7E9J: POMGNT2

Crystal Structure of POMGNT2 in complex with UDP. Determined by X-ray diffraction at 2.4 Å resolution. Released 5 May 2021.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: Bos taurus
Chains: 2
Atoms: 8,646
Mol. weight: 124.94 kDa
Ligands: NAG, UDP
Released: 5 May 2021

Explore 7E9J in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7E9J contains 58 α-helices and 66 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: 29 helices, 33 β-strands

Element	Residues	Length	Sheet
α-helix	53-63	11
β-strand	64	1	1
β-strand	66-69	4	2
α-helix	74-76	3
β-strand	79-82	4	2
β-strand	84-87	4	1
β-strand	92-97	6	1
β-strand	102-104	3	2
α-helix	108-112	5
β-strand	117-118	2	3
β-strand	129-130	2	3
β-strand	132-136	5	1
α-helix	137-142	6
α-helix	144-146	3
β-strand	147-149	3	1
β-strand	153-156	4	2
α-helix	164-166	3
α-helix	167-172	6
α-helix	173-179	7
α-helix	185-188	4
α-helix	189	1
β-strand	190-193	4	2
α-helix	203-209	7
β-strand	215-216	2	2
α-helix	217-220	4
β-strand	226-229	4	1
β-strand	232-234	3	2
β-strand	243-244	2	4
β-strand	252-253	2	4
α-helix	261-274	14
β-strand	288-292	5	5
β-strand	300	1	6
α-helix	303-314	12
β-strand	317-321	5	5
α-helix	328-336	9
β-strand	340-344	5	5
α-helix	347-354	8
α-helix	356	1
β-strand	360-365	6	5
α-helix	371-373	3
α-helix	376-381	6
β-strand	389-394	6	5
α-helix	398-400	3
β-strand	401-402	2	6
α-helix	409-411	3
α-helix	419-427	9
α-helix	431-433	3
α-helix	440-446	7
β-strand	449-450	2	6
α-helix	454-461	8
β-strand	486-496	11	7
β-strand	499-507	9	7
α-helix	508-509	2
α-helix	510-514	5
β-strand	520-528	9	8
β-strand	535-539	5	8
β-strand	543-546	4	7
α-helix	550-551	2
β-strand	555-564	10	8
β-strand	568-569	2	8
α-helix	574-575	2
β-strand	576-579	4	8

Chain B: 29 helices, 33 β-strands

Element	Residues	Length	Sheet
α-helix	53-63	11
β-strand	64	1	9
β-strand	66-69	4	10
α-helix	74-76	3
β-strand	79-82	4	10
β-strand	84-87	4	9
β-strand	92-97	6	9
β-strand	102-104	3	10
α-helix	108-112	5
β-strand	117-118	2	11
β-strand	129-130	2	11
β-strand	132-136	5	9
α-helix	137-142	6
α-helix	144-146	3
β-strand	147-149	3	9
β-strand	152-156	5	10
α-helix	164-166	3
α-helix	167-172	6
α-helix	173-181	9
α-helix	185-188	4
β-strand	189-193	5	10
α-helix	203-207	5
α-helix	213-214	2
β-strand	215-216	2	10
α-helix	217-219	3
α-helix	220-223	4
β-strand	226-229	4	9
β-strand	232-234	3	10
β-strand	243-244	2	12
β-strand	252-253	2	12
α-helix	261-274	14
β-strand	288-293	6	13
β-strand	300	1	14
α-helix	303-313	11
β-strand	317-322	6	13
α-helix	328-336	9
β-strand	340-344	5	13
α-helix	347-354	8
α-helix	356	1
β-strand	360-365	6	13
α-helix	376-381	6
β-strand	389-394	6	13
α-helix	398-400	3
β-strand	401-402	2	14
α-helix	409-411	3
α-helix	419-427	9
α-helix	431-433	3
α-helix	440-446	7
β-strand	449-450	2	14
α-helix	454-464	11
β-strand	486-494	9	15
β-strand	500-507	8	15
α-helix	508-509	2
α-helix	510-514	5
β-strand	520-528	9	16
β-strand	535-539	5	16
β-strand	543-546	4	15
β-strand	555-564	10	16
β-strand	568-569	2	16
α-helix	570-572	3
α-helix	575	1
β-strand	576-579	4	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2	A, B	protein	539	Bos taurus	Q5NDF2 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>7E9J_1 Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2 (chains A, B)
GAPPAPALRIDYPKALQILTEGGTHMVCTGRTHTDRLCRFKWLCYSSEAEEFIFFHGNAS
VMLPSLGSRRFQPALLDLSTVEDHNTQYFNFVELPAAALRFMPKPVFVPDVALIANRFNP
DNLMHVFHDDLLPLFYTLRQFPGLAREARLFFMEGWGEGAHFDLYKLLSPKQPLLRAQLK
ALGRLLCFSHAFVGLSKVTTWYQYGFVQPQGPKANILVSGNEIRQFAHFLMEKLNVSQAG
GPLGEEYILVFSRTQNRLILNEAELLLALAQEFQMKTVTVSLEDHAFADVVRLVSNASML
VSMHGAQLVTALFLPRGAAVVELFPYAVNPDHYTPYKTLATLPGMDLQYIAWQNTMPENT
VTHPERPWDQGGIAHLDRAEQARILQSREVPRHLCCRNPEWLFRIYQDTKVDIPSLIQTI
RRVVKGHPGPRKQKWTVSLYPGKVREARCQASVQGASEARLSVSWQIPWNLKYLKVREVK
YEVWLQEQGENTYVPYMLALQNHTFTENIKPFTTYLVWIRCIFNKTLLGPFADVLVCST

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4
UDP	Uridine-5'-diphosphate	C9 H14 N2 O12 P2	2

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

Primary citation

The structure of POMGNT2 provides new insights into the mechanism to determine the functional O-mannosylation site on alpha-dystroglycan. Imae, R., Kuwabara, N., Manya, H. et al. Genes Cells (2021) 26:485-494. DOI 10.1111/gtc.12853 · PubMed

Other PDB entries of the same protein (UniProt Q5NDF2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7E9K 2.05 Å, Crystal Structure of POMGNT2 in complex with UDP and mono-mannosyl peptide (379Man long…
7E9L 2.1 Å, Crystal Structure of POMGNT2 in complex with UDP and mono-mannosyl peptide (379Man short…

Browse structure collections

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