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- PDB-8zx2: Structure-Based Mechanism and Specificity of Human Galactosyltran... -

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Basic information

Entry
Database: PDB / ID: 8zx2
TitleStructure-Based Mechanism and Specificity of Human Galactosyltransferase B3GalT5
ComponentsBeta-1,3-galactosyltransferase 5
KeywordsTRANSFERASE / globo-series glycosphingolipid biosynthesis / Oxocarbenium / SNi-like / SN2-like / double displacement / inverting galactosyltransferase / Michaelis complex
Function / homology
Function and homology information


Lewis blood group biosynthesis / N-acetyl-beta-D-glucosaminide beta-(1,3)-galactosyltransferase activity / oligosaccharide biosynthetic process / protein O-linked glycosylation / Transferases; Glycosyltransferases; Hexosyltransferases / protein glycosylation / response to bacterium / lipid metabolic process / Golgi membrane / endoplasmic reticulum / Golgi apparatus
Similarity search - Function
Glycosyl transferase, family 31 / Galactosyltransferase
Similarity search - Domain/homology
: / Beta-1,3-galactosyltransferase 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLo, J.M. / Ma, C.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Academia Sinica (Taiwan) Taiwan
CitationJournal: J.Am.Chem.Soc. / Year: 2025
Title: Structure-Based Mechanism and Specificity of Human Galactosyltransferase beta 3GalT5.
Authors: Lo, J.M. / Kung, C.C. / Cheng, T.R. / Wong, C.H. / Ma, C.
History
DepositionJun 13, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-1,3-galactosyltransferase 5
B: Beta-1,3-galactosyltransferase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,27913
Polymers65,1012
Non-polymers4,17811
Water2,036113
1
A: Beta-1,3-galactosyltransferase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1846
Polymers32,5511
Non-polymers1,6335
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-1,3-galactosyltransferase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0957
Polymers32,5511
Non-polymers2,5446
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.597, 86.496, 86.219
Angle α, β, γ (deg.)90.000, 94.862, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 43 through 160 or resid 162 through 286 or resid 288 through 312))
d_2ens_1(chain "B" and (resid 43 through 160 or resid 162 through 286 or resid 288 through 312))
d_1ens_2(chain "E" and resid 1)
d_2ens_2(chain "F" and resid 1)
d_3ens_2(chain "G" and resid 1)
d_1ens_3chain "I"
d_2ens_3chain "J"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1ASNASNPHEPHEAA43 - 16013 - 130
d_12ens_1ASNASNPHEPHEAA162 - 286132 - 256
d_13ens_1LYSLYSPROPROAA288 - 308258 - 278
d_14ens_1MNMNMNMNAI401
d_15ens_1B3PB3PB3PB3PAJ402
d_21ens_1ASNASNPHEPHEBB43 - 16013 - 130
d_22ens_1ASNASNPHEPHEBB162 - 286132 - 256
d_23ens_1LYSLYSPROPROBB288 - 308258 - 278
d_24ens_1MNMNMNMNBK401
d_25ens_1B3PB3PB3PB3PBL402
d_11ens_2NAGNAGNAGNAGEC1
d_21ens_2NAGNAGNAGNAGFD1
d_31ens_2NAGNAGNAGNAGGE1
d_11ens_3GALGALGALGALIH3
d_12ens_3MANMANMANMANIH2
d_13ens_3BMABMABMABMAIH1
d_21ens_3GALGALGALGALJG3
d_22ens_3MANMANMANMANJG2
d_23ens_3BMABMABMABMAJG1

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(0.196911914415, 0.00381914048515, -0.980413745379), (-0.0252104285627, 0.999681482893, -0.00116921017613), (0.980097001451, 0.0249468821039, 0.19694547677)37.9815829866, 9.57652628729, -27.9214048518
2given(0.40630132347, -0.367863286235, 0.836418458182), (-0.522485876149, -0.844497432, -0.117612059629), (0.749618398768, -0.389230895468, -0.5353237957)-36.2436989685, 32.1983060703, 51.6582486859
3given(0.245629452418, 0.0333954066956, -0.968788376745), (-0.176227582915, 0.984290731947, -0.0107514661016), (0.953210370865, 0.173368110721, 0.24765598531)35.8296608818, 14.185409596, -30.4479204949
4given(0.200542907099, -0.0113041855841, -0.979619700598), (0.0473749434102, 0.998875504293, -0.00182802081229), (0.978538786737, -0.0460428312714, 0.200852932613)38.0716397672, 7.91374506718, -27.7422676744

