6UM2: M-6-P/IGFII Receptor and IGFII complex

Structure of M-6-P/IGFII Receptor and IGFII complex. Determined by electron microscopy at 4.32 Å resolution. Released 26 Feb 2020.

Method: Electron microscopy
Resolution: 4.32 Å
Organisms: Bos taurus, Homo sapiens
Chains: 2
Atoms: 13,094
Mol. weight: 283.99 kDa
Ligands: NAG
Released: 26 Feb 2020

Explore 6UM2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6UM2 contains 31 α-helices and 175 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: 27 helices, 173 β-strands

Element	Residues	Length	Sheet
β-strand	485-487	3	1
β-strand	492-494	3	1
β-strand	509	1	2
β-strand	524	1	2
β-strand	525	1	3
β-strand	546	1	3
β-strand	548-549	2	4
β-strand	554-555	2	4
β-strand	565-566	2	5
β-strand	571-574	4	5
β-strand	588	1	6
β-strand	590-595	6	5
β-strand	605-608	4	5
β-strand	615	1	6
β-strand	617-622	6	5
β-strand	631-632	2	7
β-strand	637	1	8
β-strand	648	1	8
α-helix	650-652	3
β-strand	659	1	9
β-strand	665-669	5	9
β-strand	684-690	7	9
β-strand	695-701	7	9
β-strand	707-708	2	7
β-strand	713-716	4	7
β-strand	722	1	10
β-strand	730	1	10
β-strand	732-737	6	7
β-strand	738	1	11
β-strand	748-753	6	7
β-strand	757-762	6	7
β-strand	763	1	11
α-helix	765-767	3
α-helix	769-774	6
β-strand	785	1	12
β-strand	802-806	5	13
β-strand	815-819	5	13
β-strand	837-840	4	13
β-strand	854-858	5	13
β-strand	864-865	2	14
β-strand	873	1	15
β-strand	875-876	2	14
β-strand	882-883	2	16
β-strand	891-892	2	16
β-strand	895	1	15
β-strand	896	1	14
β-strand	898-899	2	15
β-strand	911-915	5	15
β-strand	920-924	5	15
β-strand	932	1	12
α-helix	935-937	3
β-strand	943-946	4	17
β-strand	951-954	4	17
α-helix	956-958	3
β-strand	964-965	2	18
β-strand	974-975	2	18
β-strand	1015	1	19
β-strand	1019-1021	3	20
β-strand	1027-1029	3	20
β-strand	1033	1	19
α-helix	1036-1037	2
β-strand	1051	1	21
β-strand	1082	1	21
β-strand	1095	1	22
β-strand	1103	1	22
β-strand	1115-1117	3	23
β-strand	1118	1	24
α-helix	1125-1127	3
β-strand	1128-1131	4	23
β-strand	1151-1153	3	23
β-strand	1158-1160	3	23
β-strand	1177-1180	4	24
β-strand	1193-1196	4	24
β-strand	1197-1199	3	25
β-strand	1207-1212	6	24
β-strand	1215-1219	5	24
β-strand	1220-1222	3	25
α-helix	1223-1225	3
β-strand	1230-1232	3	26
β-strand	1234	1	27
β-strand	1237	1	27
β-strand	1239	1	28
β-strand	1246	1	28
β-strand	1257-1259	3	29
β-strand	1265-1268	4	29
α-helix	1287-1288	2
β-strand	1290-1293	4	29
β-strand	1303	1	29
α-helix	1305-1307	3
