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- PDB-9h6l: Human B4GALNT1 in Complex with UDP -

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Basic information

Entry
Database: PDB / ID: 9h6l
TitleHuman B4GALNT1 in Complex with UDP
ComponentsBeta-1,4 N-acetylgalactosaminyltransferase 1
KeywordsTRANSFERASE / Glycosyltransferase / CAZy GT12 / Ganglioside Synthase / Glycosphingolipid Synthase / UDP 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-5'-DIPHOSPHATE / Beta-1,4 N-acetylgalactosaminyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.674 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)113,41510
Polymers111,2042
Non-polymers2,2118
Water48627
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13390 Å2
ΔGint-40 kcal/mol
Surface area39550 Å2
Unit cell
Length a, b, c (Å)60.183, 133.527, 86.922
Angle α, β, γ (deg.)90, 94.83, 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 / Sugars , 2 types, 4 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
#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 33 molecules

#3: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#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-ACY / ACETIC ACID


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


Mass: 18.015 Da / Num. of mol.: 27 / 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: 3.22 Å3/Da / Density % sol: 61.87 %
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: 2.67→66.76 Å / Num. obs: 38565 / % possible obs: 99.3 % / Redundancy: 6.8 % / CC1/2: 0.989 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.079 / Rrim(I) all: 0.15 / Χ2: 0.81 / Net I/σ(I): 8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
9.25-66.766.80.07820.69750.9830.0470.0911.0399.7
2.67-2.795.61.1071.144420.4770.7841.3630.694.2

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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: 2.674→66.76 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.938 / SU B: 28.783 / SU ML: 0.257 / Cross valid method: FREE R-VALUE / ESU R: 0.533 / ESU R Free: 0.285 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2327 1897 4.951 %
Rwork0.1911 36420 -
all0.193 --
obs-38317 99.023 %
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: 79.968 Å2
Baniso -1Baniso -2Baniso -3
1-2.466 Å20 Å2-0.642 Å2
2--0.389 Å20 Å2
3----2.707 Å2
Refinement stepCycle: LAST / Resolution: 2.674→66.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7184 0 138 27 7349
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0127501
X-RAY DIFFRACTIONr_angle_refined_deg2.0061.82710218
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9565912
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.538574
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.609101170
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.39710340
X-RAY DIFFRACTIONr_chiral_restr0.1270.21172
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025678
X-RAY DIFFRACTIONr_nbd_refined0.2130.23139
X-RAY DIFFRACTIONr_nbtor_refined0.3180.25053
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2315
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2570.248
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1410.21
X-RAY DIFFRACTIONr_mcbond_it4.6864.113668
X-RAY DIFFRACTIONr_mcangle_it6.9267.374572
X-RAY DIFFRACTIONr_scbond_it6.9194.6373833
X-RAY DIFFRACTIONr_scangle_it10.1228.2915646
X-RAY DIFFRACTIONr_lrange_it13.40151.15930926
X-RAY DIFFRACTIONr_ncsr_local_group_10.1040.0514338
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.103520.05009
12BX-RAY DIFFRACTIONLocal ncs0.103520.05009
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
2.674-2.7440.361270.32423840.32628500.8980.91488.10530.323
2.744-2.8190.31270.28726230.28827580.9510.94499.70990.278
2.819-2.90.321460.27725750.2827230.9440.95299.92660.263
2.9-2.9890.2621040.24525150.24526200.9580.96499.96180.223
2.989-3.0870.2261180.2224210.2225400.970.97299.96060.197
3.087-3.1950.2371480.19823050.224530.9630.9771000.176
3.195-3.3160.2891070.20822700.21223770.9460.9741000.186
3.316-3.4510.241150.18921460.19222610.9650.981000.173
3.451-3.6040.241160.18620940.18922110.9660.98199.95480.172
3.604-3.7790.2361040.17920100.18121150.9640.98299.95270.166
3.779-3.9830.2261010.16618880.16919890.9710.9761000.155
3.983-4.2230.183990.15417830.15518830.9770.98799.94690.149
4.223-4.5140.218760.14816840.15117610.9750.98799.94320.15
4.514-4.8740.236760.14515920.14916680.970.9881000.153
4.874-5.3360.184830.16314430.16515260.9820.9841000.17
5.336-5.9610.261760.20413180.20713940.9580.9781000.212
5.961-6.8740.247600.20811570.2112170.9680.9771000.223
6.874-8.3970.225460.18110000.18310460.970.981000.202
8.397-11.7820.186450.1637640.1648090.9820.9851000.189
11.782-66.760.236230.3024480.2994760.9760.94498.94960.376
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)
11.1967-0.0064-0.37722.442-0.14942.71810.06850.0953-0.0024-0.357-0.01830.09560.1781-0.103-0.05020.1050.0539-0.00220.084-0.00730.2036-0.6745-7.909834.3941
20.884-0.0889-0.18952.30770.71662.66960.0550.04780.3031-0.388-0.00120.1107-0.04880.0866-0.05380.0840.043-0.00370.1030.03410.2766-2.07716.665233.6957
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAp51 - 702
2X-RAY DIFFRACTION2ALLBp51 - 703

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