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- PDB-5bo8: Structure of human sialyltransferase ST8SiaIII -

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Basic information

Entry
Database: PDB / ID: 5bo8
TitleStructure of human sialyltransferase ST8SiaIII
ComponentsSia-alpha-2,3-Gal-beta-1,4-GlcNAc-R:alpha 2,8-sialyltransferase
KeywordsTRANSFERASE / sialyltransferase
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
CITRIC ACID / Alpha-N-acetylneuraminate alpha-2,8-sialyltransferase ST8SIA3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsVolkers, G. / Worrall, L. / Strynadka, N.C.J.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
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: Refinement description
Revision 1.2Aug 12, 2015Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Data collection / Category: chem_comp / pdbx_audit_support
Item: _chem_comp.type / _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / diffrn_radiation_wavelength / 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.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_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site.occupancy / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.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_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 2.1Sep 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

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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)84,27211
Polymers80,2552
Non-polymers4,0179
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6620 Å2
ΔGint53 kcal/mol
Surface area27660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.170, 94.220, 126.190
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: TRP / Beg label comp-ID: TRP / End auth comp-ID: CYS / End label comp-ID: CYS / Refine code: 0 / Auth seq-ID: 90 - 379 / Label seq-ID: 53 - 342

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

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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: 40127.535 Da / Num. of mol.: 2 / Fragment: UNP residues 61-380
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 , 4 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.: 5
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 alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...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: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(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, 61 molecules

#6: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 3.27 Å3/Da / Density % sol: 62.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 18-21% PEG3350, 30 mM sodium tartrate, 100 mM sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Sep 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.7→52.43 Å / Num. obs: 28543 / % possible obs: 97.4 % / Redundancy: 3.3 % / CC1/2: 0.986 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.081 / Net I/σ(I): 5.5 / Num. measured all: 94630 / Scaling rejects: 16
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
2.7-2.833.30.9011.41238237890.4220.54299.1
8.96-52.433.10.04510.424937930.9950.02889.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
Aimless0.1.29data scaling
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WNB and 4JS2

2wnb

4js2


Resolution: 2.7→52.43 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.908 / WRfactor Rfree: 0.2449 / WRfactor Rwork: 0.1895 / FOM work R set: 0.7901 / SU B: 12.86 / SU ML: 0.247 / SU R Cruickshank DPI: 0.4311 / SU Rfree: 0.2905 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.431 / ESU R Free: 0.29 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2461 1450 5.1 %RANDOM
Rwork0.1931 ---
obs0.1958 27051 96.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 166.04 Å2 / Biso mean: 59.972 Å2 / Biso min: 27.1 Å2
Baniso -1Baniso -2Baniso -3
1--1.26 Å20 Å20 Å2
2--3.72 Å20 Å2
3----2.46 Å2
Refinement stepCycle: final / Resolution: 2.7→52.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4548 0 266 60 4874
Biso mean--85.44 49.48 -
Num. residues----553
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0194968
X-RAY DIFFRACTIONr_bond_other_d0.0050.024553
X-RAY DIFFRACTIONr_angle_refined_deg1.7991.9916762
X-RAY DIFFRACTIONr_angle_other_deg1.304310471
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2435549
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.08823.333237
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.45715771
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1951527
X-RAY DIFFRACTIONr_chiral_restr0.1320.2766
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025417
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021244
X-RAY DIFFRACTIONr_mcbond_it4.3825.5042208
X-RAY DIFFRACTIONr_mcbond_other4.3635.5022207
X-RAY DIFFRACTIONr_mcangle_it6.5668.2562753
Refine LS restraints NCS

Ens-ID: 1 / Number: 31844 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 99 -
Rwork0.349 1990 -
all-2089 -
obs--97.71 %

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