7E9L: POMGNT2

Crystal Structure of POMGNT2 in complex with UDP and mono-mannosyl peptide (379Man short peptide). Determined by X-ray diffraction at 2.1 Å resolution. Released 5 May 2021.

Method: X-ray diffraction
Resolution: 2.1 Å
Organisms: Bos taurus, Homo sapiens
Chains: 3
Atoms: 9,056
Mol. weight: 127.1 kDa
Ligands: MAN, UDP, NAG
Released: 5 May 2021

Explore 7E9L in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7E9L contains 62 α-helices and 66 β-strands across 3 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: 32 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	173-181	9
α-helix	185-188	4
α-helix	189	1
β-strand	190-193	4	2
α-helix	203-208	6
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	328-336	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	376-382	7
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
α-helix	477-479	3
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	534-539	6	8
β-strand	543-546	4	7
β-strand	555-564	10	8
β-strand	568-572	5	8
α-helix	573	1
α-helix	575	1
β-strand	576-579	4	8

Chain B: 29 helices, 33 β-strands

Element	Residues	Length	Sheet
α-helix	53-58	6
α-helix	59-63	5
β-strand	64	1	9
β-strand	66-70	5	10
α-helix	74-76	3
β-strand	78-82	5	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	203-208	6
α-helix	213-214	2
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	328-336	9
β-strand	340-344	5	13
α-helix	347-354	8
α-helix	356	1
β-strand	360-365	6	13
α-helix	371-373	3
α-helix	376-381	6
β-strand	389-394	6	13
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	480-482	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	535-539	5	16
β-strand	543-546	4	15
β-strand	555-564	10	16
β-strand	568-572	5	16
α-helix	575	1
β-strand	576-579	4	16

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-10	9

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)
mono-mannosyl peptide (379Man short peptide)	C	protein	14	Homo sapiens	Q14118 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>7E9L_1 Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2 (chains A, B)
GAPPAPALRIDYPKALQILTEGGTHMVCTGRTHTDRLCRFKWLCYSSEAEEFIFFHGNAS
VMLPSLGSRRFQPALLDLSTVEDHNTQYFNFVELPAAALRFMPKPVFVPDVALIANRFNP
DNLMHVFHDDLLPLFYTLRQFPGLAREARLFFMEGWGEGAHFDLYKLLSPKQPLLRAQLK
ALGRLLCFSHAFVGLSKVTTWYQYGFVQPQGPKANILVSGNEIRQFAHFLMEKLNVSQAG
GPLGEEYILVFSRTQNRLILNEAELLLALAQEFQMKTVTVSLEDHAFADVVRLVSNASML
VSMHGAQLVTALFLPRGAAVVELFPYAVNPDHYTPYKTLATLPGMDLQYIAWQNTMPENT
VTHPERPWDQGGIAHLDRAEQARILQSREVPRHLCCRNPEWLFRIYQDTKVDIPSLIQTI
RRVVKGHPGPRKQKWTVSLYPGKVREARCQASVQGASEARLSVSWQIPWNLKYLKVREVK
YEVWLQEQGENTYVPYMLALQNHTFTENIKPFTTYLVWIRCIFNKTLLGPFADVLVCST

Sequence of entity 2 (C), FASTA

>7E9L_2 mono-mannosyl peptide (379Man short peptide) (chains C)
XQTPTLGPIQPTRX

Ligands and cofactors

ID	Name	Formula	Copies
MAN	alpha-D-mannopyranose	C6 H12 O6	1
UDP	Uridine-5'-diphosphate	C9 H14 N2 O12 P2	2
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	5

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…
7E9J 2.4 Å, Crystal Structure of POMGNT2 in complex with UDP

Browse structure collections

About this viewer

MolViewer shows 7E9L directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.