β-strand	1312-1314	3	26
β-strand	1317-1322	6	26
β-strand	1327	1	30
α-helix	1332	1
β-strand	1333	1	30
α-helix	1334	1
β-strand	1336-1342	7	26
β-strand	1346-1352	7	26
β-strand	1360-1366	7	26
β-strand	1379	1	31
β-strand	1389	1	31
β-strand	1401	1	32
β-strand	1411-1414	4	32
α-helix	1428-1430	3
β-strand	1435-1438	4	32
β-strand	1444-1445	2	32
β-strand	1448	1	33
α-helix	1452-1454	3
β-strand	1462-1464	3	34
β-strand	1465	1	33
β-strand	1469	1	35
β-strand	1476	1	35
β-strand	1478-1484	7	34
α-helix	1494	1
β-strand	1495-1496	2	34
β-strand	1500	1	34
β-strand	1504-1510	7	34
β-strand	1526-1528	3	36
β-strand	1535-1537	3	36
β-strand	1548-1550	3	37
β-strand	1556-1559	4	37
β-strand	1574-1575	2	37
β-strand	1582	1	37
β-strand	1584-1585	2	38
β-strand	1591-1592	2	39
β-strand	1597-1601	5	39
β-strand	1602-1603	2	38
β-strand	1606	1	40
α-helix	1607	1
β-strand	1614	1	40
β-strand	1616-1621	6	39
β-strand	1623	1	41
β-strand	1638-1639	2	39
β-strand	1644-1647	4	39
β-strand	1651	1	41
β-strand	1664-1665	2	42
β-strand	1668-1669	2	42
β-strand	1682-1684	3	43
α-helix	1685-1686	2
β-strand	1699-1701	3	43
α-helix	1706-1709	4
β-strand	1721-1723	3	43
β-strand	1731-1734	4	43
β-strand	1735-1736	2	44
α-helix	1740	1
β-strand	1741	1	45
α-helix	1742	1
β-strand	1750	1	45
β-strand	1751-1754	4	44
β-strand	1768-1771	4	44
β-strand	1774-1775	2	46
β-strand	1784-1789	6	44
β-strand	1793-1798	6	44
β-strand	1799-1800	2	46
α-helix	1805-1806	2
β-strand	1814	1	47
β-strand	1825	1	47
α-helix	1826-1829	4
β-strand	1837-1838	2	48
β-strand	1841-1842	2	48
β-strand	1844-1845	2	49
β-strand	1862	1	50
β-strand	1864-1865	2	49
α-helix	1872-1873	2
β-strand	1874	1	49
β-strand	1876	1	51
β-strand	1877	1	50
α-helix	1878-1880	3
β-strand	1882-1886	5	52
β-strand	1891-1896	6	52
β-strand	1898	1	51
β-strand	1901	1	53
α-helix	1902-1904	3
β-strand	1905	1	54
β-strand	1916-1918	3	55
β-strand	1921-1923	3	55
β-strand	1927	1	56
β-strand	1935-1937	3	56
β-strand	1941	1	55
β-strand	1948-1950	3	56
β-strand	1952	1	54
β-strand	1957	1	53
β-strand	1959-1963	5	52
β-strand	1966	1	57
β-strand	1977-1981	5	52
β-strand	1985-1988	4	52
β-strand	1992	1	57
β-strand	2007	1	58
β-strand	2010	1	58
β-strand	2025-2028	4	59
β-strand	2031-2034	4	59
β-strand	2054-2056	3	60
β-strand	2057	1	59
α-helix	2062-2063	2
β-strand	2064-2066	3	60
β-strand	2074-2076	3	61
β-strand	2081-2083	3	61
β-strand	2098-2105	8	62
β-strand	2114	1	62
β-strand	2123-2130	8	62
α-helix	2131-2133	3

