: 23.7 Å2 / CC1/2: 1 / Rrim(I) all: 0.05 / Net I/σ(I): 26.3
Reflection shellResolution: 1.39→1.43 Å / Redundancy: 12 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 6880 / CC1/2: 0.53 / Rrim(I) all: 1.86 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8D0O

8d0o


Resolution: 1.39→36.9 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.172 3479 5.01 %
Rwork0.152 --
obs0.153 69390 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.39→36.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2482 0 158 302 2942
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082752
X-RAY DIFFRACTIONf_angle_d1.213788
X-RAY DIFFRACTIONf_dihedral_angle_d13.372997
X-RAY DIFFRACTIONf_chiral_restr0.095412
X-RAY DIFFRACTIONf_plane_restr0.008457
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3901-1.40910.26991410.25862620X-RAY DIFFRACTION100
1.4091-1.42920.251360.22592610X-RAY DIFFRACTION100
1.4292-1.45060.2431430.19862653X-RAY DIFFRACTION100
1.4506-1.47320.24641360.19462591X-RAY DIFFRACTION100
1.4732-1.49740.22091390.18472671X-RAY DIFFRACTION100
1.4974-1.52320.2181370.15492597X-RAY DIFFRACTION100
1.5232-1.55090.19321380.1372605X-RAY DIFFRACTION100
1.5509-1.58070.1791380.13032640X-RAY DIFFRACTION100
1.5807-1.6130.14671370.12072619X-RAY DIFFRACTION100
1.613-1.64810.14761340.11892621X-RAY DIFFRACTION100
1.6481-1.68640.16571390.12362648X-RAY DIFFRACTION100
1.6864-1.72860.18291370.12342633X-RAY DIFFRACTION100
1.7286-1.77530.17041430.12632651X-RAY DIFFRACTION100
1.7753-1.82760.16151370.12482604X-RAY DIFFRACTION100
1.8276-1.88660.18191380.13792644X-RAY DIFFRACTION100
1.8866-1.9540.19741390.14452591X-RAY DIFFRACTION99
1.954-2.03220.13381430.13832660X-RAY DIFFRACTION100
2.0322-2.12470.18891380.1382640X-RAY DIFFRACTION100
2.1247-2.23670.15751400.14412653X-RAY DIFFRACTION100
2.2367-2.37680.17351410.14842642X-RAY DIFFRACTION100
2.3768-2.56030.18341410.15482641X-RAY DIFFRACTION100
2.5603-2.81780.18941390.1622661X-RAY DIFFRACTION100
2.8178-3.22540.17981420.17832670X-RAY DIFFRACTION100
3.2254-4.06280.16011480.14592688X-RAY DIFFRACTION100
4.0628-36.8960.15941380.15542709X-RAY DIFFRACTION98

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