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- PDB-6h0b: Crystal structure of the human GalNAc-T4 in complex with UDP, man... -

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Basic information

Entry
Database: PDB / ID: 6h0b
TitleCrystal structure of the human GalNAc-T4 in complex with UDP, manganese and the diglycopeptide 6.
Components
  • ALA-THR-GLY-ALA-GLY-ALA-GLY-ALA-GLY-THR-THR-PRO-GLY-PRO-GLY
  • Polypeptide N-acetylgalactosaminyltransferase 4
KeywordsTRANSFERASE / GalNAc-Ts / GalNAc-T4 / short-range glycosylation preference / long-range glycosylation preference / (glyco)peptides / STD-NMR / Molecular dynamics / enzyme kinetics
Function / homology
Function and homology information


polypeptide N-acetylgalactosaminyltransferase / polypeptide N-acetylgalactosaminyltransferase activity / protein O-linked glycosylation via serine / O-linked glycosylation of mucins / O-glycan processing / protein O-linked glycosylation via threonine / manganese ion binding / carbohydrate binding / Golgi membrane / perinuclear region of cytoplasm ...polypeptide N-acetylgalactosaminyltransferase / polypeptide N-acetylgalactosaminyltransferase activity / protein O-linked glycosylation via serine / O-linked glycosylation of mucins / O-glycan processing / protein O-linked glycosylation via threonine / manganese ion binding / carbohydrate binding / Golgi membrane / perinuclear region of cytoplasm / extracellular exosome / integral component of membrane
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 / URIDINE-5'-DIPHOSPHATE / Polypeptide N-acetylgalactosaminyltransferase 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
Authorsde las Rivas, M. / Daniel, E.J.P. / Coelho, H. / Lira-Navarrete, E. / Raich, L. / Companon, I. / Diniz, A. / Lagartera, L. / Jimenez-Barbero, J. / Clausen, H. ...de las Rivas, M. / Daniel, E.J.P. / Coelho, H. / Lira-Navarrete, E. / Raich, L. / Companon, I. / Diniz, A. / Lagartera, L. / Jimenez-Barbero, J. / Clausen, H. / Rovira, C. / Marcelo, F. / Corzana, F. / Gerken, T.A. / Hurtado-Guerrero, R.
CitationJournal: ACS Cent Sci / Year: 2018
Title: Structural and Mechanistic Insights into the Catalytic-Domain-Mediated Short-Range Glycosylation Preferences of GalNAc-T4.
Authors: de Las Rivas, M. / Paul Daniel, E.J. / Coelho, H. / Lira-Navarrete, E. / Raich, L. / Companon, I. / Diniz, A. / Lagartera, L. / Jimenez-Barbero, J. / Clausen, H. / Rovira, C. / Marcelo, F. / ...Authors: de Las Rivas, M. / Paul Daniel, E.J. / Coelho, H. / Lira-Navarrete, E. / Raich, L. / Companon, I. / Diniz, A. / Lagartera, L. / Jimenez-Barbero, J. / Clausen, H. / Rovira, C. / Marcelo, F. / Corzana, F. / Gerken, T.A. / Hurtado-Guerrero, R.
History
DepositionJul 8, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polypeptide N-acetylgalactosaminyltransferase 4
B: Polypeptide N-acetylgalactosaminyltransferase 4
F: ALA-THR-GLY-ALA-GLY-ALA-GLY-ALA-GLY-THR-THR-PRO-GLY-PRO-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,93944
Polymers134,7113
Non-polymers3,22841
Water14,214789
1
A: Polypeptide N-acetylgalactosaminyltransferase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,87319
Polymers66,7561
Non-polymers1,11718
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Polypeptide N-acetylgalactosaminyltransferase 4
F: ALA-THR-GLY-ALA-GLY-ALA-GLY-ALA-GLY-THR-THR-PRO-GLY-PRO-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,06625
Polymers67,9552
Non-polymers2,11123
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.090, 81.332, 84.863
Angle α, β, γ (deg.)65.55, 68.66, 74.31
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A58 - 578
2010B58 - 578

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Components

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Protein / Protein/peptide / Sugars , 3 types, 5 molecules ABF

#1: Protein Polypeptide N-acetylgalactosaminyltransferase 4 / / Polypeptide GalNAc transferase 4 / pp-GaNTase 4 / Protein-UDP acetylgalactosaminyltransferase 4 / ...Polypeptide GalNAc transferase 4 / pp-GaNTase 4 / Protein-UDP acetylgalactosaminyltransferase 4 / UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase 4


Mass: 66755.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GALNT4 / Production host: Homo sapiens (human)
References: UniProt: Q8N4A0, polypeptide N-acetylgalactosaminyltransferase
#2: Protein/peptide ALA-THR-GLY-ALA-GLY-ALA-GLY-ALA-GLY-THR-THR-PRO-GLY-PRO-GLY


Mass: 1199.230 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#7: Sugar ChemComp-NGA / 2-acetamido-2-deoxy-beta-D-galactopyranose / N-Acetylgalactosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
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, 828 molecules

#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 789 / Source method: isolated from a natural source / Formula: H2O

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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: 2.84 Å3/Da / Density % sol: 56.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: PEG3350 ammonium nitrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.8→73.99 Å / Num. obs: 133764 / % possible obs: 97.3 % / Redundancy: 3.7 % / CC1/2: 0.998 / Rpim(I) all: 0.044 / Net I/σ(I): 9.2
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 0.9 / CC1/2: 0.529 / Rpim(I) all: 0.742 / % possible all: 95.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NQA

5nqa


Resolution: 1.8→73.99 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.767 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.119 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23806 3699 2.8 %RANDOM
Rwork0.18965 ---
obs0.19092 130063 97.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 54.152 Å2
Baniso -1Baniso -2Baniso -3
1--1.42 Å21.99 Å2-1.09 Å2
2---3.86 Å2-0.76 Å2
3---3.74 Å2
Refinement stepCycle: 1 / Resolution: 1.8→73.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8544 0 204 789 9537
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0199034
X-RAY DIFFRACTIONr_bond_other_d0.0070.028464
X-RAY DIFFRACTIONr_angle_refined_deg1.8231.95912197
X-RAY DIFFRACTIONr_angle_other_deg1.449319473
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.18551077
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.62623.18456
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.753151511
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9281583
X-RAY DIFFRACTIONr_chiral_restr0.1190.21269
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02110120
X-RAY DIFFRACTIONr_gen_planes_other0.0060.022197
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_it4.085.2314230
X-RAY DIFFRACTIONr_mcbond_other4.0775.2314229
X-RAY DIFFRACTIONr_mcangle_it5.8787.8265288
X-RAY DIFFRACTIONr_mcangle_other5.8797.8265289
X-RAY DIFFRACTIONr_scbond_it4.2825.594804
X-RAY DIFFRACTIONr_scbond_other4.2775.594804
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.3438.2136895
X-RAY DIFFRACTIONr_long_range_B_refined8.95441.60410945
X-RAY DIFFRACTIONr_long_range_B_other8.95541.60610946
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 62264 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 247 -
Rwork0.326 9486 -
obs--95.78 %

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