PDB-9h6j: Human B4GALNT1 Apo Structure

ID or keywords:

Entry

Database: PDB / ID: 9h6j

Title

Human B4GALNT1 Apo Structure

Components

Beta-1,4 N-acetylgalactosaminyltransferase 1

Keywords

TRANSFERASE / Glycosyltransferase / CAZy GT12 / Ganglioside Synthase / Glycosphingolipid Synthase

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 / : ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.96 Å

Authors

Welland, J.W.J. / Deane, J.E.

Funding support

United Kingdom, 1items

Citation

Journal: 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

Deposition	Oct 24, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 16, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9h6j.cif.gz	432.5 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	9h6j_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	9h6j_full_validation.pdf.gz	1.1 MB	Display
Data in XML	9h6j_validation.xml.gz	38.8 KB	Display
Data in CIF	9h6j_validation.cif.gz	49.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/h6/9h6j ftp://data.pdbj.org/pub/pdb/validation_reports/h6/9h6j	HTTPS FTP

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Related structure data

Related structure data	9h6kC 9h6lC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#254 - Feb 2021 Cellulose Synthase similarity (3) #156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (1) #4 - Apr 2000 Collagen similarity (1) #116 - Aug 2009 Sulfotransferases similarity (1)

Deposited unit

A: Beta-1,4 N-acetylgalactosaminyltransferase 1

B: Beta-1,4 N-acetylgalactosaminyltransferase 1

hetero molecules

112 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: light scattering

Unit cell

Length a, b, c (Å)	60.463, 136.486, 87.427
Angle α, β, γ (deg.)	90, 96.076, 90
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: GLN / End label comp-ID: GLN / Auth seq-ID: 53 - 533 / Label seq-ID: 19 - 499

Dom-ID	Auth asym-ID	Label asym-ID
1	A	A
2	B	B

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

#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: 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

#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.: 2 / Source method: obtained synthetically / Formula: C₈H₁₅NO₆

Identifier	Type	Program
DGlcpNAcb	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-b-D-glucopyranosamine	COMMON NAME	GMML 1.0
b-D-GlcpNAc	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
GlcNAc	SNFG CARBOHYDRATE SYMBOL	GMML 1.0

#4: Chemical

ChemComp-ACY / ACETIC ACID

Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₄O₂

#5: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H₂O

Has ligand of interest

Y

Has protein modification

Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.32 Å³/Da / Density % sol: 63 %
Crystal grow	Temperature: 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

Crystal

Density Matthews: 3.32 Å³/Da / Density % sol: 63 %

Crystal grow

Temperature: 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 ...

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

Diamond

/ Beamline: I24 / Wavelength: 0.6199 Å

Detector

Type: DECTRIS EIGER2 X CdTe 9M / Detector: PIXEL / Date: Feb 1, 2024

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.6199 Å / Relative weight: 1

Reflection

Resolution: 2.94→136.49 Å / Num. obs: 30064 / % possible obs: 100 % / Redundancy: 7.1 % / CC_1/2: 0.999 / R_merge(I) obs: 0.112 / R_pim(I) all: 0.069 / R_rim(I) all: 0.131 / Χ²: 0.94 / Net I/σ(I): 9.9

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
9.3-136.49	6.8	0.025	45	987	1	0.016	0.03	0.66	99.9
2.94-3.1	7.2	1.61	1.1	4363	0.521	0.983	1.89	0.87	100

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Processing

Software

Name	Version	Classification
DIALS		data collection
DIALS		data reduction
Aimless		data scaling
PHASER		phasing
REFMAC	5.8.0430 (refmacat 0.4.88)	refinement
ISOLDE		model building
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.96→86.936 Å / Cor.coef. F_o:F_c: 0.953 / Cor.coef. F_o:F_c free: 0.936 / SU B: 46.293 / SU ML: 0.366 / Cross valid method: FREE R-VALUE / ESU R Free: 0.387 / Details: Hydrogens have not been used

	R_factor	Num. reflection	% reflection
R_free	0.254	1456	4.979 %
R_work	0.2019	27784	-
all	0.205	-	-
obs	-	29240	99.236 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 118.931 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.023 Å²	0 Å²	1.464 Å²
2-	-	-0.81 Å²	-0 Å²
3-	-	-	-0.514 Å²

