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- PDB-4js2: Crystal structure of human Beta-galactoside alpha-2,6-sialyltrans... -

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Basic information

Entry
Database: PDB / ID: 4js2
TitleCrystal structure of human Beta-galactoside alpha-2,6-sialyltransferase 1 in complex with CMP
ComponentsBeta-galactoside alpha-2,6-sialyltransferase 1
KeywordsTRANSFERASE / Rossmann / GT-A / sialyltransferase / glycoprotein / sialylation / endoplasmatic reticulum / golgi
Function / homology
Function and homology information


beta-galactoside alpha-(2,6)-sialyltransferase / beta-galactoside alpha-2,6-sialyltransferase activity / Maturation of protein 3a / sialyltransferase activity / N-acetylneuraminate metabolic process / sialylation / Maturation of protein 3a / N-Glycan antennae elongation / Golgi trans cisterna / regulation of substrate adhesion-dependent cell spreading ...beta-galactoside alpha-(2,6)-sialyltransferase / beta-galactoside alpha-2,6-sialyltransferase activity / Maturation of protein 3a / sialyltransferase activity / N-acetylneuraminate metabolic process / sialylation / Maturation of protein 3a / N-Glycan antennae elongation / Golgi trans cisterna / regulation of substrate adhesion-dependent cell spreading / O-glycan processing / Termination of O-glycan biosynthesis / negative regulation of macrophage apoptotic process / Sialic acid metabolism / negative regulation of chemotaxis / protein N-linked glycosylation via asparagine / positive regulation of mononuclear cell proliferation / Golgi cisterna membrane / Golgi medial cisterna / humoral immune response / response to ethanol / Maturation of spike protein / viral protein processing / Golgi membrane / Golgi apparatus / protein homodimerization activity / extracellular region
Similarity search - Function
Glycosyl transferase family 29 / Glycosyl transferase family 29 / Sialyltransferase / GT29-like superfamiliy / Glycosyltransferase family 29 (sialyltransferase) / sialyltransferase cstii, chain A / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
CYTIDINE-5'-MONOPHOSPHATE / Beta-galactoside alpha-2,6-sialyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKuhn, B. / Benz, J. / Greif, M. / Engel, A.M. / Sobek, H. / Rudolph, M.G.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: The structure of human alpha-2,6-sialyltransferase reveals the binding mode of complex glycans.
Authors: Kuhn, B. / Benz, J. / Greif, M. / Engel, A.M. / Sobek, H. / Rudolph, M.G.
History
DepositionMar 22, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Dec 18, 2019Group: Database references / Derived calculations / Category: citation / struct_conn
Item: _citation.country / _citation.journal_id_CSD ..._citation.country / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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 / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 2023Group: 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
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
Revision 3.0May 29, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Refinement description
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / chem_comp_atom / chem_comp_bond / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_refine_tls_group
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_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _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_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.type / _chem_comp_atom.atom_id / _chem_comp_atom.comp_id / _chem_comp_atom.type_symbol / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.comp_id / _chem_comp_bond.value_order / _pdbx_entity_nonpoly.comp_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_refine_tls_group.selection_details
Revision 3.1Nov 20, 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: Beta-galactoside alpha-2,6-sialyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9333
Polymers36,8221
Non-polymers2,1112
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.027, 64.027, 160.571
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Beta-galactoside alpha-2,6-sialyltransferase 1 / Alpha 2 / 6-ST 1 / B-cell antigen CD75 / CMP-N-acetylneuraminate-beta-galactosamide-alpha-2 / 6- ...Alpha 2 / 6-ST 1 / B-cell antigen CD75 / CMP-N-acetylneuraminate-beta-galactosamide-alpha-2 / 6-sialyltransferase 1 / ST6Gal I / ST6GalI / Sialyltransferase 1


Mass: 36821.906 Da / Num. of mol.: 1 / Fragment: catalytic domain, UNP RESIDUES 89-406
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ST6GAL1, SIAT1 / Cell line (production host): HEK 293 / Production host: Homo sapiens (human) / References: UniProt: P15907, EC: 2.4.99.1
#2: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[beta-D-galactopyranose-(1-4)-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)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1787.631 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-2DManpa1-3[DGalpb1-4DGlcpNAcb1-2DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpb1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/5,10,9/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5][a1221m-1b_1-5]/1-1-2-3-1-4-3-1-4-5/a4-b1_a6-j1_b4-c1_c3-d1_c6-g1_d2-e1_e4-f1_g2-h1_h4-i1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}}[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-C5P / CYTIDINE-5'-MONOPHOSPHATE


Mass: 323.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N3O8P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.33 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M HEPES/NaOH, pH 7.0, 20% PEG 550 MME, 0.01M CaCl2, 0.01M MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→45.6 Å / Num. obs: 16396 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.3 % / Net I/σ(I): 11.8
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 9.9 % / Mean I/σ(I) obs: 1 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: dev_1327)refinement
XDSdata reduction
SADABSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JS1

4js1


Resolution: 2.3→38.51 Å / SU ML: 0.33 / σ(F): 1.35 / Phase error: 31.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2127 872 5.32 %
Rwork0.1754 --
obs0.1774 16396 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→38.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2594 0 142 43 2779
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112827
X-RAY DIFFRACTIONf_angle_d1.313853
X-RAY DIFFRACTIONf_dihedral_angle_d14.5441074
X-RAY DIFFRACTIONf_chiral_restr0.082434
X-RAY DIFFRACTIONf_plane_restr0.008469
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.44410.39331460.34772546X-RAY DIFFRACTION99
2.4441-2.63280.28421330.28162587X-RAY DIFFRACTION99
2.6328-2.89760.30881440.24682572X-RAY DIFFRACTION99
2.8976-3.31670.23511430.21742589X-RAY DIFFRACTION100
3.3167-4.17790.22451610.172596X-RAY DIFFRACTION100
4.1779-38.5150.16581450.13652634X-RAY DIFFRACTION100
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)
14.307-0.0621-0.52043.9527-0.29245.1493-0.19990.1439-0.24570.22830.13220.10850.3156-0.075100.70530.0140.0480.5236-0.00660.66623.039244.994332.6283
20.0446-0.02920.0403-0.02030.17630.04960.688-0.679-1.01961.1335-0.0408-0.64081.0771.2164-01.1584-0.18070.0590.9602-0.05491.3547-5.718625.909110.091
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 89:406) OR (RESID 511)
2X-RAY DIFFRACTION2CHAIN B AND (RESID 1:10)

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