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- PDB-6x5r: Human Alpha-1,6-fucosyltransferase (FUT8) bound to GDP and A2-Asn -

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Basic information

Entry
Database: PDB / ID: 6x5r
TitleHuman Alpha-1,6-fucosyltransferase (FUT8) bound to GDP and A2-Asn
Components
  • A2-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: 2.4 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: A2-Asn
D: A2-Asn
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,32615
Polymers124,3554
Non-polymers3,97111
Water11,025612
1
B: Alpha-(1,6)-fucosyltransferase
D: A2-Asn
hetero molecules

A: Alpha-(1,6)-fucosyltransferase
C: A2-Asn
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,32615
Polymers124,3554
Non-polymers3,97111
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665x-y+1,-y+1,-z1
MethodPISA
Unit cell
Length a, b, c (Å)149.880, 149.880, 480.880
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: 61845.219 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 / Production host: Homo sapiens (human)
References: UniProt: Q9BYC5, glycoprotein 6-alpha-L-fucosyltransferase
#2: Protein/peptide A2-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)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-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: 1317.209 Da / Num. of mol.: 2 / Source method: isolated from a natural source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-3[DGlcpNAcb1-2DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-1-3-1/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f2-g1WURCSPDB2Glycan 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]{}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}}}}LINUCSPDB-CARE

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Non-polymers , 5 types, 621 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#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: 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
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 612 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Sequence detailsA2-Asn was purified as a glycosylated peptide, and proteolyzed to small fragments containing the ...A2-Asn was purified as a glycosylated peptide, and proteolyzed to small fragments containing the glycosylated asparagine
Source detailsA2-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: 6.48 Å3/Da / Density % sol: 81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.0 M Lithium sulfate, 10 mM Nickel 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-BM / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 8, 2017
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: 2.4→49.409 Å / Num. obs: 124545 / % possible obs: 99.3 % / Redundancy: 10.4 % / Biso Wilson estimate: 43 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.153 / Net I/σ(I): 18.4
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 11.7 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 8849 / CC1/2: 0.761 / Rrim(I) all: 1.5 / % possible all: 97.1

