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- PDB-6vle: Crystal structure of human alpha 1,6-fucosyltransferase, FUT8 in ... -

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Basic information

Entry
Database: PDB / ID: 6vle
TitleCrystal structure of human alpha 1,6-fucosyltransferase, FUT8 in its Apo-form
ComponentsAlpha-(1,6)-fucosyltransferase
KeywordsTRANSFERASE / FUT8 / Fucosyltransferase / Glycosyltransferase / N-glycan / Core fucose / SH3 domain
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 / : / Reactions specific to the complex N-glycan synthesis pathway / oligosaccharide biosynthetic process / L-fucose catabolic process / N-glycan processing ...glycoprotein 6-alpha-L-fucosyltransferase / glycoprotein 6-alpha-L-fucosyltransferase activity / receptor metabolic process / GDP-L-fucose metabolic process / alpha-(1->6)-fucosyltransferase activity / : / Reactions specific to the complex N-glycan synthesis pathway / oligosaccharide biosynthetic process / L-fucose catabolic process / N-glycan processing / regulation of cellular response to oxidative stress / protein N-linked glycosylation via asparagine / respiratory gaseous exchange by respiratory system / 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. / ESAT-6-like / Variant SH3 domain / SH3 Domains / SH3 type barrels. ...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. / ESAT-6-like / Variant SH3 domain / SH3 Domains / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Helix Hairpins / Roll / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Alpha-(1,6)-fucosyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.28 Å
AuthorsJarva, M.A. / Dramicanin, M. / Lingford, J.P. / Mao, R. / John, A. / Goddard-Borger, E.D.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)GNT1139546 Australia
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Structural basis of substrate recognition and catalysis by fucosyltransferase 8.
Authors: Jarva, M.A. / Dramicanin, M. / Lingford, J.P. / Mao, R. / John, A. / Jarman, K.E. / Grinter, R. / Goddard-Borger, E.D.
History
DepositionJan 23, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 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
Revision 1.3Nov 20, 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: Alpha-(1,6)-fucosyltransferase
B: Alpha-(1,6)-fucosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,5923
Polymers111,4962
Non-polymers961
Water6,774376
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6530 Å2
ΔGint-42 kcal/mol
Surface area39520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.019, 62.204, 109.905
Angle α, β, γ (deg.)90.000, 90.880, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#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: 55747.973 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FUT8 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9BYC5, glycoprotein 6-alpha-L-fucosyltransferase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 376 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.91 Å3/Da / Density % sol: 57.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 12% PEG 20000, 0.1 M HEPES, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9536 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9536 Å / Relative weight: 1
ReflectionResolution: 2.28→47.5 Å / Num. obs: 58867 / % possible obs: 99.8 % / Redundancy: 5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.067 / Rrim(I) all: 0.151 / Net I/σ(I): 8.2 / Num. measured all: 293792
Reflection shellResolution: 2.28→2.34 Å / Redundancy: 5.1 % / Rmerge(I) obs: 1.711 / Num. measured all: 23265 / Num. unique obs: 4549 / CC1/2: 0.63 / Rpim(I) all: 0.833 / Rrim(I) all: 1.907 / Net I/σ(I) obs: 1 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.16_3549refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DE0

2de0


Resolution: 2.28→47.251 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.234 2918 4.96 %
Rwork0.2019 55870 -
obs0.2035 58788 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 106.98 Å2 / Biso mean: 50.8483 Å2 / Biso min: 27.04 Å2
Refinement stepCycle: final / Resolution: 2.28→47.251 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7492 0 5 376 7873
Biso mean--89.46 48.54 -
Num. residues----918
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.28-2.31740.38051360.34152652100
2.3174-2.35740.31431300.32962618100
2.3574-2.40020.39041190.31172679100
2.4002-2.44640.30341180.30032653100
2.4464-2.49630.3031490.27282648100
2.4963-2.55060.27771170.26342641100
2.5506-2.60990.31571490.25492678100
2.6099-2.67520.30841390.25052621100
2.6752-2.74750.32131130.25712681100
2.7475-2.82830.2581160.2478267099
2.8283-2.91960.25771460.23672625100
2.9196-3.0240.27081370.2323263699
3.024-3.1450.26471360.22042680100
3.145-3.28810.25031430.21972643100
3.2881-3.46140.26371610.21692639100
3.4614-3.67820.23771770.19352628100
3.6782-3.96210.19341260.1812676100
3.9621-4.36050.20491500.15712689100
4.3605-4.99090.16421370.14042675100
4.9909-6.28570.2051430.17382718100
6.2857-47.2510.19191760.1607272099
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)
10.63040.1388-0.43130.7995-0.45142.07450.113-0.11610.06350.173-0.02820.0612-0.05370.0797-0.08250.3482-0.02640.01720.3845-0.05870.350118.0166-2.221739.459
20.5744-0.0408-0.43240.63890.1831.80750.03620.05910.0864-0.10160.0502-0.0401-0.05020.1092-0.08810.30180.0168-0.00920.4030.02810.338929.9661-1.6892-7.0103
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 108 through 574)A108 - 574
2X-RAY DIFFRACTION2(chain 'B' and resid 108 through 574)B108 - 574

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