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- PDB-6s24: Crystal structure of the TgGalNAc-T3 in complex with UDP, mangane... -

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Basic information

Entry
Database: PDB / ID: 6s24
TitleCrystal structure of the TgGalNAc-T3 in complex with UDP, manganese and the peptide 3
Components
  • ALA-THR-GLY-ALA-GLY-ALA-GLY-ALA-GLY-THR-THR-PRO-GLY-PRO
  • Polypeptide N-acetylgalactosaminyltransferase
KeywordsTRANSFERASE / GalNAc-Ts / GalNAc-T3 / long-range glycosylation preference / (glyco)peptides / Molecular dynamics / specificity / enzyme kinetics / FGF23 / phosphate homeostasis
Function / homology
Function and homology information


: / polypeptide N-acetylgalactosaminyltransferase / polypeptide N-acetylgalactosaminyltransferase activity / Golgi cisterna membrane / manganese ion binding / carbohydrate binding
Similarity search - Function
N-acetylgalactosaminyltransferase / Glycosyltransferase 2-like / Glycosyl transferase family 2 / Ricin-type beta-trefoil lectin domain / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
: / 2-acetamido-2-deoxy-beta-D-galactopyranose / PHOSPHATE ION / URIDINE-5'-DIPHOSPHATE / Polypeptide N-acetylgalactosaminyltransferase 3
Similarity search - Component
Biological speciesTaeniopygia guttata (zebra finch)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
Authorsde las Rivas, M. / Daniel, E.J.P. / Narimatsu, Y. / Companon, I. / Kato, K. / Hermosilla, P. / Thureau, A. / Ceballos-Laita, L. / Coelho, H. / Bernado, P. ...de las Rivas, M. / Daniel, E.J.P. / Narimatsu, Y. / Companon, I. / Kato, K. / Hermosilla, P. / Thureau, A. / Ceballos-Laita, L. / Coelho, H. / Bernado, P. / Marcelo, F. / Hansen, L. / Lostao, A. / Corzana, F. / Clausen, H. / Gerken, T.A. / Hurtado-Guerrero, R.
CitationJournal: Nat.Chem.Biol. / Year: 2020
Title: Molecular basis for fibroblast growth factor 23 O-glycosylation by GalNAc-T3.
Authors: de Las Rivas, M. / Paul Daniel, E.J. / Narimatsu, Y. / Companon, I. / Kato, K. / Hermosilla, P. / Thureau, A. / Ceballos-Laita, L. / Coelho, H. / Bernado, P. / Marcelo, F. / Hansen, L. / ...Authors: de Las Rivas, M. / Paul Daniel, E.J. / Narimatsu, Y. / Companon, I. / Kato, K. / Hermosilla, P. / Thureau, A. / Ceballos-Laita, L. / Coelho, H. / Bernado, P. / Marcelo, F. / Hansen, L. / Maeda, R. / Lostao, A. / Corzana, F. / Clausen, H. / Gerken, T.A. / Hurtado-Guerrero, R.
History
DepositionJun 20, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year
Revision 1.2Mar 4, 2020Group: Data collection / Database references / Category: chem_comp / citation / citation_author
Item: _chem_comp.type / _citation.journal_volume ..._chem_comp.type / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _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.ptnr1_label_seq_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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 6, 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: Polypeptide N-acetylgalactosaminyltransferase
F: ALA-THR-GLY-ALA-GLY-ALA-GLY-ALA-GLY-THR-THR-PRO-GLY-PRO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,03523
Polymers73,4512
Non-polymers2,58421
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, It runs as a monomer under gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5930 Å2
ΔGint-92 kcal/mol
Surface area23700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.655, 104.661, 143.186
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AF

#1: Protein Polypeptide N-acetylgalactosaminyltransferase / Protein-UDP acetylgalactosaminyltransferase


Mass: 72365.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Taeniopygia guttata (zebra finch) / Gene: GALNT3 / Production host: Komagataella pastoris (fungus)
References: UniProt: H0ZAB5, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Protein/peptide ALA-THR-GLY-ALA-GLY-ALA-GLY-ALA-GLY-THR-THR-PRO-GLY-PRO


Mass: 1085.126 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: AT*GAGAGAGTTPGP Note that this is a monoglycopeptide and T* stands for T-O-GalNAc
Source: (synth.) Homo sapiens (human)

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Sugars , 2 types, 2 molecules

#7: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#8: Sugar ChemComp-NGA / 2-acetamido-2-deoxy-beta-D-galactopyranose / N-acetyl-beta-D-galactosamine / 2-acetamido-2-deoxy-beta-D-galactose / 2-acetamido-2-deoxy-D-galactose / 2-acetamido-2-deoxy-galactose / N-ACETYL-D-GALACTOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGalpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-galactopyranosamineCOMMON NAMEGMML 1.0
b-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 220 molecules

#3: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE


Mass: 163.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#6: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.56 Å3/Da / Density % sol: 52.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: Morpheus precipitant mix 4, nitrate phosphate buffer and Morpheus buffer System 1

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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 S 6M / Detector: PIXEL / Date: Mar 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.12→20 Å / Num. obs: 41413 / % possible obs: 94 % / Redundancy: 5.3 % / CC1/2: 0.996 / Rpim(I) all: 0.051 / Net I/σ(I): 7.7
Reflection shellResolution: 2.12→2.23 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4490 / CC1/2: 0.522 / Rpim(I) all: 0.491 / % possible all: 71.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NQA

5nqa


Resolution: 2.12→19.96 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.936 / SU B: 6.459 / SU ML: 0.157 / Cross valid method: THROUGHOUT / ESU R: 0.202 / ESU R Free: 0.181 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23738 1651 4 %RANDOM
Rwork0.19119 ---
obs0.19302 39661 93.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 41.609 Å2
Baniso -1Baniso -2Baniso -3
1--1.18 Å20 Å20 Å2
2---0.84 Å20 Å2
3---2.01 Å2
Refinement stepCycle: 1 / Resolution: 2.12→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4410 40 105 201 4756
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0134668
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174113
X-RAY DIFFRACTIONr_angle_refined_deg1.6881.6656344
X-RAY DIFFRACTIONr_angle_other_deg1.2671.5869597
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8265549
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.20922.551247
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.05415759
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0011526
X-RAY DIFFRACTIONr_chiral_restr0.0750.2581
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025110
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02975
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_it3.7084.212203
X-RAY DIFFRACTIONr_mcbond_other3.7064.2082201
X-RAY DIFFRACTIONr_mcangle_it5.6756.3022749
X-RAY DIFFRACTIONr_mcangle_other5.6746.3022750
X-RAY DIFFRACTIONr_scbond_it4.4214.7252465
X-RAY DIFFRACTIONr_scbond_other4.0464.632402
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2786.753500
X-RAY DIFFRACTIONr_long_range_B_refined8.95548.9775141
X-RAY DIFFRACTIONr_long_range_B_other8.93348.9275121
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.12→2.175 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 88 -
Rwork0.335 2021 -
obs--66.01 %

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