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- PDB-5nqa: Crystal structure of GalNAc-T4 in complex with the monoglycopeptide 3 -

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Basic information

Entry
Database: PDB / ID: 5nqa
TitleCrystal structure of GalNAc-T4 in complex with the monoglycopeptide 3
Components
  • Monoglycopeptide 3
  • Polypeptide N-acetylgalactosaminyltransferase 4
KeywordsTRANSFERASE / GalNAc-T4 / GalNAc-T2 / chimeras / Glycosylation preferences / STD-NMR / flexible linker
Function / homology
Function and homology information


protein O-linked glycosylation via threonine / polypeptide N-acetylgalactosaminyltransferase / polypeptide N-acetylgalactosaminyltransferase activity / protein O-linked glycosylation via serine / O-glycan processing / O-linked glycosylation of mucins / protein O-linked glycosylation / manganese ion binding / carbohydrate binding / Golgi membrane ...protein O-linked glycosylation via threonine / polypeptide N-acetylgalactosaminyltransferase / polypeptide N-acetylgalactosaminyltransferase activity / protein O-linked glycosylation via serine / O-glycan processing / O-linked glycosylation of mucins / protein O-linked glycosylation / manganese ion binding / carbohydrate binding / Golgi membrane / perinuclear region of cytoplasm / extracellular exosome
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 / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A ...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 / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
2-acetamido-2-deoxy-beta-D-galactopyranose / Polypeptide N-acetylgalactosaminyltransferase 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
Authorsde las Rivas, M. / Lira-Navarrete, E. / Daniel, E.J.P. / Companon, I. / Coelho, H. / Diniz, A. / Jimenez-Barbero, J. / Peregrina, J.M. / Clausen, H. / Corzana, F. ...de las Rivas, M. / Lira-Navarrete, E. / Daniel, E.J.P. / Companon, I. / Coelho, H. / Diniz, A. / Jimenez-Barbero, J. / Peregrina, J.M. / Clausen, H. / Corzana, F. / Marcelo, F. / Jimenez-Oses, G. / Gerken, T.A. / Hurtado-Guerrero, R.
CitationJournal: Nat Commun / Year: 2017
Title: The interdomain flexible linker of the polypeptide GalNAc transferases dictates their long-range glycosylation preferences.
Authors: Rivas, M.L. / Lira-Navarrete, E. / Daniel, E.J.P. / Companon, I. / Coelho, H. / Diniz, A. / Jimenez-Barbero, J. / Peregrina, J.M. / Clausen, H. / Corzana, F. / Marcelo, F. / Jimenez-Oses, G. ...Authors: Rivas, M.L. / Lira-Navarrete, E. / Daniel, E.J.P. / Companon, I. / Coelho, H. / Diniz, A. / Jimenez-Barbero, J. / Peregrina, J.M. / Clausen, H. / Corzana, F. / Marcelo, F. / Jimenez-Oses, G. / Gerken, T.A. / Hurtado-Guerrero, R.
History
DepositionApr 19, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2017Provider: 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 / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Jan 17, 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 / 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_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

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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
G: Monoglycopeptide 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,48186
Polymers134,7113
Non-polymers5,77083
Water28,2301567
1
A: Polypeptide N-acetylgalactosaminyltransferase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,82645
Polymers66,7561
Non-polymers3,07044
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Polypeptide N-acetylgalactosaminyltransferase 4
G: Monoglycopeptide 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,65541
Polymers67,9552
Non-polymers2,70039
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.447, 79.881, 88.614
Angle α, β, γ (deg.)116.47, 96.74, 104.72
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 0 / Auth seq-ID: 59 - 578 / Label seq-ID: 59 - 578

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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

#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: Komagataella pastoris (fungus)
References: UniProt: Q8N4A0, polypeptide N-acetylgalactosaminyltransferase
#2: Protein/peptide Monoglycopeptide 3


Mass: 1199.230 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#5: 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 / 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 , 3 types, 1648 molecules

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


Mass: 62.068 Da / Num. of mol.: 71 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1567 / 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: 2.87 Å3/Da / Density % sol: 57.15 %
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: Jul 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.9→76.45 Å / Num. obs: 115064 / % possible obs: 97.5 % / Redundancy: 3.6 % / CC1/2: 0.988 / Rpim(I) all: 0.068 / Net I/σ(I): 6.9
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.2 % / Rpim(I) all: 0.556 / % possible all: 95.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5AJP

5ajp


Resolution: 1.9→76.45 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.891 / SU B: 10.056 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R: 0.167 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27393 3182 2.8 %RANDOM
Rwork0.22459 ---
obs0.22594 111879 97.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.271 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å2-0.87 Å2-0.62 Å2
2---0.79 Å20.53 Å2
3---0.7 Å2
Refinement stepCycle: 1 / Resolution: 1.9→76.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8405 0 373 1567 10345
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0199024
X-RAY DIFFRACTIONr_bond_other_d0.0020.028335
X-RAY DIFFRACTIONr_angle_refined_deg1.7181.96612082
X-RAY DIFFRACTIONr_angle_other_deg1.051319317
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.78851055
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.77923.245453
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.744151506
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0641581
X-RAY DIFFRACTIONr_chiral_restr0.1070.21255
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0219754
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021929
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_it1.3812.7274141
X-RAY DIFFRACTIONr_mcbond_other1.3792.7264140
X-RAY DIFFRACTIONr_mcangle_it2.2174.0815174
X-RAY DIFFRACTIONr_mcangle_other2.2184.0815175
X-RAY DIFFRACTIONr_scbond_it1.5133.0094883
X-RAY DIFFRACTIONr_scbond_other1.5133.0094884
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3284.3726893
X-RAY DIFFRACTIONr_long_range_B_refined5.52133.81110778
X-RAY DIFFRACTIONr_long_range_B_other5.52133.81610779
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 34474 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 223 -
Rwork0.332 8037 -
obs--94.93 %
Refinement TLS params.

S22: 0 Å ° / 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 °)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)
10.03060.0537-0.00590.2269-0.01940.30820.0129-0.00040.0224-0.0460.01250.01240.0046-0.01290.0464-0.00750.00930.00830.01360.046-0.8162-0.1028-0.6185
20.073-0.0796-0.02090.1482-0.00490.2159-0.038-0.0013-0.04630.02620.0328-0.0370.02010.0380.0394-0.00630.02090.00490.00710.042232.3396-21.672233.4234
3000000000000000.0155000.015500.0155000
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A58 - 578
2X-RAY DIFFRACTION2B59 - 578

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