8v9q

Crystal structure of mGalNAc-T1 in complex with the mucin glycopeptide Muc5AC-13, Mn2+, and UDP.

Method: X-RAY DIFFRACTION

▼

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

Polypeptide N-acetylgalactosaminyltransferase 1 soluble form

Mus musculus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 5 其他Polymer 2	Mucin-5AC × 3 （P98088） ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 URIDINE-5'-DIPHOSPHATE × 2 GLYCEROL × 2 SUCCINIC ACID × 1 1,2-ETHANEDIOL × 5 MANGANESE (II) ION × 2 2-acetamido-2-deoxy-alpha-D-galactopyranose × 3 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GALT1_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–559； UniProt 1–559 Author chain B； PDBConstruct 1–559； UniProt 1–559

Mucin-5AC

OrganismNot specified

UniProt P98088

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 5 其他Polymer 2	Polypeptide N-acetylgalactosaminyltransferase 1 soluble form × 2 （O08912） ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 URIDINE-5'-DIPHOSPHATE × 2 GLYCEROL × 2 SUCCINIC ACID × 1 1,2-ETHANEDIOL × 5 MANGANESE (II) ION × 2 2-acetamido-2-deoxy-alpha-D-galactopyranose × 3 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MUC5A_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–16； UniProt 2449–2464 Author chain F； PDBConstruct 1–16； UniProt 2449–2464 Author chain H； PDBConstruct 1–16； UniProt 2449–2464

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	8v9q
Deposition date deposition_date	2023-12-08
Structure title title	Crystal structure of mGalNAc-T1 in complex with the mucin glycopeptide Muc5AC-13, Mn2+, and UDP.
Keywords keywords	GT-A fold catalytic domain, Lectin domain, Golgi membrane, Mucin-type O-glycosyltransferase, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

8v9q__assembly_1__model_1

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

Download this curve (.dat)

8v9q__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8v9q__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	37.06 Å
Rg (electron density)	36.64 Å
Total Rg	37.22 Å
Atom count	16137
Residues	987
Excluded volume	145130 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8v9q__assembly_1__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (12)

Entity 1 Entity 1 polymer

Description description	Polypeptide N-acetylgalactosaminyltransferase 1 soluble form
Molecular weight formula_weight	64340.9 kDa
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	16274

MRKFAYCKVVLATSLVWVLLDMFLLLYFSECNKCEEKQERGLPAGDVLELVQKPHEGPGEMGKPVVIPKEDQEKMKEMFKINQFNLMASEMIALNRSLPDVRLEGCKTKVYPDNLPTTSVVIVFHNEAWSTLLRTVHSVINRSPRHMIEEIVLVDDASERDFLKRPLESYVKKLKVPVHVIRMEQRSGLIRARLKGAAVSRGQVITFLDAHCECTAGWLEPLLARIKHDRRTVVCPIIDVISDDTFEYMAGSDMTYGGFNWKLNFRWYPVPQREMDRRKGDRTLPVRTPTMAGGLFSIDRDYFQEIGTYDAGMDIWGGENLEISFRIWQCGGTLEIVTCSHVGHVFRKATPYTFPGGTGQIINKNNRRLAEVWMDEFKNFFYIISPGVTKVDYGDISSRLGLRRKLQCKPFSWYLENIYPDSQIPRHYFSLGEIRNVETNQCLDNMARKENEKVGIFNCHGMGGNQVFSYTANKEIRTDDLCLDVSKLNGPVTMLKCHHLKGNQLWEYDPVKLTLQHVNSNQCLDKATEEDSQVPSIRDCTGSRSQQWLLRNVTLPEIF

Source Source

Source organism organism	Mus musculus
Common name common_name	house mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Komagataella pastoris

Entity 2 Entity 2 polymer

Description description	Mucin-5AC
Molecular weight formula_weight	1501.6 kDa
Source method src_method	syn
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,F,H

GTTPSPVPTTSTTSAP

Entity 3 Entity 3 branched

Description description	;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	910.8 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 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 6 Entity 6 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	SUCCINIC ACID
Molecular weight formula_weight	118.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 9 Entity 9 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 10 Entity 10 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	3

Entity 11 Entity 11 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 12 Entity 12 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	137

▶

Unit-cell length a length_a	59.635 Å
Unit-cell length b length_b	72.761 Å
Unit-cell length c length_c	148.498 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.44 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	monoclinic

Resolution resolution	2.290 Å
Low-resolution limit resolution_low	29.900 Å
R factor r_factor	0.2494
R_work r_work	0.2479
R_free r_free	0.2777

Crystal structure of mGalNAc-T1 in complex with the mucin glycopeptide Muc5AC-13, Mn2+, and UDP.

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

Polypeptide N-acetylgalactosaminyltransferase 1 soluble form

State in the Current Structure

Other States of the Same Protein in the Database

Mucin-5AC

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

8v9q__assembly_1__model_1

8v9q__assembly_1__model_1 | I(q)

8v9q__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 (12)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 branched

Entity 4 Entity 4 branched

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 non-polymer

Entity 12 Entity 12 water

7. Citations (1)

Crystal structure of mGalNAc-T1 in complex with the mucin glycopeptide Muc5AC-13, Mn2+, and UDP.

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

Polypeptide N-acetylgalactosaminyltransferase 1 soluble form

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Mucin-5AC

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

8v9q__assembly_1__model_1

8v9q__assembly_1__model_1 | I(q)

8v9q__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 (12)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 branched

Entity 4 Entity 4 branched

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 non-polymer

Entity 12 Entity 12 water

7. Citations (1)