6Z32: Cation-independent mannose-6-phosphate receptor

Human cation-independent mannose 6-phosphate/IGF2 receptor domains 7-11. Determined by X-ray diffraction at 3.47 Å resolution. Released 19 Aug 2020.

Method: X-ray diffraction
Resolution: 3.47 Å
Organism: Homo sapiens
Chains: 2
Atoms: 10,549
Mol. weight: 164.57 kDa
Ligands: NAG
Released: 19 Aug 2020

Explore 6Z32 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6Z32 contains 40 α-helices and 148 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: 21 helices, 73 β-strands

Element	Residues	Length	Sheet
β-strand	935-937	3	1
β-strand	944-946	3	1
α-helix	948-950	3
β-strand	956-959	4	2
β-strand	964-967	4	2
α-helix	983-984	2
β-strand	986-989	4	2
β-strand	1002-1005	4	2
β-strand	1008-1013	6	3
β-strand	1019-1029	11	3
β-strand	1032-1042	11	3
β-strand	1048-1059	12	3
α-helix	1060-1062	3
β-strand	1064-1073	10	3
β-strand	1085-1087	3	4
β-strand	1093-1095	3	4
α-helix	1097-1100	4
β-strand	1106-1111	6	5
β-strand	1117-1122	6	5
α-helix	1127-1130	4
β-strand	1131	1	6
β-strand	1134	1	6
β-strand	1139	1	7
β-strand	1141-1145	5	5
β-strand	1148-1151	4	5
β-strand	1154	1	7
β-strand	1160	1	8
β-strand	1167-1171	5	8
β-strand	1172	1	7
α-helix	1174	1
β-strand	1176-1177	2	9
β-strand	1180-1181	2	9
β-strand	1183-1190	8	8
β-strand	1198-1203	6	8
β-strand	1206-1213	8	8
α-helix	1214-1216	3
α-helix	1218-1219	2
β-strand	1221-1224	4	10
β-strand	1228-1230	3	11
β-strand	1237-1239	3	11
α-helix	1241-1244	4
β-strand	1248-1251	4	12
β-strand	1255-1259	5	12
β-strand	1279-1285	7	12
α-helix	1286	1
β-strand	1292-1297	6	12
β-strand	1302-1305	4	10
β-strand	1308-1313	6	10
β-strand	1318-1319	2	13
β-strand	1323-1324	2	13
β-strand	1326-1332	7	10
α-helix	1338-1340	3
β-strand	1341-1345	5	10
β-strand	1350-1356	7	10
α-helix	1358-1360	3
β-strand	1366	1	14
β-strand	1370-1372	3	15
β-strand	1378-1380	3	15
α-helix	1382-1384	3
β-strand	1391-1392	2	16
β-strand	1394	1	17
β-strand	1403-1405	3	16
β-strand	1409	1	14
α-helix	1410-1413	4
α-helix	1419-1421	3
β-strand	1426-1428	3	16
β-strand	1435-1436	2	16
β-strand	1439-1440	2	17
β-strand	1445-1447	3	17
β-strand	1450-1456	7	17
β-strand	1460	1	18
α-helix	1461	1
β-strand	1467	1	18
β-strand	1469-1476	8	17
α-helix	1485	1
β-strand	1486-1491	6	17
β-strand	1495-1502	8	17
α-helix	1503-1505	3
β-strand	1517-1519	3	19
α-helix	1525	1
β-strand	1526-1528	3	19
α-helix	1530-1532	3
β-strand	1538-1541	4	20
β-strand	1547-1550	4	20
β-strand	1563	1	21
β-strand	1565-1566	2	20
β-strand	1573	1	20
β-strand	1576	1	21
β-strand	1582-1584	3	22
β-strand	1587-1592	6	22
β-strand	1607-1614	8	22
β-strand	1625-1630	6	22
β-strand	1635-1642	8	22
α-helix	1643-1645	3

