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- PDB-8d0x: Human FUT9 bound to LNnT -

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Basic information

Entry
Database: PDB / ID: 8d0x
TitleHuman FUT9 bound to LNnT
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 / : / : ...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 / : / : / glycosphingolipid biosynthetic process / fucosyltransferase activity / oligosaccharide biosynthetic process / L-fucose catabolic process / protein O-linked glycosylation / polysaccharide biosynthetic process / protein N-linked 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: 1.33 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 1.4Oct 30, 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)39,87112
Polymers37,8531
Non-polymers2,01911
Water7,494416
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)79,74324
Polymers75,7052
Non-polymers4,03822
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_555x,-y,-z+1/21
Buried area10350 Å2
ΔGint-53 kcal/mol
Surface area26990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.170, 127.170, 127.170
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-1023-

HOH

21A-1095-

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 , 2 types, 2 molecules

#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: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 545.490 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-3DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2112h-1b_1-5][a2122h-1b_1-5_2*NCC/3=O]/1-2-1/a3-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(3+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 425 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 416 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 8.5 / Details: 1.8 M Ammonium sulfate, 100 mM Tris pH 8.5

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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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.33→31.8 Å / Num. obs: 78129 / % possible obs: 99.9 % / Redundancy: 20.9 % / Biso Wilson estimate: 15.8 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.134 / Net I/σ(I): 13.3
Reflection shellResolution: 1.33→1.36 Å / Redundancy: 11.9 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 7822 / CC1/2: 0.485 / Rrim(I) all: 2.07 / % 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: 1.33→31.793 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1791 3896 4.99 %
Rwork0.1556 --
obs0.1568 78111 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.33→31.793 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2482 0 129 416 3027
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052792
X-RAY DIFFRACTIONf_angle_d0.9043830
X-RAY DIFFRACTIONf_dihedral_angle_d14.5661033
X-RAY DIFFRACTIONf_chiral_restr0.082419
X-RAY DIFFRACTIONf_plane_restr0.006470
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.33-1.34630.27621380.26212634X-RAY DIFFRACTION100
1.3463-1.36330.31051350.24892676X-RAY DIFFRACTION100
1.3633-1.38120.26991370.23142612X-RAY DIFFRACTION100
1.3812-1.40020.2631400.2212619X-RAY DIFFRACTION100
1.4002-1.42020.26761360.19282618X-RAY DIFFRACTION100
1.4202-1.44140.22661420.18462662X-RAY DIFFRACTION100
1.4414-1.46390.23551370.17062623X-RAY DIFFRACTION100
1.4639-1.48790.20981400.16422661X-RAY DIFFRACTION100
1.4879-1.51350.17591390.15082619X-RAY DIFFRACTION100
1.5135-1.54110.18981350.13952622X-RAY DIFFRACTION100
1.5411-1.57070.18121380.142642X-RAY DIFFRACTION100
1.5707-1.60280.18071390.13642636X-RAY DIFFRACTION100
1.6028-1.63760.17491400.13672623X-RAY DIFFRACTION100
1.6376-1.67570.18291430.13882664X-RAY DIFFRACTION100
1.6757-1.71760.19271370.13582644X-RAY DIFFRACTION100
1.7176-1.7640.19361390.1452636X-RAY DIFFRACTION100
1.764-1.81590.16151430.13432632X-RAY DIFFRACTION100
1.8159-1.87460.19271370.13562635X-RAY DIFFRACTION100
1.8746-1.94150.17151390.13022642X-RAY DIFFRACTION100
1.9415-2.01930.18621370.14232655X-RAY DIFFRACTION100
2.0193-2.11110.17081380.14092657X-RAY DIFFRACTION100
2.1111-2.22240.1741390.1442660X-RAY DIFFRACTION100
2.2224-2.36160.15761420.14732662X-RAY DIFFRACTION100
2.3616-2.54390.17331370.1592678X-RAY DIFFRACTION100
2.5439-2.79980.20241420.15922661X-RAY DIFFRACTION100
2.7998-3.20460.17361350.16652672X-RAY DIFFRACTION100
3.2046-4.03610.14371470.14892700X-RAY DIFFRACTION100
4.0361-31.790.17791450.16812770X-RAY DIFFRACTION99

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