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- PDB-8d0p: Human FUT9, unliganded -

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Basic information

Entry
Database: PDB / ID: 8d0p
TitleHuman FUT9, unliganded
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 / Lewis x epitope biosynthetic process / regulation of leukocyte cell-cell adhesion / regulation of leukocyte tethering or rolling / alpha-(1->3)-fucosyltransferase activity / 4-galactosyl-N-acetylglucosaminide 3-alpha-L-fucosyltransferase / 4-galactosyl-N-acetylglucosaminide 3-alpha-L-fucosyltransferase activity / Lewis blood group biosynthesis / fucosylation / N-glycan fucosylation ...neuronal stem cell division / Lewis x epitope biosynthetic process / regulation of leukocyte cell-cell adhesion / regulation of leukocyte tethering or rolling / alpha-(1->3)-fucosyltransferase activity / 4-galactosyl-N-acetylglucosaminide 3-alpha-L-fucosyltransferase / 4-galactosyl-N-acetylglucosaminide 3-alpha-L-fucosyltransferase activity / Lewis blood group biosynthesis / fucosylation / N-glycan fucosylation / glycosphingolipid biosynthetic process / fucosyltransferase activity / oligosaccharide biosynthetic process / L-fucose catabolic process / polysaccharide biosynthetic process / protein O-linked glycosylation / protein N-linked glycosylation / protein glycosylation / trans-Golgi network membrane / trans-Golgi network / positive regulation of neuron projection development / neuron differentiation / 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
4-galactosyl-N-acetylglucosaminide 3-alpha-L-fucosyltransferase 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.09 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 24, 2023Provider: repository / Type: Initial release
Revision 1.1May 31, 2023Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 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 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)39,0487
Polymers37,8531
Non-polymers1,1956
Water6,702372
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)78,09514
Polymers75,7052
Non-polymers2,39012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation14_665-x+1,-y+3/2,z1
Buried area7120 Å2
ΔGint-81 kcal/mol
Surface area26920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.350, 127.350, 127.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213

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Components

#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
#2: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 372 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: RAYONIX MX300-HS / Detector: CCD / Date: Jul 9, 2015
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: 1.09→30 Å / Num. obs: 140941 / % possible obs: 99.9 % / Redundancy: 17 % / Biso Wilson estimate: 13.2 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.087 / Net I/σ(I): 15.7
Reflection shellResolution: 1.09→1.12 Å / Redundancy: 12 % / Num. unique obs: 13870 / CC1/2: 0.51 / Rrim(I) all: 1.7 / % possible all: 98.9

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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: 1.09→30 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1599 7065 5.01 %
Rwork0.1414 --
obs0.1423 140939 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.4 Å2
Refinement stepCycle: LAST / Resolution: 1.09→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2482 0 74 372 2928
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072806
X-RAY DIFFRACTIONf_angle_d1.143867
X-RAY DIFFRACTIONf_dihedral_angle_d12.8871049
X-RAY DIFFRACTIONf_chiral_restr0.089413
X-RAY DIFFRACTIONf_plane_restr0.008485
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.09-1.10440.28182290.27494304X-RAY DIFFRACTION97
1.1044-1.11740.24252370.22994436X-RAY DIFFRACTION100
1.1174-1.1310.22812320.21354432X-RAY DIFFRACTION100
1.131-1.14540.22752340.20844415X-RAY DIFFRACTION100
1.1454-1.16040.24022340.19244486X-RAY DIFFRACTION100
1.1604-1.17630.20362360.18154410X-RAY DIFFRACTION100
1.1763-1.19310.182340.17064484X-RAY DIFFRACTION100
1.1931-1.2110.18422370.16654419X-RAY DIFFRACTION100
1.211-1.22990.16972270.15924418X-RAY DIFFRACTION100
1.2299-1.250.16042400.15224485X-RAY DIFFRACTION100
1.25-1.27160.17932290.14754427X-RAY DIFFRACTION100
1.2716-1.29470.16042370.14244445X-RAY DIFFRACTION100
1.2947-1.31960.16192330.13474474X-RAY DIFFRACTION100
1.3196-1.34660.13912350.1254443X-RAY DIFFRACTION100
1.3466-1.37580.15662340.12744436X-RAY DIFFRACTION100
1.3758-1.40780.14882370.12444473X-RAY DIFFRACTION100
1.4078-1.4430.15252350.12374461X-RAY DIFFRACTION100
1.443-1.48210.1522370.12084432X-RAY DIFFRACTION100
1.4821-1.52570.14222390.11774460X-RAY DIFFRACTION100
1.5257-1.57490.13332360.1144464X-RAY DIFFRACTION100
1.5749-1.63120.13192370.11454469X-RAY DIFFRACTION100
1.6312-1.69650.13562340.1194478X-RAY DIFFRACTION100
1.6965-1.77370.15582390.11554464X-RAY DIFFRACTION100
1.7737-1.86720.13082360.11794475X-RAY DIFFRACTION100
1.8672-1.98420.1372320.12134478X-RAY DIFFRACTION100
1.9842-2.13730.14292320.12184502X-RAY DIFFRACTION100
2.1373-2.35230.13252360.12794512X-RAY DIFFRACTION100
2.3523-2.69250.15752410.14044510X-RAY DIFFRACTION100
2.6925-3.39160.17542400.15614541X-RAY DIFFRACTION100
3.3916-300.17292460.15614641X-RAY DIFFRACTION100

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