Chain B: 19 helices, 75 β-strands

Element	Residues	Length	Sheet
β-strand	935-937	3	23
β-strand	944-946	3	23
α-helix	948-950	3
β-strand	956-958	3	24
β-strand	965-967	3	24
α-helix	974-976	3
α-helix	982-984	3
β-strand	986-988	3	24
β-strand	1002-1005	4	24
β-strand	1008-1013	6	25
β-strand	1019-1027	9	25
β-strand	1033-1042	10	25
β-strand	1048-1059	12	25
α-helix	1060-1062	3
β-strand	1064-1073	10	25
β-strand	1085-1087	3	26
β-strand	1093-1095	3	26
α-helix	1097-1101	5
β-strand	1106-1109	4	27
β-strand	1119-1122	4	27
α-helix	1127-1130	4
β-strand	1139	1	28
β-strand	1141	1	27
β-strand	1144-1145	2	27
β-strand	1148-1149	2	27
β-strand	1154	1	28
β-strand	1167-1171	5	29
β-strand	1172	1	28
β-strand	1176-1177	2	30
β-strand	1180-1181	2	30
β-strand	1183-1190	8	29
β-strand	1198-1203	6	29
β-strand	1206-1213	8	29
β-strand	1221-1222	2	31
β-strand	1228-1230	3	32
β-strand	1237-1239	3	32
α-helix	1241-1244	4
β-strand	1248-1252	5	33
β-strand	1255-1259	5	33
β-strand	1279-1284	6	33
β-strand	1296-1297	2	33
β-strand	1303-1305	3	31
β-strand	1308-1313	6	31
β-strand	1318-1319	2	34
β-strand	1323-1324	2	34
β-strand	1326-1332	7	31
β-strand	1337	1	35
α-helix	1338-1340	3
β-strand	1341-1345	5	31
β-strand	1350-1356	7	31
β-strand	1357	1	35
α-helix	1358-1360	3
β-strand	1366	1	36
β-strand	1370-1372	3	37
β-strand	1378-1380	3	37
α-helix	1382-1384	3
β-strand	1391-1392	2	38
α-helix	1393	1
β-strand	1394	1	39
β-strand	1403-1405	3	38
β-strand	1409	1	36
α-helix	1410-1414	5
α-helix	1419-1421	3
β-strand	1424	1	39
β-strand	1426-1428	3	38
β-strand	1436	1	38
β-strand	1439-1440	2	39
β-strand	1445-1447	3	39
β-strand	1450-1456	7	39
β-strand	1460	1	40
α-helix	1461	1
β-strand	1467	1	40
β-strand	1469-1476	8	39
α-helix	1485	1
β-strand	1486-1491	6	39
β-strand	1495-1502	8	39
α-helix	1503-1505	3
β-strand	1517-1519	3	41
α-helix	1525	1
β-strand	1526-1528	3	41
α-helix	1530-1532	3
β-strand	1538-1539	2	42
β-strand	1549-1550	2	42
β-strand	1563	1	43
β-strand	1565	1	42
β-strand	1576	1	43
β-strand	1582-1584	3	44
β-strand	1587-1592	6	44
β-strand	1597	1	45
β-strand	1605	1	45
β-strand	1607-1614	8	44
β-strand	1625-1630	6	44
β-strand	1635-1642	8	44
α-helix	1643-1645	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cation-independent mannose-6-phosphate receptor	A, B	protein	737	Homo sapiens	P11717 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6Z32_1 Cation-independent mannose-6-phosphate receptor (chains A, B)
ETGQLKHHHHHHEFTTDTDQACSIRDPNSGFVFNLNPLNSSQGYNVSGIGKIFMFNVCGT
MPVCGTILGKPASGCEAETQTEELKNWKPARPVGIEKSLQLSTEGFITLTYKGPLSAKGT
ADAFIVRFVCNDDVYSGPLKFLHQDIDSGQGIRNTYFEFETALACVPSPVDCQVTDLAGN
EYDLTGLSTVRKPWTAVDTSVDGRKRTFYLSVCNPLPYIPGCQGSAVGSCLVSEGNSWNL
GVVQMSPQAAANGSLSIMYVNGDKCGNQRFSTRITFECAQISGSPAFQLQDGCEYVFIWR
TVEACPVVRVEGDNCEVKDPRHGNLYDLKPLGLNDTIVSAGEYTYYFRVCGKLSSDVCPT
SDKSKVVSSCQEKREPQGFHKVAGLLTQKLTYENGLLKMNFTGGDTCHKVYQRSTAIFFY
CDRGTQRPVFLKETSDCSYLFEWRTQYACPPFDLTECSFKDGAGNSFDLSSLSRYSDNWE
AITGTGDPEHYLINVCKSLAPQAGTEPCPPEAAACLLGGSKPVNLGRVRDGPQWRDGIIV
LKYVDGDLCPDGIRKKSTTIRFTCSESQVNSRPMFISAVEDCEYTFAWPTATACPMKSNE
HDDCQVTNPSTGHLFDLSSLSGRAGFTAAYSEKGLVYMSICGENENCPPGVGACFGQTRI
SVGKANKRLRYVDQVLQLVYKDGSPCPSKSGLSYKSVISFVCRPEAGPTNRPMLISLDKQ
TCTLFFSWHTPLACEQA

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3

Water and common crystallization additives (SO4) are not listed.

Primary citation

Structure of the Human Cation-Independent Mannose 6-Phosphate/IGF2 Receptor Domains 7-11 Uncovers the Mannose 6-Phosphate Binding Site of Domain 9. Bochel, A.J., Williams, C., McCoy, A.J. et al. Structure (2020) 28:1300-1312.e5. DOI 10.1016/j.str.2020.08.002 · PubMed

Other PDB entries of the same protein (UniProt P11717 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1GP0 1.4 Å, Human IGF2R domain 11
6Z30 1.5 Å, Human cation-independent mannose 6-phosphate/ IGF2 receptor domains 9-10
1E6F 1.75 Å, Human MIR-receptor, repeat 11
1GQB 1.8 Å, Human mir-receptor, repeat 11
1GP3 1.95 Å, Human IGF2R domain 11
1JWG 2.0 Å, VHS Domain of human GGA1 complexed with cation-independent M6PR C-terminal Peptide
6N5X 2.05 Å, Crystal structure of the SNX5 PX domain in complex with the CI-MPR (space group P212121…
6N5Y 2.26 Å, Crystal structure of the SNX5 PX domain in complex with the CI-MPR (space group P212121…
1LF8 2.3 Å, Complex of GGA3-VHS Domain and CI-MPR C-terminal Phosphopeptide
1JPL 2.4 Å, GGA3 VHS domain complexed with C-terminal peptide from cation-independent mannose…
6V02 2.46 Å, N-terminal 5 domains of CI-MPR
6P8I 2.54 Å, N-terminal 5 domains of IGFIIR

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