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- PDB-9h6k: Human B4GALNT1 in Complex with UDP-GalNac -

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Basic information

Entry
Database: PDB / ID: 9h6k
TitleHuman B4GALNT1 in Complex with UDP-GalNac
ComponentsBeta-1,4 N-acetylgalactosaminyltransferase 1
KeywordsTRANSFERASE / Glycosyltransferase / CAZy GT12 / Ganglioside Synthase / Glycosphingolipid Synthase / UDP-GalNac Complex
Function / homology
Function and homology information


(N-acetylneuraminyl)-galactosylglucosylceramide N-acetylgalactosaminyltransferase / (N-acetylneuraminyl)-galactosylglucosylceramide N-acetylgalactosaminyltransferase activity / acetylgalactosaminyltransferase activity / Glycosphingolipid biosynthesis / ganglioside biosynthetic process / glycosphingolipid metabolic process / nerve development / vacuole organization / lipid storage / : ...(N-acetylneuraminyl)-galactosylglucosylceramide N-acetylgalactosaminyltransferase / (N-acetylneuraminyl)-galactosylglucosylceramide N-acetylgalactosaminyltransferase activity / acetylgalactosaminyltransferase activity / Glycosphingolipid biosynthesis / ganglioside biosynthetic process / glycosphingolipid metabolic process / nerve development / vacuole organization / lipid storage / : / limb development / motor behavior / determination of adult lifespan / spermatogenesis / carbohydrate metabolic process / Golgi membrane / Golgi apparatus / membrane
Similarity search - Function
Ganglioside GM2 synthase / Glycosyltransferase 2-like / Glycosyl transferase family 2 / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
ACETIC ACID / : / URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE / Beta-1,4 N-acetylgalactosaminyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsWelland, J.W.J. / Deane, J.E.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: Nat Commun / Year: 2025
Title: Conformational dynamics and membrane insertion mechanism of B4GALNT1 in ganglioside synthesis.
Authors: Welland, J.W.J. / Barrow, H.G. / Stansfeld, P.J. / Deane, J.E.
History
DepositionOct 24, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-1,4 N-acetylgalactosaminyltransferase 1
B: Beta-1,4 N-acetylgalactosaminyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,38214
Polymers111,2042
Non-polymers3,17812
Water1,33374
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15020 Å2
ΔGint-29 kcal/mol
Surface area40620 Å2
Unit cell
Length a, b, c (Å)60.1, 134.922, 86.584
Angle α, β, γ (deg.)90, 95.907, 90
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: GLN / End label comp-ID: GLN / Auth seq-ID: 51 - 533 / Label seq-ID: 17 - 499

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

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Beta-1,4 N-acetylgalactosaminyltransferase 1 / (N-acetylneuraminyl)-galactosylglucosylceramide / GM2/GD2 synthase / GalNAc-T


Mass: 55601.836 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B4GALNT1, GALGT, SIAT2 / Cell line (production host): HEK293-F / Production host: Homo sapiens (human)
References: UniProt: Q00973, (N-acetylneuraminyl)-galactosylglucosylceramide N-acetylgalactosaminyltransferase

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Sugars , 2 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: isolated from a genetically manipulated source
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: 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.: 4 / Source method: obtained synthetically / 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 , 4 types, 80 molecules

#4: 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
#5: Chemical ChemComp-UD2 / URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE / (2R,3R,4R,5R,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate


