1SYO: N-terminal 3 domains of CI-MPR

N-terminal 3 domains of CI-MPR bound to mannose 6-phosphate. Determined by X-ray diffraction at 2.2 Å resolution. Released 29 Jun 2004.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Bos taurus
Chains: 2
Atoms: 6,891
Mol. weight: 97.19 kDa
Ligands: M6P, NAG
Released: 29 Jun 2004

Explore 1SYO in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1SYO contains 38 α-helices and 80 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: 22 helices, 40 β-strands

Element	Residues	Length	Sheet
α-helix	10-12	3
β-strand	17-21	5	1
β-strand	26-30	5	1
α-helix	39-41	3
β-strand	45-51	7	1
β-strand	56-62	7	1
α-helix	63-65	3
β-strand	66-68	3	2
β-strand	72-80	9	2
β-strand	87-96	10	2
β-strand	103-108	6	2
β-strand	112-119	8	2
α-helix	120-122	3
α-helix	126-128	3
β-strand	133	1	3
β-strand	137-139	3	4
β-strand	145-147	3	4
α-helix	149-151	3
β-strand	156	1	5
β-strand	158-159	2	6
β-strand	161	1	7
β-strand	167-171	5	6
β-strand	175	1	3
β-strand	178	1	5
α-helix	191	1
β-strand	196-200	5	6
β-strand	205-206	2	6
β-strand	209-210	2	7
β-strand	215-216	2	7
β-strand	222-227	6	7
α-helix	235-237	3
α-helix	240-242	3
β-strand	243-249	7	7
α-helix	260	1
β-strand	261-264	4	7
α-helix	266-268	3
β-strand	269-275	7	7
α-helix	277-279	3
α-helix	282-285	4
β-strand	286-287	2	8
β-strand	291-292	2	9
α-helix	294-297	4
β-strand	301-302	2	9
α-helix	304-307	4
β-strand	317-320	4	10
β-strand	324-328	5	10
α-helix	333-336	4
α-helix	337-339	3
β-strand	346-350	5	10
β-strand	353-359	7	10
β-strand	362-371	10	8
β-strand	374-380	7	8
α-helix	383	1
β-strand	384	1	11
α-helix	385	1
α-helix	389	1
β-strand	390	1	11
α-helix	391	1
β-strand	392-399	8	8
β-strand	411-416	6	8
β-strand	420-427	8	8
α-helix	428-430	3

Chain B: 16 helices, 40 β-strands

Element	Residues	Length	Sheet
α-helix	1010-1012	3
β-strand	1017-1021	5	12
β-strand	1026-1030	5	12
β-strand	1045-1051	7	12
β-strand	1056-1062	7	12
β-strand	1066-1069	4	13
β-strand	1072-1076	5	13
β-strand	1089-1096	8	13
β-strand	1103-1108	6	13
β-strand	1112-1119	8	13
α-helix	1120-1122	3
β-strand	1133	1	14
β-strand	1137-1139	3	15
β-strand	1145-1147	3	15
α-helix	1149-1151	3
β-strand	1156	1	16
β-strand	1158-1160	3	17
β-strand	1161	1	18
β-strand	1167-1171	5	17
β-strand	1175	1	14
β-strand	1178	1	16
α-helix	1185-1188	4
β-strand	1196-1200	5	17
β-strand	1203-1208	6	17
β-strand	1209-1210	2	18
β-strand	1215-1218	4	18
β-strand	1221-1227	7	18
α-helix	1240-1242	3
β-strand	1243-1249	7	18
β-strand	1261-1265	5	18
β-strand	1269-1275	7	18
α-helix	1277-1279	3
α-helix	1282-1284	3
β-strand	1286-1287	2	19
β-strand	1291-1292	2	20
α-helix	1294-1297	4
β-strand	1301-1302	2	20
α-helix	1304-1307	4
β-strand	1317-1320	4	21
β-strand	1324-1328	5	21
α-helix	1333-1336	4
α-helix	1337-1339	3
β-strand	1346-1350	5	21
β-strand	1357-1359	3	21
β-strand	1366-1371	6	19
β-strand	1374-1379	6	19
α-helix	1383	1
β-strand	1384	1	22
α-helix	1385	1
α-helix	1389	1
β-strand	1390	1	22
α-helix	1391	1
β-strand	1392-1399	8	19
β-strand	1412-1417	6	19
β-strand	1420-1427	8	19
α-helix	1428-1430	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
cation-independent mannose 6-phosphate receptor	A, B	protein	432	Bos taurus	P08169 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>1SYO_1 cation-independent mannose 6-phosphate receptor (chains A, B)
AAGTQGAEFPELCSYTWEAVDTKNNMLYKINICGNMGVAQCGPSSAVCMHDLKTDSFHSV
GDSLLKTASRSLLEFNTTVNCKQQNHKIQSSITFLCGKTLGTPEFVTATDCVHYFEWRTT
AACKKNIFKANKEVPCYAFDRELKKHDLNPLIKTSGAYLVDDSDPDTSLFINVCRDIEVL
RASSPQVRVCPTGAAACLVRGDRAFDVGRPQEGLKLVSNDRLVLSYVKEGAGQPDFCDGH
SPAVTITFVCPSERREGTIPKLTAKSNCRFEIEWVTEYACHRDYLESRSCSLSSAQHDVA
VDLQPLSRVEASDSLFYTSEADEYTYYLSICGGSQAPICNKKDAAVCQVKKADSTQVKVA
GRPQNLTLRYSDGDLTLIYFGGEECSSGFQRMSVINFECNQTAGNNGRGAPVFTGEVDCT
YFFTWDTKYACV

Ligands and cofactors

ID	Name	Formula	Copies
M6P	6-O-phosphono-alpha-D-mannopyranose	C6 H13 O9 P	2
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3

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

Primary citation

The N-terminal carbohydrate recognition site of the cation-independent mannose 6-phosphate receptor. Olson, L.J., Dahms, N.M., Kim, J.-J.P. J Biol Chem (2004) 279:34000-34009. DOI 10.1074/jbc.M404588200 · PubMed

Other PDB entries of the same protein (UniProt P08169 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1Q25 1.8 Å, Crystal structure of N-terminal 3 domains of CI-MPR
1SZ0 2.1 Å, N-terminal 3 domains of CI-MPR bound to mannose 6-phosphate
6UM1 3.46 Å, Structure of M-6-P/IGFII Receptor at pH 4.5
6UM2 4.32 Å, Structure of M-6-P/IGFII Receptor and IGFII complex
2KVA SOLUTION STRUCTURE OF CI-MPR ligand-free domain 5
2KVB Solution structure of CI-MPR domain 5 bound to N-acetylglucosaminyl…

Browse structure collections

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