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- PDB-6vld: Crystal structure of human alpha 1,6-fucosyltransferase, FUT8 bou... -

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Basic information

Entry
Database: PDB / ID: 6vld
TitleCrystal structure of human alpha 1,6-fucosyltransferase, FUT8 bound to GDP and A2SGP
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 / 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. / 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
ASPARAGINE / GUANOSINE-5'-DIPHOSPHATE / 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
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 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 16, 2020Group: Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / struct_conn
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _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 / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Oct 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
G: Alpha-(1,6)-fucosyltransferase
H: Alpha-(1,6)-fucosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,82826
Polymers222,9924
Non-polymers7,83622
Water11,313628
1
A: Alpha-(1,6)-fucosyltransferase
H: Alpha-(1,6)-fucosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,70216
Polymers111,4962
Non-polymers4,20614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14360 Å2
ΔGint-70 kcal/mol
Surface area38800 Å2
MethodPISA
2
B: Alpha-(1,6)-fucosyltransferase
G: Alpha-(1,6)-fucosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,12610
Polymers111,4962
Non-polymers3,6308
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13540 Å2
ΔGint-5 kcal/mol
Surface area39250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)208.307, 68.453, 249.983
Angle α, β, γ (deg.)90.000, 111.210, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein / Sugars , 2 types, 8 molecules ABGH

#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.: 4
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: 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.: 4
Source method: isolated from a genetically manipulated 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 , 4 types, 646 molecules

#3: Chemical
ChemComp-ASN / ASPARAGINE


Type: L-peptide linking / Mass: 132.118 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H8N2O3 / Feature type: SUBJECT OF INVESTIGATION
#4: 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
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 628 / 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: 3.73 Å3/Da / Density % sol: 66.99 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 2 M NH4SO4, 0.2 M NaCl, 0.1 M sodium cacodylate, pH 6.5

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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→48.65 Å / Num. obs: 150224 / % possible obs: 99.9 % / Redundancy: 5.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.047 / Rrim(I) all: 0.114 / Net I/σ(I): 10.2 / Num. measured all: 849036 / Scaling rejects: 1
Reflection shellResolution: 2.28→2.32 Å / Redundancy: 5.6 % / Rmerge(I) obs: 1.517 / Num. measured all: 41177 / Num. unique obs: 7302 / CC1/2: 0.435 / Rpim(I) all: 0.7 / Rrim(I) all: 1.676 / Net I/σ(I) obs: 1.1 / % possible all: 99.9

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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: 2.28→48.55 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.43
RfactorNum. reflection% reflection
Rfree0.2239 7492 4.99 %
Rwork0.1914 --
obs0.193 150193 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 181.57 Å2 / Biso mean: 64.0252 Å2 / Biso min: 25.16 Å2
Refinement stepCycle: final / Resolution: 2.28→48.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15083 0 508 628 16219
Biso mean--69.89 55.28 -
Num. residues----1854
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.28-2.30590.35332660.31044595100
2.3059-2.3330.33142500.29934775100
2.333-2.36150.30392480.29244747100
2.3615-2.39140.32532360.28094693100
2.3914-2.42280.30852390.27854737100
2.4228-2.4560.33182330.27874737100
2.456-2.49110.31032580.27714743100
2.4911-2.52830.29362250.27434760100
2.5283-2.56780.30632720.26134691100
2.5678-2.60990.28762690.25064751100
2.6099-2.65490.26822440.24414683100
2.6549-2.70320.25282260.23744766100
2.7032-2.75520.29922360.24264748100
2.7552-2.81140.26932520.24194793100
2.8114-2.87250.26952330.24034721100
2.8725-2.93930.29192640.24864734100
2.9393-3.01280.25022410.23474701100
3.0128-3.09430.26732570.22024758100
3.0943-3.18530.2422570.2174766100
3.1853-3.28810.24482660.21884746100
3.2881-3.40560.22452460.2054788100
3.4056-3.54190.21222660.18964725100
3.5419-3.70310.21812060.17334783100
3.7031-3.89820.19732300.16124809100
3.8982-4.14230.19082910.14794727100
4.1423-4.46190.1772680.13534791100
4.4619-4.91060.14922700.13124812100
4.9106-5.62030.20442340.1564816100
5.6203-7.07740.21872630.18064846100
7.0774-48.550.1842460.167495999
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)
11.4489-0.3082-0.58670.46140.09060.6932-0.0856-0.2050.0090.01260.0668-0.00210.33010.38990.01480.50870.2618-0.01790.55280.01870.400956.362712.5689.0465
20.64580.23360.21851.23120.59791.2266-0.039-0.0105-0.09170.00990.2089-0.31860.1950.261-0.12840.71090.32630.00050.6291-0.05850.51172.41850.235649.0899
30.39170.24990.32281.56490.7681.143-0.0564-0.0517-0.0243-0.02990.06160.15830.1305-0.125-0.01760.81720.13340.00180.53080.03130.392746.371924.061418.7681
41.224-0.402-0.26530.72040.07131.65950.04110.0753-0.0285-0.0185-0.07730.04280.0972-0.09650.02410.23760.0080.0040.227-0.00280.350414.808433.147697.2803
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 107 through 572)A107 - 572
2X-RAY DIFFRACTION2(chain 'B' and resid 107 through 572)B107 - 572
3X-RAY DIFFRACTION3(chain 'G' and resid 107 through 573)G107 - 573
4X-RAY DIFFRACTION4(chain 'H' and resid 107 through 573)H107 - 573

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