Mass: 607.354 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H27N3O17P2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 3.23 Å3/Da / Density % sol: 61.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris-BICINE, 30% w/v GOL_P4K (40% v/v Glycerol, 20% w/v PEG 4000), 0.2 M Sodium formate, 0.2 M Ammonium acetate, 0.2 M Sodium citrate tribasic dihydrate, 0.2 M Potassium sodium ...Details: 0.1 M Tris-BICINE, 30% w/v GOL_P4K (40% v/v Glycerol, 20% w/v PEG 4000), 0.2 M Sodium formate, 0.2 M Ammonium acetate, 0.2 M Sodium citrate tribasic dihydrate, 0.2 M Potassium sodium tartrate tetrahydrate, 0.2 M Sodium oxamate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.6199 Å
DetectorType: DECTRIS EIGER2 X CdTe 9M / Detector: PIXEL / Date: Feb 1, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6199 Å / Relative weight: 1
ReflectionResolution: 2.75→54.66 Å / Num. obs: 35584 / % possible obs: 99.5 % / Redundancy: 7 % / CC1/2: 0.992 / Rmerge(I) obs: 0.186 / Rpim(I) all: 0.114 / Rrim(I) all: 0.219 / Χ2: 0.8 / Net I/σ(I): 6.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
9.12-54.6670.05315.210150.9980.0320.0620.5999.4
2.75-2.886.31.442145650.3890.9641.7420.5396.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.88)refinement
DIALSdata collection
Aimlessdata scaling
PHASERphasing
ISOLDEmodel building
Cootmodel building
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→54.656 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.937 / SU B: 33.55 / SU ML: 0.288 / Cross valid method: FREE R-VALUE / ESU R: 0.785 / ESU R Free: 0.298 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2248 1761 4.952 %
Rwork0.1887 33797 -
all0.19 --
obs-35558 99.602 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 75.617 Å2
Baniso -1Baniso -2Baniso -3
1-0.834 Å20 Å2-0.836 Å2
2---0.845 Å2-0 Å2
3---0.18 Å2
Refinement stepCycle: LAST / Resolution: 2.75→54.656 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7316 0 200 74 7590
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0127697
X-RAY DIFFRACTIONr_angle_refined_deg1.8841.8310496
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8385930
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.629580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.28101186
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.93210348
X-RAY DIFFRACTIONr_chiral_restr0.1230.21210
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025814
X-RAY DIFFRACTIONr_nbd_refined0.2060.23063
X-RAY DIFFRACTIONr_nbtor_refined0.3090.25206
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2276
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2960.272
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3230.21
X-RAY DIFFRACTIONr_mcbond_it4.6064.2763740
X-RAY DIFFRACTIONr_mcangle_it7.1157.6794662
X-RAY DIFFRACTIONr_scbond_it6.3314.7583957
X-RAY DIFFRACTIONr_scangle_it9.5298.5595834
X-RAY DIFFRACTIONr_lrange_it13.3553.83731531
X-RAY DIFFRACTIONr_ncsr_local_group_10.0910.0514642
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.090780.0501
12BX-RAY DIFFRACTIONLocal ncs0.090780.0501
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.75-2.8210.3451220.33223620.33326100.9250.92295.17240.33
2.821-2.8980.3621310.33724380.33825700.9160.92199.96110.33
2.898-2.9820.2981080.29923790.29924870.9450.9461000.287
2.982-3.0740.292980.26122900.26323880.9350.961000.243
3.074-3.1740.2471450.21722330.21923780.9620.9711000.194
3.174-3.2850.276970.20121510.20422480.9510.9751000.178
3.285-3.4090.2331170.18820640.1921810.9620.981000.164
3.409-3.5470.2351150.1820280.18321430.9710.9821000.162
3.547-3.7040.229920.17119140.17320060.9650.9841000.157
3.704-3.8840.2421040.17218210.17619250.9630.9841000.161
3.884-4.0930.187880.15617500.15718380.9780.9871000.15
4.093-4.340.222850.16116830.16417680.9740.9861000.159
4.34-4.6370.202760.15215570.15416330.9730.9881000.152
4.637-5.0060.202710.14414730.14615440.9710.9881000.15
5.006-5.4790.181800.16813170.16913970.9810.9831000.171
5.479-6.1180.251670.18312170.18612840.9680.9821000.189
6.118-7.050.227620.18710630.18911250.9760.9821000.195
7.05-8.5990.188390.1739330.1739720.9770.9821000.194
8.599-12.0130.14430.1417040.1417470.9890.9881000.172
12.013-54.6560.231200.3164190.3134420.9670.93499.32130.412
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)
11.2605-0.2013-0.31162.1349-0.19832.61510.10960.10870.0165-0.3174-0.09580.09670.1961-0.1011-0.01380.15250.0530.04080.03260.02070.0423-1.7112-7.225234.9205
20.9355-0.2703-0.23132.12210.5332.11820.06850.02450.3036-0.2778-0.040.0163-0.05440.1405-0.02850.10250.05120.03130.07960.05750.144-2.66538.14734.2501
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAp51 - 601
2X-RAY DIFFRACTION2ALLBp51 - 602

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