7E9K: POMGNT2

Crystal Structure of POMGNT2 in complex with UDP and mono-mannosyl peptide (379Man long peptide). Determined by X-ray diffraction at 2.05 Å resolution. Released 5 May 2021.

Method: X-ray diffraction
Resolution: 2.05 Å
Organisms: Bos taurus, Homo sapiens
Chains: 6
Atoms: 18,493
Mol. weight: 256.19 kDa
Ligands: NAG, UDP, MAN
Released: 5 May 2021

Explore 7E9K in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7E9K contains 117 α-helices and 144 β-strands across 6 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: 30 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
β-strand	190-193	4	2
α-helix	203-207	5
α-helix	213-214	2
β-strand	215-216	2	2
α-helix	217-219	3
α-helix	220-223	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	328-335	8
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	454-462	9
β-strand	486-491	6	7
β-strand	502-507	6	7
α-helix	508-509	2
α-helix	510-514	5
β-strand	520-528	9	8
β-strand	534-539	6	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	570-572	3
β-strand	576-579	4	8

Chain B: 27 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	49	1	9
α-helix	54-63	10
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	153-156	4	10
α-helix	164-166	3
α-helix	167-172	6
α-helix	173-179	7
α-helix	185-188	4
β-strand	190-193	4	10
α-helix	203-207	5
β-strand	215-216	2	10
α-helix	217-223	7
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	288-292	5	13
β-strand	300	1	14
α-helix	303-314	12
β-strand	317-321	5	13
α-helix	328-335	8
β-strand	340-344	5	13
α-helix	347-354	8
α-helix	356	1
β-strand	360-365	6	13
α-helix	371-373	3
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	454-462	9
α-helix	477-479	3
β-strand	486-492	7	15
β-strand	502-507	6	15
α-helix	508-509	2
α-helix	510-514	5
β-strand	520-528	9	16
β-strand	533	1	17
β-strand	535-539	5	16
β-strand	543-546	4	15
β-strand	555-564	10	16
β-strand	568-569	2	16
β-strand	576-579	4	16

Chain C: 0 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	34
β-strand	4	1	35
β-strand	6	1	17
β-strand	9	1	34
β-strand	11	1	35

Chain D: 31 helices, 33 β-strands

Element	Residues	Length	Sheet
α-helix	53-58	6
α-helix	59-63	5
β-strand	64	1	18
β-strand	66-69	4	19
α-helix	74-76	3
β-strand	79-82	4	19
β-strand	84-87	4	18
β-strand	92-97	6	18
β-strand	102-104	3	19
α-helix	108-112	5
β-strand	117-118	2	20
β-strand	129-130	2	20
β-strand	132-136	5	18
α-helix	137-142	6
α-helix	144-146	3
β-strand	147-149	3	18
β-strand	153-156	4	19
α-helix	164-166	3
α-helix	167-172	6
α-helix	173-179	7
α-helix	185-188	4
β-strand	190-193	4	19
α-helix	203-208	6
α-helix	213-214	2
β-strand	215-216	2	19
α-helix	217-219	3
α-helix	220-223	4
β-strand	226-229	4	18
β-strand	232-234	3	19
β-strand	243-244	2	21
β-strand	252-253	2	21
α-helix	261-274	14
β-strand	288-293	6	22
β-strand	300	1	23
α-helix	303-314	12
β-strand	317-322	6	22
α-helix	328-336	9
β-strand	340-344	5	22
α-helix	347-354	8
α-helix	356	1
β-strand	360-365	6	22
α-helix	371-373	3
α-helix	376-381	6
β-strand	389-394	6	22
α-helix	398-400	3
β-strand	401-402	2	23
α-helix	409-411	3
α-helix	419-426	8
α-helix	431-433	3
α-helix	440-446	7
β-strand	449-450	2	23
α-helix	454-462	9
β-strand	486-491	6	24
β-strand	502-507	6	24
α-helix	508-509	2
α-helix	510-514	5
β-strand	520-528	9	25
β-strand	535-539	5	25
β-strand	543-546	4	24
α-helix	550-551	2
β-strand	555-564	10	25
β-strand	568-569	2	25
α-helix	575	1
β-strand	576-579	4	25

