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- PDB-6x5s: Human Alpha-1,6-fucosyltransferase (FUT8) bound to GDP and A3'-Asn -

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Basic information

Entry
Database: PDB / ID: 6x5s
TitleHuman Alpha-1,6-fucosyltransferase (FUT8) bound to GDP and A3'-Asn
Components
  • A3'-Asn
  • Alpha-(1,6)-fucosyltransferase
KeywordsTRANSFERASE / Glycosyl transferase / Fucosyl transferase / GT-B fold / Inverting
Function / homology
Function and homology information


glycoprotein 6-alpha-L-fucosyltransferase / glycoprotein 6-alpha-L-fucosyltransferase activity / receptor metabolic process / GDP-L-fucose metabolic process / alpha-(1->6)-fucosyltransferase activity / N-glycan fucosylation / Reactions specific to the complex N-glycan synthesis pathway / L-fucose catabolic process / oligosaccharide biosynthetic process / regulation of cellular response to oxidative stress ...glycoprotein 6-alpha-L-fucosyltransferase / glycoprotein 6-alpha-L-fucosyltransferase activity / receptor metabolic process / GDP-L-fucose metabolic process / alpha-(1->6)-fucosyltransferase activity / N-glycan fucosylation / Reactions specific to the complex N-glycan synthesis pathway / L-fucose catabolic process / oligosaccharide biosynthetic process / regulation of cellular response to oxidative stress / N-glycan processing / respiratory gaseous exchange by respiratory system / protein N-linked glycosylation via asparagine / fibroblast migration / protein N-linked glycosylation / Golgi cisterna membrane / transforming growth factor beta receptor signaling pathway / integrin-mediated signaling pathway / SH3 domain binding / regulation of gene expression / Maturation of spike protein / in utero embryonic development / viral protein processing / Golgi membrane / Golgi apparatus / extracellular exosome / membrane
Similarity search - Function
Alpha-(1,6)-fucosyltransferase / Alpha-(1,6)-fucosyltransferase, SH3 domain / Alpha-(1,6)-fucosyltransferase, N- and catalytic domain / Alpha-(1,6)-fucosyltransferase N- and catalytic domains / Glycosyltransferase family 23 (GT23) domain / Glycosyltransferase family 23 (GT23) domain profile. / Variant SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Alpha-(1,6)-fucosyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 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)R01GM130915, P41GM103390 and P01GM107012 United States
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Characterizing human alpha-1,6-fucosyltransferase (FUT8) substrate specificity and structural similarities with related fucosyltransferases.
Authors: Boruah, B.M. / Kadirvelraj, R. / Liu, L. / Ramiah, A. / Li, C. / Zong, G. / Bosman, G.P. / Yang, J.Y. / Wang, L.X. / Boons, G.J. / Wood, Z.A. / Moremen, K.W.
History
DepositionMay 26, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 23, 2020Group: 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 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-(1,6)-fucosyltransferase
B: Alpha-(1,6)-fucosyltransferase
C: A3'-Asn
D: A3'-Asn
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,70522
Polymers108,2254
Non-polymers4,48018
Water1267
1
A: Alpha-(1,6)-fucosyltransferase
C: A3'-Asn
hetero molecules

B: Alpha-(1,6)-fucosyltransferase
D: A3'-Asn
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,70522
Polymers108,2254
Non-polymers4,48018
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_565x-y,-y+1,-z1
MethodPISA
Unit cell
Length a, b, c (Å)150.500, 150.500, 480.310
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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Protein / Protein/peptide / Sugars , 3 types, 6 molecules ABCD

#1: Protein Alpha-(1,6)-fucosyltransferase / Alpha1-6FucT / Fucosyltransferase 8 / GDP-L-Fuc:N-acetyl-beta-D-glucosaminide alpha1 / 6- ...Alpha1-6FucT / Fucosyltransferase 8 / GDP-L-Fuc:N-acetyl-beta-D-glucosaminide alpha1 / 6-fucosyltransferase / GDP-fucose--glycoprotein fucosyltransferase / Glycoprotein 6-alpha-L-fucosyltransferase


Mass: 53779.883 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FUT8 / Cell (production host): HEK293 / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
References: UniProt: Q9BYC5, glycoprotein 6-alpha-L-fucosyltransferase
#2: Protein/peptide A3'-Asn


Mass: 332.376 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken)
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)] ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1520.401 Da / Num. of mol.: 2 / Source method: isolated from a natural source
DescriptorTypeProgram
DGlcpNAcb1-2[DGlcpNAcb1-4]DManpa1-3[DGlcpNAcb1-2DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-1-1-3-1/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_d4-f1_g2-h1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}[(4+1)][b-D-GlcpNAc]{}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 23 molecules

