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- PDB-6vlg: Crystal structure of mouse alpha 1,6-fucosyltransferase, FUT8 bou... -

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Basic information

Entry
Database: PDB / ID: 6vlg
TitleCrystal structure of mouse alpha 1,6-fucosyltransferase, FUT8 bound to GDP
ComponentsAlpha-(1,6)-fucosyltransferase
KeywordsTRANSFERASE / FUT8 / Fucosyltransferase / Glycosyltransferase / N-glycan / Core fucose / SH3 domain
Function / homology
Function and homology information


Reactions specific to the complex N-glycan synthesis pathway / 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 / protein N-linked glycosylation via asparagine / N-glycan processing / regulation of cellular response to oxidative stress ...Reactions specific to the complex N-glycan synthesis pathway / 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 / protein N-linked glycosylation via asparagine / N-glycan processing / regulation of cellular response to oxidative stress / respiratory gaseous exchange by respiratory system / fibroblast migration / protein N-linked glycosylation / Golgi cisterna membrane / glycosyltransferase activity / transforming growth factor beta receptor signaling pathway / integrin-mediated signaling pathway / SH3 domain binding / cell migration / regulation of gene expression
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 / Src homology 3 domains ...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 / Src homology 3 domains / SH3 type barrels. / 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
GUANOSINE-5'-DIPHOSPHATE / TRIETHYLENE GLYCOL / Alpha-(1,6)-fucosyltransferase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsJarva, M.A. / Dramicanin, M. / Lingford, J.P. / Mao, R. / John, A. / Goddard-Borger, E.D.
Funding support Australia, 1items
OrganizationGrant numberCountry
Other governmentGNT1139546 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

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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: Alpha-(1,6)-fucosyltransferase
D: Alpha-(1,6)-fucosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)252,91714
Polymers250,4154
Non-polymers2,50110
Water16,664925
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C: Alpha-(1,6)-fucosyltransferase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)126,4807
Polymers125,2082
Non-polymers1,2735
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555y,-x+y,z+1/61
Buried area8680 Å2
ΔGint-66 kcal/mol
Surface area39060 Å2
MethodPISA
2
D: Alpha-(1,6)-fucosyltransferase
hetero molecules

B: Alpha-(1,6)-fucosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,4367
Polymers125,2082
Non-polymers1,2295
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_564x-y,x+1,z-1/61
Buried area8620 Å2
ΔGint-66 kcal/mol
Surface area39020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.820, 150.820, 472.139
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

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Protein , 1 types, 4 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: 62603.777 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Fut8 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9WTS2, glycoprotein 6-alpha-L-fucosyltransferase

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Non-polymers , 5 types, 935 molecules

#2: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 925 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.1 Å3/Da / Density % sol: 60.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 12% PEG 3350, 0.25 M NH4SO4, 0.1 M Tris, pH 7.4

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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: Nov 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9536 Å / Relative weight: 1
ReflectionResolution: 2.5→49.37 Å / Num. obs: 109145 / % possible obs: 98.8 % / Redundancy: 10.4 % / CC1/2: 0.995 / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.049 / Rrim(I) all: 0.164 / Net I/σ(I): 9.5 / Num. measured all: 1135283 / Scaling rejects: 3
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.713 / Num. measured all: 28905 / Num. unique obs: 4637 / CC1/2: 0.811 / Rpim(I) all: 0.279 / Rrim(I) all: 0.772 / Net I/σ(I) obs: 2 / % possible all: 85.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2de0

2de0


Resolution: 2.5→49.367 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.06
RfactorNum. reflection% reflection
Rfree0.2273 5440 5 %
Rwork0.1822 --
obs0.1844 108860 98.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 111.86 Å2 / Biso mean: 43.3464 Å2 / Biso min: 19.94 Å2
Refinement stepCycle: final / Resolution: 2.5→49.367 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15248 0 187 925 16360
Biso mean--49.46 43 -
Num. residues----1872
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5-2.52840.31641460.2517292285
2.5284-2.55820.30551530.2484307389
2.5582-2.58940.27871690.2526317393
2.5894-2.62220.29221790.2423330297
2.6222-2.65670.27021680.2464342899
2.6567-2.6930.30791970.2323458100
2.693-2.73150.27681800.23423386100
2.7315-2.77230.27761790.22153459100
2.7723-2.81560.2891650.21163453100
2.8156-2.86180.25571760.20063432100
2.8618-2.91110.24681790.20313458100
2.9111-2.9640.29551740.2043470100
2.964-3.0210.25342010.19763436100
3.021-3.08270.24771830.2013423100
3.0827-3.14970.25461860.20463477100
3.1497-3.2230.27281770.21063468100
3.223-3.30350.23371840.21183458100
3.3035-3.39280.2512000.19973444100
3.3928-3.49270.24731620.19983501100
3.4927-3.60540.24491930.18153476100
3.6054-3.73420.22431860.17683485100
3.7342-3.88360.21181920.16913483100
3.8836-4.06030.20771810.1583516100
4.0603-4.27430.20071870.14653500100
4.2743-4.54190.17451800.13363544100
4.5419-4.89230.16182050.12923511100
4.8923-5.38410.17061810.14433599100
5.3841-6.16190.19251910.16943575100
6.1619-7.75850.20121920.1783663100
7.7585-49.3670.22311940.1788384798
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)
10.7256-0.2027-0.38011.10650.82321.63870.05290.01240.1307-0.01040.0437-0.0583-0.21150.0675-0.07440.24650.00250.04420.2331-0.01080.2773-59.1069-15.672835.8296
20.68560.2475-0.3961.2677-0.62331.32010.0484-0.02370.10350.12940.0410.0588-0.1363-0.1565-0.0660.27550.01670.0390.2360.01670.2756-90.6996-16.028184.455
30.52490.08430.01291.15470.83171.172-0.07530.0001-0.13850.19690.0644-0.06990.25840.08810.01710.3380.04040.00240.2366-0.03830.2874-57.31887.614586.1215
40.6267-0.26130.19431.4063-1.25981.8797-0.0394-0.026-0.1093-0.35420.10880.10680.4751-0.1646-0.05580.47530.0258-0.00440.31940.04760.2891-92.44428.239134.1049
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 107 through 574)A107 - 574
2X-RAY DIFFRACTION2(chain 'B' and resid 107 through 574)B107 - 574
3X-RAY DIFFRACTION3(chain 'C' and resid 107 through 574)C107 - 574
4X-RAY DIFFRACTION4(chain 'D' and resid 107 through 574)D107 - 574

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