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- PDB-8d0o: Human alpha1,3-fucosyltransferase FUT9, heavy atom derivative -

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Basic information

Entry
Database: PDB / ID: 8d0o
TitleHuman alpha1,3-fucosyltransferase FUT9, heavy atom derivative
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
: / IODIDE ION / 4-galactosyl-N-acetylglucosaminide 3-alpha-L-fucosyltransferase 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 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 1.1Jun 7, 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 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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)41,25025
Polymers37,8531
Non-polymers3,39724
Water3,909217
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)82,50050
Polymers75,7052
Non-polymers6,79448
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation14_665-x+1,-y+3/2,z1
MethodPISA
Unit cell
Length a, b, c (Å)127.120, 127.120, 127.120
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-414-

IOD

21A-419-

CS

31A-625-

HOH

41A-662-

HOH

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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 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-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: I / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cs / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / Source method: isolated from a natural source / Formula: H2O
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: 1.7 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Apr 2, 2015
RadiationMonochromator: Si (111) Rosenbaum-Rock double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7 Å / Relative weight: 1
ReflectionResolution: 2.1→51.9 Å / Num. obs: 19803 / % possible obs: 99.1 % / Redundancy: 43 % / Biso Wilson estimate: 19.7 Å2 / CC1/2: 1 / Rrim(I) all: 0.093 / Net I/σ(I): 42.4
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 15 % / Mean I/σ(I) obs: 6.4 / Num. unique obs: 1771 / CC1/2: 0.95 / Rrim(I) all: 0.45 / % possible all: 88.3

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→51.9 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 19.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2088 1880 4.93 %
Rwork0.1643 --
obs0.1665 19803 98.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.5 Å2
Refinement stepCycle: LAST / Resolution: 2.1→51.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2482 0 51 217 2750
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082622
X-RAY DIFFRACTIONf_angle_d0.8993587
X-RAY DIFFRACTIONf_dihedral_angle_d9.9391535
X-RAY DIFFRACTIONf_chiral_restr0.058381
X-RAY DIFFRACTIONf_plane_restr0.006453
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1041-2.1610.27391290.20092486X-RAY DIFFRACTION87
2.161-2.22460.23721520.15582816X-RAY DIFFRACTION100
2.2246-2.29640.18221440.1552780X-RAY DIFFRACTION100
2.2964-2.37850.27541460.1552813X-RAY DIFFRACTION100
2.3785-2.47370.2021500.15972844X-RAY DIFFRACTION100
2.4737-2.58630.25051440.1592773X-RAY DIFFRACTION100
2.5863-2.72270.22411430.15942853X-RAY DIFFRACTION100
2.7227-2.89320.21281460.17452824X-RAY DIFFRACTION100
2.8932-3.11660.23711480.17532802X-RAY DIFFRACTION100
3.1166-3.43020.22251420.16982828X-RAY DIFFRACTION100
3.4302-3.92650.15461460.14222800X-RAY DIFFRACTION100
3.9265-4.94670.16781580.14242818X-RAY DIFFRACTION100
4.9467-51.90.23041320.20542835X-RAY DIFFRACTION100
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)
12.25790.0382-0.12573.89470.93371.8821-0.00870.09530.1298-0.05040.0257-0.05460.00120.109-0.02060.0919-0.01310.02660.13410.01780.083977.6805107.978833.187
23.1792-1.50431.85133.5854-1.48952.23440.02480.00810.25690.2223-0.054-0.1175-0.18790.12920.04540.1207-0.00550.03820.1461-0.01160.132972.7802108.311644.38
31.2121-0.18360.39031.7171-0.84260.4881-0.03040.0453-0.0859-0.08250.1273-0.00830.01870.0138-0.06830.10760.00460.00120.1568-0.01660.10973.208287.429237.9114
42.53730.54760.93641.9360.45842.4242-0.06980.10620.2212-0.1238-0.1358-0.0939-0.37970.19130.11610.21180.0489-0.07810.1679-0.01140.181190.435680.027552.4392
53.31620.3769-0.57690.6141.52574.8819-0.01450.28210.1695-0.2382-0.0433-0.3111-0.67850.54460.11680.2192-0.0183-0.05090.1760.01090.214896.217581.307146.2011
60.5469-0.9822-0.06752.61610.96941.4632-0.0866-0.06660.0770.21390.1198-0.17120.0930.05-0.04710.11240.0184-0.0240.13210.00770.126782.548582.566747.6003
72.3387-0.61770.33542.77320.72492.16110.0798-0.1431-0.244-0.00930.01550.10110.2187-0.0984-0.08060.1001-0.0162-0.0220.10970.01320.146778.42572.394550.333
80.441-1.2986-0.20875.63090.06590.31890.03790.0509-0.1631-0.0610.008-0.03380.01050.023-0.07160.12430.0054-0.00630.1554-0.01110.105874.266193.473332.7898
98.0617-1.62823.91594.0508-0.07765.3412-0.1145-0.64390.19810.31280.1269-0.1908-0.1699-0.6564-0.00550.1276-0.03130.06940.1580.00290.155565.9147105.115446.7993
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 63 through 122 )
2X-RAY DIFFRACTION2chain 'A' and (resid 123 through 156 )
3X-RAY DIFFRACTION3chain 'A' and (resid 157 through 178 )
4X-RAY DIFFRACTION4chain 'A' and (resid 179 through 211 )
5X-RAY DIFFRACTION5chain 'A' and (resid 212 through 237 )
6X-RAY DIFFRACTION6chain 'A' and (resid 238 through 270 )
7X-RAY DIFFRACTION7chain 'A' and (resid 271 through 320 )
8X-RAY DIFFRACTION8chain 'A' and (resid 321 through 343 )
9X-RAY DIFFRACTION9chain 'A' and (resid 344 through 359 )

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