8ujg

X-ray crystal structure of Toxoplasma gondii GalNAc-T3 in complex with UDP-GalNAc, Mn2+, and the mono-glycopeptide Srs13.2

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Glycosyl transferase

Toxoplasma gondii ME49

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	SAG-related sequence SRS13 × 1 （S8F856） MANGANESE (II) ION × 4 URIDINE-5'-DIPHOSPHATE × 2 GLYCEROL × 10 DI(HYDROXYETHYL)ETHER × 2 2-acetamido-2-deoxy-alpha-D-galactopyranose × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A125YMZ8_TOXGM
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–563； UniProt 74–635 Author chain B； PDBConstruct 2–563； UniProt 74–635

SAG-related sequence SRS13

OrganismNot specified

UniProt S8F856

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Glycosyl transferase × 2 （A0A125YMZ8） MANGANESE (II) ION × 4 URIDINE-5'-DIPHOSPHATE × 2 GLYCEROL × 10 DI(HYDROXYETHYL)ETHER × 2 2-acetamido-2-deoxy-alpha-D-galactopyranose × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	S8F856_TOXGM
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–19； UniProt 525–543

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8ujg
Deposition date deposition_date	2023-10-11
Structure title title	X-ray crystal structure of Toxoplasma gondii GalNAc-T3 in complex with UDP-GalNAc, Mn2+, and the mono-glycopeptide Srs13.2
Keywords keywords	GT-A fold GalNAc Glycosyltransferase, Mucin-type O-glycosylation, Toxoplasma gondii cyst wall glycosylation, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

8ujg__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

8ujg__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8ujg__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	33.94 Å
Rg (electron density)	33.33 Å
Total Rg	33.85 Å
Atom count	16936
Residues	1062
Excluded volume	152490 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8ujg__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	Glycosyl transferase
Molecular weight formula_weight	63514.1 kDa
EC 编号 ec_number	2.4.1.41
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	17581

GARDVQEGVSSFEESGGAQLPPRVHALEVLEGAGPGRLHGRLGIKPDGQPGYTRAPSPPTDLSMPQALARGGGFNLYLSDHLELDRTAPDARHASCRQLHYDLSTLPKASVIIVFYNEPFSTLMRSVHSVLNGTPPQILEELILVDDGSTLPYIREDGNQQLVEYLKLLPAKVRLIRNEVRKGIVGARMKGIRASRAPIFAILDSHIEVSPQWLEPLLLRIKEDSRRVVMPQIDGIDAETFKHIAGGIGCKLGFLWKLMEHSYEGHQTARLPPEERQPSPTDFQTSPAMAGGLFAANKAFFFDVGAYDEDFQFWGTENLELSFRLWQCGGVLECAPCSRVYHIFRKGGSGYSSPGDSITINKMRTMLWMDEYADLAWRVIGKPRVNYRPESLEKRREWRKRKGCKSFRWFMENVFPEGDVVTLDDVPYLGPLRNDKIGMCLDNMGWASPGHAVGLEYCHGGDTQTFMFFRKVGHVMPVNDDEACLQPSGRLDWCRGTAQFWWDFTSSGQLMFRETKQCLSAFGRKLRMVECDDTDPYQIWSWTAYNPPDTFTFPSVSRSIRSG

Source Source

Source organism organism	Toxoplasma gondii ME49
NCBI taxonomy ID ncbi_taxonomy_id	508771
Host organism host_organism	Komagataella pastoris

Entity 2 Entity 2 polymer

Description description	SAG-related sequence SRS13
Molecular weight formula_weight	1970.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

PETTTVAPPAKTQPETTTV

Entity 3 Entity 3 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	URIDINE-5'-DIPHOSPHATE
Molecular weight formula_weight	404.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 6 Entity 6 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	2-acetamido-2-deoxy-alpha-D-galactopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	241

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Unit-cell length a length_a	66.614 Å
Unit-cell length b length_b	122.624 Å
Unit-cell length c length_c	165.655 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	orthorhombic

Resolution resolution	2.270 Å
Low-resolution limit resolution_low	29.660 Å
R factor r_factor	0.1945
R_work r_work	0.1923
R_free r_free	0.2369

X-ray crystal structure of Toxoplasma gondii GalNAc-T3 in complex with UDP-GalNAc, Mn2+, and the mono-glycopeptide Srs13.2

1. Protein Identity and Related Structures Protein Identity & Related Structures

Glycosyl transferase

State in the Current Structure

Other States of the Same Protein in the Database

SAG-related sequence SRS13

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8ujg__assembly_1__model_1

8ujg__assembly_1__model_1 | I(q)

8ujg__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Citations (1)

X-ray crystal structure of Toxoplasma gondii GalNAc-T3 in complex with UDP-GalNAc, Mn2+, and the mono-glycopeptide Srs13.2

1. Protein Identity and Related Structures Protein Identity & Related Structures

Glycosyl transferase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

SAG-related sequence SRS13

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8ujg__assembly_1__model_1

8ujg__assembly_1__model_1 | I(q)

8ujg__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Citations (1)