Chain B: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	13-20	8
α-helix	22-24	3
β-strand	26	1	63
α-helix	43-46	4
α-helix	55-58	4
β-strand	60	1	63

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cation-independent mannose-6-phosphate receptor	A	protein	2499	Bos taurus	P08169 (AlphaFold model)
Insulin-like growth factor II	B	protein	68	Homo sapiens	P01344 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6UM2_1 Cation-independent mannose-6-phosphate receptor (chains A)
MEAAAGRSSHLGPAPAGRPPRCPLLLQLQLLLLLLLLPPGWVPGAAGTQGAEFPELCSYT
WEAVDTKNNMLYKINICGNMGVAQCGPSSAVCMHDLKTDSFHSVGDSLLKTASRSLLEFN
TTVNCKQQNHKIQSSITFLCGKTLGTPEFVTATDCVHYFEWRTTAACKKNIFKANKEVPC
YAFDRELKKHDLNPLIKTSGAYLVDDSDPDTSLFINVCRDIEVLRASSPQVRVCPTGAAA
CLVRGDRAFDVGRPQEGLKLVSNDRLVLSYVKEGAGQPDFCDGHSPAVTITFVCPSERRE
GTIPKLTAKSNCRFEIEWVTEYACHRDYLESRSCSLSSAQHDVAVDLQPLSRVEASDSLF
YTSEADEYTYYLSICGGSQAPICNKKDAAVCQVKKADSTQVKVAGRPQNLTLRYSDGDLT
LIYFGGEECSSGFQRMSVINFECNQTAGNNGRGAPVFTGEVDCTYFFTWDTKYACVHEKE
ALLCGVSDGKQRFDLSALARHSELEQNWEAVDGSQREAEKKHFFINICHRVLQTGQARGC
PEDAAVCAVDKNGSKNLGRFISSPTREKGNIQLSYSDGDECGGGQKIITNITLMCKPGDL
ESAPVLTTSRADGCFYEFEWRTAAACVLSRTEGDNCTVFDSQAGFSFDLTPLTKKDAYKV
ETDKYEFHINVCGPVSVGACPPDSGACQVSRSDRKSWNLGRSNAKLSYYDGMIQLTYRDG
TPYNNEKRTPRATLITFLCDRDAGVGFPEYQEEDNSTYNFRWYTSYACPEEPLECIVTDP
VTLDQYDLSRLAKSEGGPGGNWYSLDNGGARSTWRKYYINVCRPLNPVPGCDRYASACQM
KYQGEQGSYSETVSISNLGVAKTGPMVEDSGSLLLEYVNGSACTTSDQRRTTYTTRIHLV
CSTGSLYTHPIFSLNWECVVSFLWNTAAACPIRITTDIDQVCSIKDPNSGYVFDLNPLNN
SRGYVVLGIGKTFLFNVCGDMPACGTLDGKPASGCEAEVQMDDMKTLKPGRLVGLEKSLQ
LSTEGFITLNYTGLPSHPNGRADAFIIRFVCNDDVYPGTPKFLHQDIDSSLGIRDTFFEF
ETALACVPSPVDCQVTDPAGNEYDLSGLSKARKPWTAVDTFDEGKKRTFYLSVCTPLPYI
PGCHGTAVGCCLVTEDSKLNLGVVQISPQVGANGSLSLVYVNGDKCKNQRFSTRINLECA
HTTGSPTFQLQNDCEYVFLWRTVEACPVVRAEGDYCEVRDPRHGNLYNLIPLGLNDTVVR
AGEYTYYFRVCGELTSGVCPTSDKSKVISSCQEKRGPQGFQKVAGLFNQKLTYENGVLKM
NYTGGDTCHKVYQRSTTIFFYCDRSTQAPVFLQETSDCSYLFEWRTQYACPPYDLTECSF
KNEAGETYDLSSLSRYSDNWEAVTGTGSTEHYLINVCKSLSPQAGSDPCPPEAAVCLLGG
PKPVNLGRVRDSPQWSQGLTLLKYVDGDLCPDQIRKKSTTIRFTCSESHVNSRPMFISAV
EDCEYTFSWPTAAACAVKSNVHDDCQVTNPATGHLFDLSSLSGRAGFTAAYSEKGLVYLS
VCGDNENCANGVGACFGQTRISVGKASKRLTYVDQVLQLVYEGGSPCPSKTGLSYKSVIS
FVCRPEVGPTNRPMLISLDKRTCTLFFSWHTPLACEQTTECSVRNGSSLIDLSPLIHRTG
GYEAYDESEDDGSDTSPDFYINICQPLNPMHGLACPAGTAVCKVPVDGPPIDIGRVAGPP
ILNPIANEVYLNFESSTPCLADRHFNYTSLITFHCKRGVSMGTPKLLRTSVCDFVFEWET
PLVCPDEVKTDGCSLTDEQLYYSFNLSSLSKSTFKVTRGPHTYSVGVCTAAAGLDEGGCK
DGAVCLLSGSKGASFGRLASMKLDYRHQDEAVILSYANGDTCPPETEDGEPCVFPFVFNG
KSYEECVVESRARLWCATTANYDRDHEWGFCKHSTSHRTSVIIFKCDEDADVGRPQVFSE
VRGCEVTFEWKTKVVCPPKKMECKFVQKHRTYDLRLLSSLTGSWSFVHNGASYYINLCQK
IYKGPQDCSERASVCKKSTSGEVQVLGLVHTQKLDVVDDRVIVTYSKGHYCGDNKTASAV
IELTCAKTVGRPSFTRFDVDSCTYHFSWDSRAACAVKPQEVQMVNGTITNPANGRSFSLG
DIYFKRFSASGDVRTNGDRYIYEIQLSSITGSSSPACSGASICQRKANDQHFSRKVGTSN
QTRYYVQDGDLDVVFTSSSKCGKDKTKSVSSTIFFHCDPLVKDGIPEFSHETADCQYLFS
WHTSAVCPLGAGFDEEIAGDDAQEHKGLSERSQAVGAVLSLLLVALTACLLTLLLYKKER
REMVMSRLTNCCRRSANVSYKYSKVNKEEEADENETEWLMEEIQPPAPRPGKEGQENGHV
AAKSVRAADTLSALHGDEQDSEDEVLTLPEVKVRPPGRAPGAEGGPPLRPLPRKAPPPLR
ADDRVGLVRGEPARRGRPRAAATPISTFHDDSDEDLLHV

Sequence of entity 2 (B), FASTA

>6UM2_2 Insulin-like growth factor II (chains B)
MAYRPSETLCGGELVDTLQFVCGDRGFYFSRPASRVSRRSRGIVEECCFRSCDLALLETY
CATPAKSE

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	7

Primary citation

Marked structural rearrangement of mannose 6-phosphate/IGF2 receptor at different pH environments. Wang, R., Qi, X., Schmiege, P. et al. Sci Adv (2020) 6:eaaz1466. DOI 10.1126/sciadv.aaz1466

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
1SYO 2.2 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
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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