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- PDB-5ajo: Crystal structure of the inactive form of GalNAc-T2 in complex wi... -

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Basic information

Entry
Database: PDB / ID: 5ajo
TitleCrystal structure of the inactive form of GalNAc-T2 in complex with the glycopeptide MUC5AC-3,13
Components
  • MUCIN
  • POLYPEPTIDE N-ACETYLGALACTOSAMINYLTRANSFERASE 2
KeywordsTRANSFERASE / AFM / SAXS / LECTIN DOMAIN / COARSE-GRAINED MODEL / GLYCOPEPTIDES / INACTIVE FORM / ACTIVE FORM / COMPACT FORM / EXTENDED FORM
Function / homology
Function and homology information


: / : / polypeptide N-acetylgalactosaminyltransferase / mucus layer / polypeptide N-acetylgalactosaminyltransferase activity / protein O-linked glycosylation via N-acetyl-galactosamine / Defective GALNT3 causes HFTC / Defective C1GALT1C1 causes TNPS / Defective GALNT12 causes CRCS1 / Termination of O-glycan biosynthesis ...: / : / polypeptide N-acetylgalactosaminyltransferase / mucus layer / polypeptide N-acetylgalactosaminyltransferase activity / protein O-linked glycosylation via N-acetyl-galactosamine / Defective GALNT3 causes HFTC / Defective C1GALT1C1 causes TNPS / Defective GALNT12 causes CRCS1 / Termination of O-glycan biosynthesis / O-linked glycosylation of mucins / protein O-linked glycosylation / Golgi stack / COPI-independent Golgi-to-ER retrograde traffic / extracellular matrix structural constituent / positive regulation of immunoglobulin production / Golgi cisterna membrane / Dectin-2 family / extracellular matrix / protein maturation / Golgi lumen / manganese ion binding / carbohydrate binding / Golgi membrane / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / extracellular space / extracellular exosome / extracellular region / metal ion binding / membrane / plasma membrane
Similarity search - Function
N-acetylgalactosaminyltransferase / WxxW domain / Mucin-2 protein WxxW repeating region / : / C8 domain / Uncharacterised domain, cysteine-rich / C8 / von Willebrand factor, type D domain / von Willebrand factor type D domain / VWFD domain profile. ...N-acetylgalactosaminyltransferase / WxxW domain / Mucin-2 protein WxxW repeating region / : / C8 domain / Uncharacterised domain, cysteine-rich / C8 / von Willebrand factor, type D domain / von Willebrand factor type D domain / VWFD domain profile. / von Willebrand factor (vWF) type D domain / von Willebrand factor (vWF) type C domain / Trypsin Inhibitor-like, cysteine rich domain / Serine protease inhibitor-like superfamily / Trypsin Inhibitor like cysteine rich domain / C-terminal cystine knot signature. / C-terminal cystine knot domain profile. / Cystine knot, C-terminal / C-terminal cystine knot-like domain (CTCK) / Glycosyltransferase 2-like / Glycosyl transferase family 2 / VWFC domain signature. / VWFC domain profile. / von Willebrand factor (vWF) type C domain / VWFC domain / 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-alpha-D-galactopyranose / Mucin-5AC / Polypeptide N-acetylgalactosaminyltransferase 2 / Mucin
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsLira-Navarrete, E. / delasRivas, M. / Companon, I. / Pallares, M.C. / Kong, Y. / Iglesias-Fernandez, J. / Bernardes, G.J.L. / Peregrina, J.M. / Rovira, C. / Bernado, P. ...Lira-Navarrete, E. / delasRivas, M. / Companon, I. / Pallares, M.C. / Kong, Y. / Iglesias-Fernandez, J. / Bernardes, G.J.L. / Peregrina, J.M. / Rovira, C. / Bernado, P. / Bruscolini, P. / Clausen, H. / Lostao, A. / Corzana, F. / Hurtado-Guerrero, R.
CitationJournal: Nat.Commun. / Year: 2015
Title: Dynamic Interplay between Catalytic and Lectin Domains of Galnac-Transferases Modulates Protein O-Glycosylation.
Authors: Lira-Navarrete, E. / De Las Rivas, M. / Companon, I. / Pallares, M.C. / Kong, Y. / Iglesias-Fernandez, J. / Bernardes, G.J.L. / Peregrina, J.M. / Rovira, C. / Bernado, P. / Bruscolini, P. / ...Authors: Lira-Navarrete, E. / De Las Rivas, M. / Companon, I. / Pallares, M.C. / Kong, Y. / Iglesias-Fernandez, J. / Bernardes, G.J.L. / Peregrina, J.M. / Rovira, C. / Bernado, P. / Bruscolini, P. / Clausen, H. / Lostao, A. / Corzana, F. / Hurtado-Guerrero, R.
History
DepositionFeb 26, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1May 20, 2015Group: Database references
Revision 1.2Sep 13, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _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.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 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 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: POLYPEPTIDE N-ACETYLGALACTOSAMINYLTRANSFERASE 2
B: MUCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,79235
Polymers66,3712
Non-polymers3,42033
Water14,268792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7950 Å2
ΔGint-323.3 kcal/mol
Surface area22360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.203, 87.203, 179.074
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
Components on special symmetry positions
IDModelComponents
11A-2110-

