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Basic information

Entry
Database: PDB / ID: 8zwy
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
: / URIDINE-5'-DIPHOSPHATE / Beta-1,3-galactosyltransferase 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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)69,65214
Polymers65,1012
Non-polymers4,55112
Water4,107228
1
A: Beta-1,3-galactosyltransferase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4817
Polymers32,5511
Non-polymers1,9316
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-1,3-galactosyltransferase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1717
Polymers32,5511
Non-polymers2,6206
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.645, 86.700, 86.996
Angle α, β, γ (deg.)90.000, 95.252, 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...
d_2ens_1(chain "B" and (resid 43 through 160 or resid 162...
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_4ens_2(chain "I" and resid 1)
d_5ens_2(chain "J" and resid 1)

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_1ASNASNLYSLYSAA162 - 202132 - 172
d_13ens_1GLUGLUPHEPHEAA204 - 286174 - 256
d_14ens_1LYSLYSPROPROAA288 - 308258 - 278
d_15ens_1MNMNMNMNAI401
d_16ens_1UDPUDPUDPUDPAJ402
d_17ens_1B3PB3PB3PB3PAK403
d_21ens_1ASNASNPHEPHEBB43 - 16013 - 130
d_22ens_1ASNASNLYSLYSBB162 - 202132 - 172
d_23ens_1GLUGLUPHEPHEBB204 - 286174 - 256
d_24ens_1LYSLYSPROPROBB288 - 308258 - 278
d_25ens_1MNMNMNMNBL401
d_26ens_1UDPUDPUDPUDPBM402
d_27ens_1B3PB3PB3PB3PBN403
d_11ens_2NAGNAGNAGNAGEC1
d_21ens_2NAGNAGNAGNAGFD1
d_31ens_2NAGNAGNAGNAGGE1
d_41ens_2NAGNAGNAGNAGIG2
d_51ens_2NAGNAGNAGNAGJH2

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.194966536517, 0.00891245708529, -0.980769400903), (-0.0254757758911, 0.999667357406, 0.00401987320183), (0.980478982172, 0.0242021207028, 0.195128734102)38.5337191704, 9.26216383042, -27.6608837816
2given(0.392595926149, -0.463352579736, 0.794463860489), (-0.503250926288, -0.831255172723, -0.236121458178), (0.76980968035, -0.307114351136, -0.559530009352)-34.1182494344, 34.950324733, 51.5969554397
3given(0.10014712322, 0.0317090930594, -0.994467237835), (0.00933378150048, 0.999418124415, 0.0328069064893), (0.994928858881, -0.012567657214, 0.0997928843076)41.3688194849, 7.56157714645, -24.9841793451
4given(-0.811492019534, 0.494314023907, 0.311663838137), (-0.0555907758569, 0.465618605075, -0.883237782394), (-0.581713303847, -0.734066046332, -0.350366482059)30.4615629489, 23.2906098237, 81.8863263396
5given(0.300404393491, 0.823728574351, 0.480862180015), (-0.00375985056456, 0.50516654591, -0.863013687271), (-0.953804520798, 0.25744513336, 0.154851346181)-34.7025139235, 29.6911588736, 23.204084309

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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 , 4 types, 6 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 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-methyl beta-D-galactopyranoside


Type: oligosaccharide / Mass: 397.375 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-3DGalp[1Me]b1-OMEGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5_1*OC][a2122h-1b_1-5_2*NCC/3=O]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][b-D-Galp]{[(3+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 234 molecules

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


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#8: 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.: 228 / 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: 2.75 Å3/Da / Density % sol: 55.25 %
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: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: May 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 47592 / % possible obs: 98.1 % / Redundancy: 4.9 % / Biso Wilson estimate: 17.27 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 16.2
Reflection shellResolution: 1.95→2.02 Å / Rmerge(I) obs: 0.362 / Mean I/σ(I) obs: 3.45 / Num. unique obs: 3613 / % possible all: 89

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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: 1.95→47.44 Å / SU ML: 0.2078 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.2476
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2268 2272 4.77 %
Rwork0.2082 45316 -
obs0.2091 47588 92.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.13 Å2
Refinement stepCycle: LAST / Resolution: 1.95→47.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4382 0 295 228 4905
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01284809
X-RAY DIFFRACTIONf_angle_d1.53166518
X-RAY DIFFRACTIONf_chiral_restr0.0926749
X-RAY DIFFRACTIONf_plane_restr0.0423787
X-RAY DIFFRACTIONf_dihedral_angle_d16.46311810
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.922539680335
ens_2d_2CEX-RAY DIFFRACTIONTorsion NCS0.110864546118
ens_2d_3CEX-RAY DIFFRACTIONTorsion NCS0.182525310246
ens_2d_4CEX-RAY DIFFRACTIONTorsion NCS0.558363913443
ens_2d_5CEX-RAY DIFFRACTIONTorsion NCS0.569822532078
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.990.2965900.2442103X-RAY DIFFRACTION68.79
1.99-2.040.2794970.23522282X-RAY DIFFRACTION75.26
2.04-2.090.24331330.22772438X-RAY DIFFRACTION80.09
2.09-2.150.24771180.22732629X-RAY DIFFRACTION85.07
2.15-2.210.24081360.2352663X-RAY DIFFRACTION89.17
2.21-2.280.26881390.23172876X-RAY DIFFRACTION93.34
2.28-2.360.23421700.23462918X-RAY DIFFRACTION97.23
2.36-2.460.25811420.24393025X-RAY DIFFRACTION99.43
2.46-2.570.28661710.23223022X-RAY DIFFRACTION99.72
2.57-2.710.24671830.23222987X-RAY DIFFRACTION99.87
2.71-2.880.26331960.23243015X-RAY DIFFRACTION99.94
2.88-3.10.28831300.22953083X-RAY DIFFRACTION99.97
3.1-3.410.20271240.20883121X-RAY DIFFRACTION99.78
3.41-3.90.2121550.18642995X-RAY DIFFRACTION99.18
3.9-4.920.17761510.16123079X-RAY DIFFRACTION99.78
4.92-47.440.15781370.17433080X-RAY DIFFRACTION97.96
Refinement TLS params.Method: refined / Origin x: 8.86178001402 Å / Origin y: 8.15854858127 Å / Origin z: 15.1899140322 Å
111213212223313233
T0.25196087809 Å2-0.0420307894587 Å2-0.000848542688763 Å2-0.147344447868 Å20.00951039380225 Å2--0.219864458089 Å2
L0.464010066507 °2-0.206631730062 °20.645499779405 °2-0.333785550358 °2-0.0929749975243 °2--0.979252994657 °2
S-0.0223844944996 Å °0.177174001957 Å °-0.00363676839335 Å °-0.28799466419 Å °0.00123555473644 Å °0.0502962261799 Å °-0.0502794966088 Å °0.16033936913 Å °0.0362401441956 Å °
Refinement TLS groupSelection details: all

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