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- PDB-6tkv: Crystal structure of the human FUT8 in complex with GDP and a bia... -

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Basic information

Entry
Database: PDB / ID: 6tkv
TitleCrystal structure of the human FUT8 in complex with GDP and a biantennary complex N-glycan
Components(Alpha-(1,6)-fucosyltransferase) x 2
KeywordsSUGAR BINDING PROTEIN / Glycosyltransferase / sugar nucleotide / acceptor substrate / catalysis
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
GUANOSINE-5'-DIPHOSPHATE / Alpha-(1,6)-fucosyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsGarcia-Garcia, A. / Ceballos-Laita, L. / Serna, L. / Artschwager, R. / Reichardt, N.C. / Corzana, F. / Hurtado-Guerrero, R.
CitationJournal: Nat Commun / Year: 2020
Title: Structural basis for substrate specificity and catalysis of alpha 1,6-fucosyltransferase.
Authors: Garcia-Garcia, A. / Ceballos-Laita, L. / Serna, S. / Artschwager, R. / Reichardt, N.C. / Corzana, F. / Hurtado-Guerrero, R.
History
DepositionNov 29, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Data collection / Database references / Category: chem_comp / citation
Item: _chem_comp.type / _citation.country ..._chem_comp.type / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Mar 4, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / 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.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 2.2Oct 16, 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)111,37223
Polymers106,2852
Non-polymers5,08621
Water9,080504
1
B: Alpha-(1,6)-fucosyltransferase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)111,37223
Polymers106,2852
Non-polymers5,08621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area18260 Å2
ΔGint21 kcal/mol
Surface area36630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)208.039, 68.589, 173.921
Angle α, β, γ (deg.)90.00, 149.90, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 108 - 574

Dom-IDAuth asym-IDLabel asym-IDLabel seq-ID
1AA2 - 468
2BB1 - 452

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Components

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Protein , 2 types, 2 molecules AB

#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: 53966.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FUT8 / Production host: Homo sapiens (human)
References: UniProt: Q9BYC5, glycoprotein 6-alpha-L-fucosyltransferase
#2: 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: 52319.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FUT8 / Production host: Homo sapiens (human)
References: UniProt: Q9BYC5, glycoprotein 6-alpha-L-fucosyltransferase

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Sugars , 1 types, 2 molecules

#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 genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-3[DGlcpNAcb1-2DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][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 , 3 types, 523 molecules

#4: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 504 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.34 Å3/Da / Density % sol: 47.33 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Carboxilic acids 0.1 M Buffer system 3 pH 8.5 30% Precipitant mix 1 (Molecular Dimensions).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 X 1M / Detector: PIXEL / Date: Nov 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.95→20.01 Å / Num. obs: 89000 / % possible obs: 99.9 % / Redundancy: 4.4 % / CC1/2: 0.995 / Rmerge(I) obs: 0.133 / Net I/σ(I): 6.4
Reflection shellResolution: 1.95→2.06 Å / Rmerge(I) obs: 1.368 / Mean I/σ(I) obs: 1.4 / Num. measured obs: 394687 / Num. unique obs: 12914 / CC1/2: 0.447

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DE0

2de0


Resolution: 1.95→20 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / SU B: 9.511 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.136 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21884 3478 3.9 %RANDOM
Rwork0.18547 ---
obs0.1868 85092 99.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 36.105 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å20.05 Å2
2---2.21 Å20 Å2
3---0.27 Å2
Refinement stepCycle: 1 / Resolution: 1.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7493 0 338 506 8337
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0138054
X-RAY DIFFRACTIONr_bond_other_d0.0010.0187295
X-RAY DIFFRACTIONr_angle_refined_deg2.0651.6910929
X-RAY DIFFRACTIONr_angle_other_deg1.4911.62416982
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8075924
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.51421.95441
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.295151330
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.4221555
X-RAY DIFFRACTIONr_chiral_restr0.1090.21036
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.028686
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021699
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.511.6543689
X-RAY DIFFRACTIONr_mcbond_other1.5021.6523688
X-RAY DIFFRACTIONr_mcangle_it2.4432.474610
X-RAY DIFFRACTIONr_mcangle_other2.4432.4714611
X-RAY DIFFRACTIONr_scbond_it2.2612.0174364
X-RAY DIFFRACTIONr_scbond_other2.262.0174365
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.632.8926318
X-RAY DIFFRACTIONr_long_range_B_refined6.92420.7159159
X-RAY DIFFRACTIONr_long_range_B_other6.87620.2939082
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 14753 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.953→2.004 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 264 -
Rwork0.285 6019 -
obs--95.36 %
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)
10.77720.031-0.23680.0479-0.00590.1405-0.0706-0.13480.0372-0.01080.0410.00350.06090.07660.02960.04180.06640.04860.49030.01470.161826.22272.282616.2482
20.21070.23830.01820.43090.08420.1810.0062-0.00210.0269-0.0386-0.0164-0.02160.0122-0.00870.01020.0298-0.00630.06250.42470.0050.183415.600823.054-24.0494
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A107 - 574
2X-RAY DIFFRACTION2B108 - 575

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