HOH

21A-2147-

HOH

31A-2210-

HOH

41A-2211-

HOH

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Components

#1: Protein POLYPEPTIDE N-ACETYLGALACTOSAMINYLTRANSFERASE 2 / POLYPEPTIDE GALNAC TRANSFERASE 2 / GALNAC-T2 / PP-GANTASE 2 / PROTEIN-UDP ACETYLGALACTOSAMINYLTRANSFERASE 2 /


Mass: 64824.703 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: KOMAGATAELLA PASTORIS (fungus) / Strain (production host): SMD1168
References: UniProt: Q10471, polypeptide N-acetylgalactosaminyltransferase
#2: Protein/peptide MUCIN / MUC5AC


Mass: 1546.632 Da / Num. of mol.: 1 / Fragment: RESIDUES 65-79 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: KOMAGATAELLA PASTORIS (fungus) / Strain (production host): SMD1168 / References: UniProt: Q14886, UniProt: P98088*PLUS
#3: Sugar ChemComp-A2G / 2-acetamido-2-deoxy-alpha-D-galactopyranose / N-acetyl-alpha-D-galactosamine / 2-acetamido-2-deoxy-alpha-D-galactose / 2-acetamido-2-deoxy-D-galactose / 2-acetamido-2-deoxy-galactose / N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGalpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-galactopyranosamineCOMMON NAMEGMML 1.0
a-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 31 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 792 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 52.04 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.48→20 Å / Num. obs: 110205 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 8.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.6
Reflection shellResolution: 1.48→1.56 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.3 / % possible all: 97.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4D0T

4d0t


Resolution: 1.48→89.54 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.135 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.057 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.1806 3028 2.7 %RANDOM
Rwork0.1576 ---
obs0.15824 107151 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.137 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2---0.08 Å20 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.48→89.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4068 0 183 792 5043
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194410
X-RAY DIFFRACTIONr_bond_other_d0.0010.024046
X-RAY DIFFRACTIONr_angle_refined_deg1.6131.9856015
X-RAY DIFFRACTIONr_angle_other_deg0.88139317
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8815537
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.09123.507211
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.26415739
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7361539
X-RAY DIFFRACTIONr_chiral_restr0.1090.2655
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214902
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021035
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_it1.2871.3732071
X-RAY DIFFRACTIONr_mcbond_other1.2861.3722070
X-RAY DIFFRACTIONr_mcangle_it2.0422.062594
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.221.8692339
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.48→1.518 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 189 -
Rwork0.265 7563 -
obs--95.37 %
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)
10.33320.0282-0.00080.03370.04730.0977-0.0110.0024-0.0419-0.0050.01010.0006-0.0011-0.01680.00090.0133-0.0034-0.00450.04340.00140.026130.215933.7233-0.3879
20.78630.1895-0.86340.2102-0.61021.9570.030.1421-0.09670.1456-0.03750.0063-0.3903-0.03620.00750.119-0.02950.02470.0639-0.01770.023133.522739.6363-7.504
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A75 - 569
2X-RAY DIFFRACTION2B1 - 16

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