7Q4I: DmC1GalT1

Crystal structure of DmC1GalT1 in complex with UDP-Mn2+ and the APD-TGalNAc-RP. Determined by X-ray diffraction at 2.4 Å resolution. Released 13 Apr 2022.

Method: X-ray diffraction
Resolution: 2.4 Å
Organisms: Drosophila melanogaster, Homo sapiens
Chains: 4
Atoms: 4,830
Mol. weight: 75.39 kDa
Ligands: A2G, MN, UDP
Released: 13 Apr 2022

Explore 7Q4I in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7Q4I contains 33 α-helices and 34 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 16 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	88	1	1
α-helix	90-98	9
β-strand	101-106	6	2
α-helix	109-111	3
α-helix	112-116	5
α-helix	117-121	5
α-helix	123-126	4
β-strand	129-134	6	2
β-strand	144-145	2	2
α-helix	152-154	3
α-helix	155-170	16
β-strand	176-181	6	2
β-strand	184-186	3	3
α-helix	188-195	8
β-strand	204-206	3	2
β-strand	209-210	2	4
β-strand	218-219	2	4
β-strand	225-228	4	2
α-helix	229-234	6
α-helix	235-239	5
α-helix	254-264	11
β-strand	268-269	2	2
β-strand	279	1	5
β-strand	281	1	3
α-helix	286-290	5
α-helix	300-304	5
β-strand	305	1	4
β-strand	316	1	5
β-strand	322-324	3	3
α-helix	328-335	8
α-helix	336-340	5
β-strand	347-348	2	6
α-helix	350-358	9

Chain B: 17 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	87-88	2	6
α-helix	90-98	9
β-strand	101-106	6	7
α-helix	109-111	3
α-helix	112-116	5
α-helix	117-121	5
α-helix	124-126	3
β-strand	129-134	6	7
β-strand	144-145	2	7
α-helix	152-154	3
α-helix	155-170	16
β-strand	176-181	6	7
β-strand	184-186	3	8
α-helix	188-195	8
β-strand	204-206	3	7
β-strand	209-210	2	9
β-strand	218-219	2	9
β-strand	225-228	4	7
α-helix	229-234	6
α-helix	235-239	5
α-helix	254-264	11
β-strand	268-269	2	7
β-strand	279	1	10
β-strand	281	1	8
α-helix	286-290	5
α-helix	300-304	5
β-strand	305	1	9
β-strand	316	1	10
β-strand	322-324	3	8
α-helix	328-335	8
α-helix	336-340	5
β-strand	347	1	1
α-helix	350-358	9
α-helix	363-365	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase 1	A, B	protein	316	Drosophila melanogaster	Q7K237 (AlphaFold model)
Mucin-1	F, G	protein	6	Homo sapiens	P15941 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>7Q4I_1 Glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase 1 (chains A, B)
SGPEQDVGGHEHVHENSTIAERLYSEVRVLCWIMTNPSNHQKKARHVKRTWGKRCNKLIF
MSSAKDDELDAVALPVGEGRNNLWGKTKEAYKYIYEHHINDADWFLKADDDTYTIVENMR
YMLYPYSPETPVYFGCKFKPYVKQGYMSGGAGYVLSREAVRRFVVEALPNPKLCKSDNSG
AEDVEIGKCLQNVNVLAGDSRDSNGRGRFFPFVPEHHLIPSHTDKKFWYWQYIFYKTDEG
LDCCSDNAISFHYVSPNQMYVLDYLIYHLRPYGIINTPDALPNKLAVGELMPEIKEQATE
STSDGVSKRSAETKTQ

Sequence of entity 2 (F, G), FASTA

>7Q4I_2 Mucin-1 (chains F, G)
APDTRP

Ligands and cofactors

ID	Name	Formula	Copies
A2G	2-acetamido-2-deoxy-alpha-D-galactopyranose	C8 H15 N O6	2
MN	Manganese (II) ion	Mn	2
UDP	Uridine-5'-diphosphate	C9 H14 N2 O12 P2	2

Water and common crystallization additives (EDO) are not listed.

Primary citation

Structural basis for the synthesis of the core 1 structure by C1GalT1. Gonzalez-Ramirez, A.M., Grosso, A.S., Yang, Z. et al. Nat Commun (2022) 13:2398-2398. DOI 10.1038/s41467-022-29833-0 · PubMed

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