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- PDB-8d0u: Human FUT9 bound to GDP -

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Basic information

Entry
Database: PDB / ID: 8d0u
TitleHuman FUT9 bound to GDP
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
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: 1.29 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 13, 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)39,73912
Polymers37,8531
Non-polymers1,88611
Water6,323351
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)79,47824
Polymers75,7052
Non-polymers3,77322
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation14_665-x+1,-y+3/2,z1
Buried area9640 Å2
ΔGint-80 kcal/mol
Surface area26790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.330, 127.330, 127.330
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-713-

HOH

21A-778-

HOH

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Components

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Protein / Sugars , 2 types, 2 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
#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

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Non-polymers , 4 types, 361 molecules

#3: Chemical ChemComp-GDP / GUANOSINE-5'-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
#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.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / 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 / 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: Apr 19, 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: 1.29→63.7 Å / Num. obs: 85310 / % possible obs: 99.2 % / Redundancy: 30.8 % / Biso Wilson estimate: 15.2 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.117 / Net I/σ(I): 20.2
Reflection shellResolution: 1.29→1.32 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 7987 / CC1/2: 0.47 / Rrim(I) all: 1.4 / % possible all: 89.8

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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: 1.29→63.665 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1722 4284 5.02 %
Rwork0.1519 --
obs0.1529 85310 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.29→63.665 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2482 0 118 351 2951
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052778
X-RAY DIFFRACTIONf_angle_d0.9693812
X-RAY DIFFRACTIONf_dihedral_angle_d14.2321031
X-RAY DIFFRACTIONf_chiral_restr0.084408
X-RAY DIFFRACTIONf_plane_restr0.006469
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.29-1.30420.3591170.35212084X-RAY DIFFRACTION77
1.3042-1.31950.28271410.25272711X-RAY DIFFRACTION100
1.3195-1.33560.23741390.21172708X-RAY DIFFRACTION100
1.3356-1.35250.20221450.17872684X-RAY DIFFRACTION100
1.3525-1.37030.24291430.17222680X-RAY DIFFRACTION100
1.3703-1.38910.2251430.16382746X-RAY DIFFRACTION100
1.3891-1.40890.17831450.15722706X-RAY DIFFRACTION100
1.4089-1.430.18821400.15492714X-RAY DIFFRACTION100
1.43-1.45230.20961450.14572669X-RAY DIFFRACTION100
1.4523-1.47610.18071480.142749X-RAY DIFFRACTION100
1.4761-1.50160.16851400.13582652X-RAY DIFFRACTION100
1.5016-1.52890.15071460.12812732X-RAY DIFFRACTION100
1.5289-1.55830.15381410.12262687X-RAY DIFFRACTION100
1.5583-1.59010.15491440.12232714X-RAY DIFFRACTION100
1.5901-1.62470.14461470.12482740X-RAY DIFFRACTION100
1.6247-1.66250.14681420.12522674X-RAY DIFFRACTION100
1.6625-1.70410.16791420.13052746X-RAY DIFFRACTION100
1.7041-1.75010.16691450.12742719X-RAY DIFFRACTION100
1.7501-1.80160.16061430.13652703X-RAY DIFFRACTION100
1.8016-1.85980.14921420.13352709X-RAY DIFFRACTION100
1.8598-1.92630.16891430.13432743X-RAY DIFFRACTION100
1.9263-2.00340.15251420.13722724X-RAY DIFFRACTION100
2.0034-2.09460.15271430.142716X-RAY DIFFRACTION100
2.0946-2.2050.15191410.14042729X-RAY DIFFRACTION100
2.205-2.34320.16311420.14772748X-RAY DIFFRACTION100
2.3432-2.52410.20771450.1572732X-RAY DIFFRACTION100
2.5241-2.77810.16691440.16532738X-RAY DIFFRACTION100
2.7781-3.18010.21391460.17322749X-RAY DIFFRACTION100
3.1801-4.00650.14221480.14842768X-RAY DIFFRACTION100
4.0065-63.6650.17871520.16132861X-RAY DIFFRACTION100

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