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- PDB-5bo7: Structure of human sialyltransferase ST8SiaIII in complex with CTP -

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Basic information

Entry
Database: PDB / ID: 5bo7
TitleStructure of human sialyltransferase ST8SiaIII in complex with CTP
ComponentsSia-alpha-2,3-Gal-beta-1,4-GlcNAc-R:alpha 2,8-sialyltransferase
KeywordsTRANSFERASE / sialyltransferase / CTP
Function / homology
Function and homology information


alpha-N-acetylneuraminate alpha-2,8-sialyltransferase / Transferases; Glycosyltransferases; Sialyltransferases / ganglioside biosynthetic process / alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity / sialylation / N-Glycan antennae elongation / glycoprotein metabolic process / glycosphingolipid biosynthetic process / Sialic acid metabolism / sialic acid binding ...alpha-N-acetylneuraminate alpha-2,8-sialyltransferase / Transferases; Glycosyltransferases; Sialyltransferases / ganglioside biosynthetic process / alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity / sialylation / N-Glycan antennae elongation / glycoprotein metabolic process / glycosphingolipid biosynthetic process / Sialic acid metabolism / sialic acid binding / oligosaccharide metabolic process / N-glycan processing / protein glycosylation / Golgi membrane / identical protein binding
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'-TRIPHOSPHATE / Alpha-N-acetylneuraminate alpha-2,8-sialyltransferase ST8SIA3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsVolkers, G. / Worrall, L. / Strynadka, N.C.J.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2015
Title: Structure of human ST8SiaIII sialyltransferase provides insight into cell-surface polysialylation.
Authors: Volkers, G. / Worrall, L.J. / Kwan, D.H. / Yu, C.C. / Baumann, L. / Lameignere, E. / Wasney, G.A. / Scott, N.E. / Wakarchuk, W. / Foster, L.J. / Withers, S.G. / Strynadka, N.C.
History
DepositionMay 27, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2015Group: Database references
Revision 1.2Aug 12, 2015Group: Database references
Revision 1.3Nov 1, 2017Group: Author supporting evidence / Derived calculations / Refinement description
Category: pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list / refine
Item: _pdbx_struct_oper_list.symmetry_operation / _refine.pdbx_method_to_determine_struct
Revision 2.0Nov 29, 2017Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Refinement description / Structure summary
Category: atom_site / diffrn_radiation_wavelength ...atom_site / diffrn_radiation_wavelength / entity / pdbx_refine_tls / pdbx_refine_tls_group / struct_conn
Item: _atom_site.auth_comp_id / _atom_site.label_comp_id ..._atom_site.auth_comp_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.id / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _pdbx_refine_tls.origin_x / _pdbx_refine_tls.origin_y / _pdbx_refine_tls.origin_z / _pdbx_refine_tls_group.beg_auth_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id
Revision 3.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / 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 / struct_asym / struct_conn / struct_site / struct_site_gen
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_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Sep 27, 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 / 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_conn.pdbx_leaving_atom_flag / _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: Sia-alpha-2,3-Gal-beta-1,4-GlcNAc-R:alpha 2,8-sialyltransferase
B: Sia-alpha-2,3-Gal-beta-1,4-GlcNAc-R:alpha 2,8-sialyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,14212
Polymers75,8382
Non-polymers4,30410
Water6,557364
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7370 Å2
ΔGint38 kcal/mol
Surface area27270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.335, 96.497, 124.655
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 0 / Auth seq-ID: 89 - 380 / Label seq-ID: 32 - 323

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsDimer by SEC-MALS

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Sia-alpha-2,3-Gal-beta-1,4-GlcNAc-R:alpha 2,8-sialyltransferase / Alpha-2 / 8-sialyltransferase 8C / 8-sialyltransferase III / ST8 alpha-N-acetyl-neuraminide alpha-2 ...Alpha-2 / 8-sialyltransferase 8C / 8-sialyltransferase III / ST8 alpha-N-acetyl-neuraminide alpha-2 / 8-sialyltransferase 3 / Sialyltransferase 8C / SIAT8-C / Sialyltransferase St8Sia III / ST8SiaIII