#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Sequence detailsA3'-Asn was purified as a glycosylated peptide, and proteolyzed to small fragments containing the ...A3'-Asn was purified as a glycosylated peptide, and proteolyzed to small fragments containing the glycosylated asparagine
Source detailsA3'-Asn was purified from egg yolk powder

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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: 6.5 Å3/Da / Density % sol: 81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.2 M Lithium sulfate, 12 mM Nickel (II) chloride, 100 mM Tris pH 8.5
Temp details: Room temperature

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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: Oct 25, 2019
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: 3.3→65.17 Å / Num. obs: 44367 / % possible obs: 89.4 % / Redundancy: 3.4 % / Biso Wilson estimate: 77.1 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.192 / Net I/σ(I): 7.9
Reflection shellResolution: 3.3→3.39 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3352 / CC1/2: 0.689 / Rrim(I) all: 0.93 / % possible all: 93.6

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6X5H

6x5h


Resolution: 3.3→65.168 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2237 2224 5.02 %
Rwork0.1976 --
obs0.199 44340 89.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.3→65.168 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7584 0 297 7 7888
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0118095
X-RAY DIFFRACTIONf_angle_d1.30211011
X-RAY DIFFRACTIONf_dihedral_angle_d21.6684846
X-RAY DIFFRACTIONf_chiral_restr0.0711208
X-RAY DIFFRACTIONf_plane_restr0.0071378
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3001-3.37180.38171420.33572676X-RAY DIFFRACTION93
3.3718-3.45030.3131430.28882701X-RAY DIFFRACTION94
3.4503-3.53660.30641380.27142694X-RAY DIFFRACTION94
3.5366-3.63220.32041420.25232714X-RAY DIFFRACTION94
3.6322-3.7390.24681450.23832661X-RAY DIFFRACTION93
3.739-3.85970.25071400.21322631X-RAY DIFFRACTION91
3.8597-3.99760.22361390.19522620X-RAY DIFFRACTION91
3.9976-4.15770.21251380.18512597X-RAY DIFFRACTION89
4.1577-4.34690.20071350.17182506X-RAY DIFFRACTION86
4.3469-4.5760.20391400.16092638X-RAY DIFFRACTION90
4.576-4.86260.19251360.15122631X-RAY DIFFRACTION90
4.8626-5.23790.19481410.16912663X-RAY DIFFRACTION91
5.2379-5.76470.21771360.17612636X-RAY DIFFRACTION89
5.7647-6.59820.18841370.18572613X-RAY DIFFRACTION88
6.5982-8.31030.19211340.18682531X-RAY DIFFRACTION83
8.3103-65.1680.19371380.18562604X-RAY DIFFRACTION80
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)
12.2116-0.39241.22480.4781-1.01792.2735-0.0974-0.1501-0.08070.00860.31680.23010.0714-0.2664-0.2420.6227-0.0407-0.04020.582-0.03880.5189-11.262357.3736-2.3645
21.4828-0.2121-0.08961.58890.31991.72450.035-0.0446-0.142-0.05440.0123-0.18660.13560.1871-0.04530.46950.0217-0.07990.59380.0080.549115.624554.891514.1637
31.18570.08570.50531.00360.68182.542-0.00970.11210.1208-0.09050.05790.0341-0.11350.0941-0.05280.41350.0038-0.00920.4646-0.01490.46815.472163.32825.0219
42.01590.09960.31162.1147-0.72752.6868-0.0581-0.1987-0.15140.58920.088-0.18020.12530.35380.03960.59780.0370.09290.6753-0.03480.636267.801867.252712.6514
53.0777-0.89160.31243.4415-0.91242.916-0.01080.23310.3884-0.10140.10150.1238-0.2924-0.2363-0.15220.55510.022-0.00280.4487-0.02960.474436.293795.692719.8169
61.9165-1.58151.44654.1796-2.42714.5633-0.2233-0.23140.38470.46910.32280.3884-0.5121-0.8969-0.2820.61910.18570.06190.66930.0290.721528.422595.722531.5839
70.507-0.1048-0.34510.8042-0.06751.25060.00620.00480.0024-0.0175-0.0094-0.0266-0.13010.1356-0.00570.54730.00930.0050.59230.00820.573542.564680.221423.0885
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 108 through 199 )
2X-RAY DIFFRACTION2chain 'A' and (resid 200 through 395 )
3X-RAY DIFFRACTION3chain 'A' and (resid 396 through 573 )
4X-RAY DIFFRACTION4chain 'B' and (resid 108 through 172 )
5X-RAY DIFFRACTION5chain 'B' and (resid 173 through 237 )
6X-RAY DIFFRACTION6chain 'B' and (resid 238 through 267 )
7X-RAY DIFFRACTION7chain 'B' and (resid 268 through 573 )

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