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Beta-1,3-galactosyltransferase 5 / Beta-1 / 3-GalTase 5 / Beta3Gal-T5 / Beta3GalT5 / b3Gal-T5 / Beta-3-Gx-T5 / UDP-Gal:beta-GlcNAc ...Beta-1 / 3-GalTase 5 / Beta3Gal-T5 / Beta3GalT5 / b3Gal-T5 / Beta-3-Gx-T5 / UDP-Gal:beta-GlcNAc beta-1 / 3-galactosyltransferase 5 / UDP-galactose:beta-N-acetylglucosamine beta-1


Mass: 32550.551 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B3GALT5 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9Y2C3, Transferases; Glycosyltransferases; Hexosyltransferases

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Sugars , 5 types, 7 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.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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: 1056.964 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-3-4/a4-b1_a6-f1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#5: Polysaccharide beta-D-galactopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
DGalpb1-3DManpa1-6DManpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5]/1-2-3/a6-b1_b3-c1WURCSPDB2Glycan 1.1.0
[][b-D-Manp]{[(6+1)][a-D-Manp]{[(3+1)][b-D-Galp]{}}}LINUCSPDB-CARE
#8: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: isolated from a natural 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 , 3 types, 117 molecules

#6: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mn
#7: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.72 Å3/Da / Density % sol: 54.72 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 0.1M BIS-TRIS Propane pH8.5, 0.2M Potassium Sodium Tartrate, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: May 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.86→50 Å / Num. obs: 24939 / % possible obs: 99.4 % / Redundancy: 5.7 % / Biso Wilson estimate: 27.46 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 21.76
Reflection shellResolution: 1.86→1.93 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.724 / Mean I/σ(I) obs: 2.15 / Num. unique obs: 1763 / % possible all: 97.7

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
Blu-Icedata collection
HKL-2000data scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→27.33 Å / SU ML: 0.3039 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.9015
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2337 1260 5.05 %
Rwork0.1885 23679 -
obs0.1908 24939 91.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.37 Å2
Refinement stepCycle: LAST / Resolution: 2.4→27.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4382 0 273 113 4768
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00834781
X-RAY DIFFRACTIONf_angle_d1.14766470
X-RAY DIFFRACTIONf_chiral_restr0.0644755
X-RAY DIFFRACTIONf_plane_restr0.0202783
X-RAY DIFFRACTIONf_dihedral_angle_d15.59161863
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.772458174781
ens_2d_2CEX-RAY DIFFRACTIONTorsion NCS0.530291907921
ens_2d_3CEX-RAY DIFFRACTIONTorsion NCS0.931620340467
ens_3d_2HIX-RAY DIFFRACTIONTorsion NCS0.340110552203
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.50.291990.24191860X-RAY DIFFRACTION64.87
2.5-2.610.32351380.23482112X-RAY DIFFRACTION74.18
2.61-2.750.278930.23292477X-RAY DIFFRACTION85.84
2.75-2.920.2591700.22792747X-RAY DIFFRACTION96.46
2.92-3.140.26961500.21762886X-RAY DIFFRACTION99.97
3.14-3.460.25781520.2032882X-RAY DIFFRACTION99.97
3.46-3.960.22211550.17272896X-RAY DIFFRACTION100
3.96-4.980.18381420.14522874X-RAY DIFFRACTION99.67
4.99-27.330.20071610.16732945X-RAY DIFFRACTION99.94
Refinement TLS params.Method: refined / Origin x: 8.87853938109 Å / Origin y: 8.27350470508 Å / Origin z: 14.4433325605 Å
111213212223313233
T0.352647550973 Å2-0.0611058176929 Å20.0237945484436 Å2-0.218469494781 Å20.0240831417407 Å2--0.230930605862 Å2
L0.499102387582 °2-0.177160561983 °20.850089893997 °2-0.473590105766 °20.0583260143893 °2--1.25424272973 °2
S-0.0604755247256 Å °0.247627287193 Å °0.00500775497641 Å °-0.369107433791 Å °0.0285231539677 Å °0.0481588990133 Å °-0.139681039142 Å °0.255094227203 Å °0.0370199331704 Å °
Refinement TLS groupSelection details: all

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