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DE0

2de0


Resolution: 2.4→49.409 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2311 6210 4.99 %
Rwork0.2054 --
obs0.2067 124419 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→49.409 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7602 0 274 612 8488
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018117
X-RAY DIFFRACTIONf_angle_d1.04311034
X-RAY DIFFRACTIONf_dihedral_angle_d26.2623107
X-RAY DIFFRACTIONf_chiral_restr0.0551203
X-RAY DIFFRACTIONf_plane_restr0.0061385
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4001-2.42730.44761950.39963746X-RAY DIFFRACTION96
2.4273-2.45590.40531980.36923825X-RAY DIFFRACTION98
2.4559-2.48580.38381970.34473812X-RAY DIFFRACTION99
2.4858-2.51730.40522060.3443848X-RAY DIFFRACTION99
2.5173-2.55040.36441950.34263845X-RAY DIFFRACTION98
2.5504-2.58540.37672060.32713865X-RAY DIFFRACTION99
2.5854-2.62230.35632000.31123881X-RAY DIFFRACTION99
2.6223-2.66140.35122070.29793842X-RAY DIFFRACTION99
2.6614-2.7030.29592030.2953874X-RAY DIFFRACTION99
2.703-2.74730.36312020.28283861X-RAY DIFFRACTION99
2.7473-2.79470.31292040.28963914X-RAY DIFFRACTION99
2.7947-2.84550.32782070.26823893X-RAY DIFFRACTION99
2.8455-2.90020.34412090.26263913X-RAY DIFFRACTION100
2.9002-2.95940.29072030.25813899X-RAY DIFFRACTION100
2.9594-3.02380.27672050.24163914X-RAY DIFFRACTION99
3.0238-3.09410.27122070.22923924X-RAY DIFFRACTION100
3.0941-3.17150.25772060.21633934X-RAY DIFFRACTION100
3.1715-3.25720.24292120.20743962X-RAY DIFFRACTION100
3.2572-3.3530.23292040.20633916X-RAY DIFFRACTION100
3.353-3.46120.25342100.1963956X-RAY DIFFRACTION100
3.4612-3.58490.2072070.19543948X-RAY DIFFRACTION100
3.5849-3.72840.21832100.17813970X-RAY DIFFRACTION100
3.7284-3.8980.17332090.15773967X-RAY DIFFRACTION100
3.898-4.10340.18952100.14933984X-RAY DIFFRACTION100
4.1034-4.36040.17552110.14674010X-RAY DIFFRACTION100
4.3604-4.69680.1622120.13964032X-RAY DIFFRACTION100
4.6968-5.1690.15532110.14554043X-RAY DIFFRACTION100
5.169-5.91590.17662150.16824077X-RAY DIFFRACTION100
5.9159-7.44930.19322180.18684151X-RAY DIFFRACTION100
7.4493-49.4090.17872310.19594403X-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)
11.0659-0.45350.44966.3241-7.43478.6745-0.25660.24610.0467-0.26310.44320.0460.0884-0.3999-0.24210.26080.0202-0.06430.5349-0.02330.3923-19.337660.8217-11.4959
23.2363-2.39682.22921.9689-2.08022.7258-0.1554-0.161-0.06240.09720.2536-0.01270.1161-0.3816-0.09950.4104-0.0363-0.03020.4531-0.04970.3558-7.359654.95253.3591
31.06820.1045-0.03640.67430.44021.1229-0.0014-0.0743-0.05950.07510.0681-0.03940.08970.0559-0.07460.2840.0409-0.0510.4069-0.01340.289111.019658.810715.5247
40.9525-0.24421.16722.2326-1.16513.09350.00920.3633-0.072-0.27260.1046-0.06080.1060.3892-0.10940.3063-0.0008-0.01350.5657-0.06510.36258.079658.1284-7.0279
51.95762.0851-1.59663.2566-3.31523.8426-0.35030.0391-0.0977-0.38630.4296-0.40450.24570.18790.04430.27220.03620.01090.5466-0.04740.368968.472367.40027.6779
62.3436-2.1102-0.45793.42990.87860.8096-0.1758-0.17660.16540.03580.3127-0.2316-0.08050.1574-0.15970.4271-0.03980.02720.5192-0.00840.310657.034181.1716.599
71.1167-0.45050.49370.7613-0.20921.4584-0.0235-0.04790.1926-0.02670.00140.1217-0.3629-0.15120.01640.41760.07730.03950.4667-0.02210.407832.242590.359724.797
82.8228-0.6464-1.85111.00960.19713.0374-0.0286-0.15030.0540.1126-0.0115-0.1188-0.11360.37220.01440.33970.026-0.03870.4777-0.05510.33350.147176.540836.8181
90.94070.77040.44961.26350.06971.97620.0070.08040.16350.0301-0.04190.0936-0.0156-0.15640.00030.31220.05720.01360.4614-0.00480.320643.996377.942719.0265
100.73430.0352-0.59218.6551.8792.1369-0.08560.2481-0.0125-0.45530.0099-0.00960.1043-0.3405-0.05510.3045-0.00490.05160.58730.00290.294341.090464.24766.1054
110.374-1.3726-0.40163.78671.25811.315-0.06240.14020.0124-0.07210.16280.2943-0.1907-0.3888-0.16560.34260.0660.03480.55110.0670.445839.218282.23877.108
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 108 through 141 )
2X-RAY DIFFRACTION2chain 'A' and (resid 142 through 199 )
3X-RAY DIFFRACTION3chain 'A' and (resid 200 through 481 )
4X-RAY DIFFRACTION4chain 'A' and (resid 482 through 574 )
5X-RAY DIFFRACTION5chain 'B' and (resid 108 through 141 )
6X-RAY DIFFRACTION6chain 'B' and (resid 142 through 199 )
7X-RAY DIFFRACTION7chain 'B' and (resid 200 through 378 )
8X-RAY DIFFRACTION8chain 'B' and (resid 379 through 458 )
9X-RAY DIFFRACTION9chain 'B' and (resid 459 through 514 )
10X-RAY DIFFRACTION10chain 'B' and (resid 515 through 548 )
11X-RAY DIFFRACTION11chain 'B' and (resid 549 through 574 )

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