Chain E: 28 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	50	1	26
α-helix	54-63	10
β-strand	64	1	26
β-strand	66-69	4	27
α-helix	74-76	3
β-strand	79-82	4	27
β-strand	84-87	4	26
β-strand	92-97	6	26
β-strand	102-104	3	27
α-helix	108-112	5
β-strand	117-118	2	28
β-strand	129-130	2	28
β-strand	132-136	5	26
α-helix	137-142	6
α-helix	144-146	3
β-strand	147-149	3	26
β-strand	153-156	4	27
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	27
α-helix	203-206	4
β-strand	215-216	2	27
α-helix	217-221	5
β-strand	226-229	4	26
β-strand	232-234	3	27
β-strand	243-244	2	29
β-strand	252-253	2	29
α-helix	261-274	14
β-strand	288-292	5	30
β-strand	300	1	31
α-helix	303-313	11
β-strand	317-321	5	30
α-helix	328-336	9
β-strand	340-344	5	30
α-helix	347-354	8
α-helix	356	1
β-strand	360-365	6	30
α-helix	371-373	3
α-helix	376-381	6
β-strand	389-394	6	30
α-helix	398-400	3
β-strand	401-402	2	31
α-helix	409-411	3
α-helix	419-426	8
α-helix	431-433	3
α-helix	440-446	7
β-strand	449-450	2	31
α-helix	454-462	9
β-strand	486-491	6	32
β-strand	502-507	6	32
α-helix	508-509	2
α-helix	510-514	5
β-strand	520-528	9	33
β-strand	535-539	5	33
β-strand	543-546	4	32
β-strand	555-564	10	33
β-strand	568-569	2	33
α-helix	575	1
β-strand	576-579	4	33

Chain F: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
α-helix	-5-0	6
β-strand	2	1	36
β-strand	4	1	37
β-strand	9	1	36
β-strand	11	1	37

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2	A, B, D, E	protein	539	Bos taurus	Q5NDF2 (AlphaFold model)
mono-mannosyl peptide (379Man long peptide)	C, F	protein	23	Homo sapiens	Q14118 (AlphaFold model)

Sequence of entity 1 (A, B, D, E), FASTA

>7E9K_1 Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2 (chains A, B, D, E)
GAPPAPALRIDYPKALQILTEGGTHMVCTGRTHTDRLCRFKWLCYSSEAEEFIFFHGNAS
VMLPSLGSRRFQPALLDLSTVEDHNTQYFNFVELPAAALRFMPKPVFVPDVALIANRFNP
DNLMHVFHDDLLPLFYTLRQFPGLAREARLFFMEGWGEGAHFDLYKLLSPKQPLLRAQLK
ALGRLLCFSHAFVGLSKVTTWYQYGFVQPQGPKANILVSGNEIRQFAHFLMEKLNVSQAG
GPLGEEYILVFSRTQNRLILNEAELLLALAQEFQMKTVTVSLEDHAFADVVRLVSNASML
VSMHGAQLVTALFLPRGAAVVELFPYAVNPDHYTPYKTLATLPGMDLQYIAWQNTMPENT
VTHPERPWDQGGIAHLDRAEQARILQSREVPRHLCCRNPEWLFRIYQDTKVDIPSLIQTI
RRVVKGHPGPRKQKWTVSLYPGKVREARCQASVQGASEARLSVSWQIPWNLKYLKVREVK
YEVWLQEQGENTYVPYMLALQNHTFTENIKPFTTYLVWIRCIFNKTLLGPFADVLVCST

Sequence of entity 2 (C, F), FASTA

>7E9K_2 mono-mannosyl peptide (379Man long peptide) (chains C, F)
XTIRTRGAIIQTPTLGPIQPTRX

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	12
UDP	Uridine-5'-diphosphate	C9 H14 N2 O12 P2	4
MAN	alpha-D-mannopyranose	C6 H12 O6	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:

7E9L 2.1 Å, Crystal Structure of POMGNT2 in complex with UDP and mono-mannosyl peptide (379Man short…
7E9J 2.4 Å, Crystal Structure of POMGNT2 in complex with UDP

Browse structure collections

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