Refinement step

Cycle: LAST / Resolution: 2.96→86.936 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7015	0	38	14	7067

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.012	7210
X-RAY DIFFRACTION	r_angle_refined_deg	1.87	1.825	9808
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.094	5	888
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	11.478	5	72
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.054	10	1150
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.786	10	334
X-RAY DIFFRACTION	r_chiral_restr	0.12	0.2	1117
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	5500
X-RAY DIFFRACTION	r_nbd_refined	0.216	0.2	2905
X-RAY DIFFRACTION	r_nbtor_refined	0.309	0.2	4869
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.136	0.2	210
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.25	0.2	48
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.653	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	6.953	6.671	3578
X-RAY DIFFRACTION	r_mcangle_it	10.447	11.984	4456
X-RAY DIFFRACTION	r_scbond_it	8.378	6.96	3632
X-RAY DIFFRACTION	r_scangle_it	12.206	12.635	5352
X-RAY DIFFRACTION	r_lrange_it	16.317	82.307	29350
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.105	0.05	13863

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.10526	0.05009
1	2	B	X-RAY DIFFRACTION	Local ncs	0.10526	0.05009

LS refinement shell

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

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.96-3.037	0.385	85	0.355	1890	0.356	2193	0.889	0.921	90.0593	0.35
3.037-3.12	0.301	99	0.293	2009	0.294	2108	0.939	0.945	100	0.281
3.12-3.21	0.315	122	0.266	1917	0.269	2039	0.943	0.957	100	0.249
3.21-3.309	0.31	89	0.252	1913	0.255	2002	0.943	0.962	100	0.23
3.309-3.417	0.301	100	0.24	1814	0.243	1914	0.939	0.967	100	0.214
3.417-3.537	0.243	105	0.199	1787	0.201	1892	0.964	0.978	100	0.177
3.537-3.67	0.276	80	0.199	1709	0.202	1790	0.952	0.979	99.9441	0.177
3.67-3.82	0.253	102	0.177	1660	0.181	1762	0.964	0.983	100	0.159
3.82-3.989	0.245	70	0.177	1604	0.18	1674	0.967	0.984	100	0.162
3.989-4.184	0.287	86	0.186	1501	0.191	1587	0.954	0.982	100	0.171
4.184-4.409	0.265	71	0.185	1458	0.189	1529	0.965	0.981	100	0.173
4.409-4.676	0.26	63	0.186	1376	0.189	1439	0.961	0.98	100	0.171
4.676-4.998	0.28	65	0.175	1282	0.18	1347	0.956	0.981	100	0.16
4.998-5.397	0.242	69	0.203	1190	0.205	1259	0.97	0.977	100	0.187
5.397-5.91	0.265	68	0.221	1102	0.223	1170	0.96	0.975	100	0.203
5.91-6.603	0.255	51	0.208	996	0.211	1047	0.971	0.977	100	0.192
6.603-7.618	0.235	46	0.185	892	0.187	938	0.97	0.981	100	0.175
7.618-9.312	0.188	38	0.176	756	0.177	794	0.979	0.982	100	0.166
9.312-13.094	0.165	31	0.167	584	0.167	615	0.982	0.984	100	0.156
13.094-86.936	0.301	16	0.28	343	0.281	360	0.954	0.947	99.7222	0.27

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	2.3207	-0.191	-0.5077	2.7314	0.1204	2.6254	0.1618	0.1889	0.0476	-0.5245	-0.0928	0.0197	0.2449	-0.0042	-0.0689	0.1898	0.0732	0.0382	0.0531	0.0353	0.4847	-1.1728	-6.3899	34.4704
2	1.7349	-0.3014	-0.1342	2.6578	0.6494	2.7841	0.0747	0.1209	0.4057	-0.4983	-0.0514	-0.0012	0.0495	0.2158	-0.0233	0.1049	0.0262	0.004	0.0372	0.0839	0.5194	-2.7858	8.0331	33.4394

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	53 - 701
2	X-RAY DIFFRACTION	2	ALL	B	53 - 701

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