Mass: 37919.012 Da / Num. of mol.: 2 / Fragment: UNP residues 81-380
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ST8SIA3, SIAT8C / Plasmid: pFHMSP LIC N / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: O43173, EC: 2.4.99.-

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Sugars , 3 types, 8 molecules

#2: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 366 molecules

#4: Chemical ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE / Cytidine triphosphate


Mass: 483.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H16N3O14P3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 364 / 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: 2.83 Å3/Da / Density % sol: 56.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8 / Details: 0.2 M (NH4)3PO4, 50 mM PIPES, 18-22% PEG2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.97947 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Apr 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 1.85→46.94 Å / Num. obs: 70613 / % possible obs: 95.8 % / Redundancy: 4.9 % / CC1/2: 1 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.021 / Net I/σ(I): 21.7 / Num. measured all: 349276
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.85-1.893.50.6642.11378438970.7450.39886.9
9.06-46.944.70.01878.629646280.9990.00988.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
Aimless0.2.17data scaling
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BO8

5bo8


Resolution: 1.85→46.94 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / WRfactor Rfree: 0.1841 / WRfactor Rwork: 0.1578 / FOM work R set: 0.854 / SU B: 5.048 / SU ML: 0.078 / SU R Cruickshank DPI: 0.1107 / SU Rfree: 0.1077 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2002 3484 4.9 %RANDOM
Rwork0.17 ---
obs0.1715 67081 95.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 117.58 Å2 / Biso mean: 35.902 Å2 / Biso min: 17.91 Å2
Baniso -1Baniso -2Baniso -3
1-1.63 Å20 Å20 Å2
2---0.75 Å20 Å2
3----0.89 Å2
Refinement stepCycle: final / Resolution: 1.85→46.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4667 0 278 364 5309
Biso mean--47.45 39.92 -
Num. residues----569
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0195107
X-RAY DIFFRACTIONr_bond_other_d0.0090.024665
X-RAY DIFFRACTIONr_angle_refined_deg1.9881.9926957
X-RAY DIFFRACTIONr_angle_other_deg1.695310719
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5455567
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.05323.388242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.15415795
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7161527
X-RAY DIFFRACTIONr_chiral_restr0.1590.2778
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.025577
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021288
X-RAY DIFFRACTIONr_mcbond_it1.822.2862274
X-RAY DIFFRACTIONr_mcbond_other1.8172.2852273
X-RAY DIFFRACTIONr_mcangle_it2.6813.4092836
Refine LS restraints NCS

Ens-ID: 1 / Number: 31814 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.14 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 225 -
Rwork0.267 4486 -
all-4711 -
obs--86.95 %
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)
10.79920.065-0.7410.9187-0.95672.8477-0.0138-0.08450.10250.14510.0495-0.1246-0.23890.0284-0.03570.11550.0032-0.03260.0309-0.03530.0559-7.801-2.5133.5
20.54780.0559-0.31861.1021-0.34411.3352-0.0849-0.009-0.0041-0.01080.0879-0.05890.0492-0.0745-0.0030.03490.0031-0.02050.0112-0.00670.0263-12.126-14.88729.514
31.3076-0.3992-0.09311.68190.13671.5209-0.1625-0.1238-0.12960.14170.1294-0.19310.23520.16110.03310.11330.0641-0.02070.05010.00250.0764-4.525-27.87341.407
40.8884-0.3409-0.44260.6307-0.08372.19130.08250.08950.0511-0.0998-0.0435-0.11410.12390.0938-0.03910.09830.05150.01610.03360.00370.0230.548-1.668-13.818
51.23410.081-0.08540.54540.42513.7640.0586-0.0431-0.1044-0.0852-0.0242-0.09770.16150.177-0.03430.05560.02950.0130.02310.00950.02440.514-4.543-2.715
63.1344-0.6111-0.0731.31360.96040.78250.04680.0094-0.27510.04820.0266-0.05320.12450.0769-0.07340.24230.11320.04910.17910.02570.114811.332-10.265-20.824
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A89 - 155
2X-RAY DIFFRACTION2A156 - 321
3X-RAY DIFFRACTION3A322 - 380
4X-RAY DIFFRACTION4B88 - 208
5X-RAY DIFFRACTION5B209 - 299
6X-RAY DIFFRACTION6B300 - 380

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