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- PDB-4js1: crystal structure of human Beta-galactoside alpha-2,6-sialyltrans... -

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Basic information

Entry
Database: PDB / ID: 4js1
Titlecrystal structure of human Beta-galactoside alpha-2,6-sialyltransferase 1 in complex with cytidine and phosphate
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 / Termination of O-glycan biosynthesis ...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 / Termination of O-glycan biosynthesis / regulation of substrate adhesion-dependent cell spreading / negative regulation of chemotaxis / O-glycan processing / Sialic acid metabolism / negative regulation of macrophage apoptotic process / protein N-linked glycosylation via asparagine / positive regulation of mononuclear cell proliferation / Golgi cisterna membrane / humoral immune response / Golgi medial cisterna / 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
4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE / PHOSPHATE ION / Beta-galactoside alpha-2,6-sialyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.09 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_2 / _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

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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)38,8024
Polymers36,8221
Non-polymers1,9803
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.292, 65.292, 162.232
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, beta-galactoside alpha-(2,6)-sialyltransferase
#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)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1641.490 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-2DManpa1-3[DGalpb1-4DGlcpNAcb1-2DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,9,8/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5]/1-1-2-3-1-4-3-1-4/a4-b1_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]{}}}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CTN / 4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE / CYTIDINE / Cytidine


Mass: 243.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N3O5
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.71 Å3/Da / Density % sol: 54.63 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: 0.1M MES/NaOH, pH 5.8, 20% PEG 2000 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: 2.09→46.4 Å / Num. obs: 22378 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.9 % / Net I/σ(I): 13.5
Reflection shellResolution: 2.09→2.16 Å / Redundancy: 10.2 % / Mean I/σ(I) obs: 1.3 / Num. unique all: 2292 / % possible all: 99.4

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Processing

Software
NameVersionClassification
SHARPphasing
PHENIX(phenix.refine: dev_1327)refinement
XDSdata reduction
SADABSdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 2.09→46.387 Å / SU ML: 0.24 / σ(F): 1.35 / Phase error: 34.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2282 1143 5.16 %random
Rwork0.1934 ---
obs0.1953 22159 95.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.09→46.387 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2594 0 133 41 2768
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092816
X-RAY DIFFRACTIONf_angle_d1.2523835
X-RAY DIFFRACTIONf_dihedral_angle_d25.9931087
X-RAY DIFFRACTIONf_chiral_restr0.081428
X-RAY DIFFRACTIONf_plane_restr0.005472
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.0901-2.18520.37331280.33192712271299
2.1852-2.30050.43741040.34171973197372
2.3005-2.44460.35791450.28482707270799
2.4446-2.63330.32031360.2752741274199
2.6333-2.89830.29621610.24462688268899
2.8983-3.31760.30061450.226427512751100
3.3176-4.17940.21851690.17832681268199
4.1794-46.3980.15621550.141527632763100
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)
13.6997-1.0168-1.62554.04483.12228.6045-0.2335-0.0938-0.1271.03910.2734-0.08651.47090.2644-0.06260.82660.01850.04310.311-0.00730.31122.339544.887732.642
21.2595-0.3638-1.02750.4733-0.09031.27891.68-0.3088-0.92080.23950.068-1.03181.43991.0577-1.21640.91-0.1058-0.23861.109-0.18950.9239-7.824925.7529.7658
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESID 89:406 )A89 - 406
2X-RAY DIFFRACTION2CHAIN A AND (RESID 501:509 )A501 - 509

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