6UM1: M-6-P/IGFII Receptor at pH 4.5

Structure of M-6-P/IGFII Receptor at pH 4.5. Determined by electron microscopy at 3.46 Å resolution. Released 26 Feb 2020.

Method: Electron microscopy
Resolution: 3.46 Å
Organism: Bos taurus
Chains: 1
Atoms: 17,134
Mol. weight: 276.5 kDa
Ligands: NAG
Released: 26 Feb 2020

Explore 6UM1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6UM1 contains 34 α-helices and 229 β-strands across 1 chain. 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: 34 helices, 229 β-strands

Element	Residues	Length	Sheet
β-strand	61-63	3	1
β-strand	70-74	5	1
β-strand	89	1	2
β-strand	91-95	5	1
β-strand	101-103	3	1
β-strand	106	1	2
α-helix	107-109	3
β-strand	110-112	3	3
β-strand	116-124	9	3
α-helix	125	1
β-strand	131-140	10	3
β-strand	149-152	4	3
β-strand	156-163	8	3
β-strand	177	1	4
β-strand	181-183	3	5
β-strand	189-191	3	5
α-helix	193-195	3
β-strand	202-204	3	6
β-strand	205	1	7
β-strand	213-215	3	6
β-strand	219	1	4
α-helix	235	1
β-strand	243	1	8
β-strand	248	1	8
β-strand	254	1	7
β-strand	259	1	7
β-strand	266-271	6	7
α-helix	284-286	3
β-strand	287-293	7	7
β-strand	304-308	5	7
β-strand	313-319	7	7
α-helix	321-323	3
α-helix	325-327	3
β-strand	328-331	4	9
α-helix	348-350	3
β-strand	361-363	3	10
β-strand	370-372	3	10
β-strand	390-393	4	10
β-strand	401-405	5	10
β-strand	410-415	6	9
β-strand	418-423	6	9
β-strand	428	1	11
β-strand	434	1	11
β-strand	436-443	8	9
α-helix	448-451	4
β-strand	455-457	3	9
β-strand	461	1	9
β-strand	464-471	8	9
β-strand	485-488	4	12
β-strand	491-494	4	12
β-strand	510	1	13
β-strand	511-512	2	14
β-strand	522-525	4	13
α-helix	531-532	2
β-strand	546-549	4	13
β-strand	555-556	2	13
β-strand	559	1	15
β-strand	565-567	3	14
β-strand	570-575	6	14
β-strand	576	1	15
β-strand	580	1	16
β-strand	586	1	16
β-strand	588	1	17
β-strand	589-595	7	14
β-strand	605-606	2	14
β-strand	615	1	17
β-strand	618-622	5	14
β-strand	631-633	3	18
β-strand	637-639	3	19
β-strand	646-648	3	19
α-helix	650-652	3
β-strand	660-661	2	20
β-strand	665-669	5	20
β-strand	684	1	21
β-strand	686-690	5	20
β-strand	696-698	3	20
β-strand	701	1	21
β-strand	706-709	4	18
β-strand	712-717	6	18
β-strand	722	1	22
β-strand	730	1	22
β-strand	733-739	7	18
β-strand	748-750	3	18
β-strand	758-764	7	18
β-strand	777-778	2	23
β-strand	785-786	2	23
β-strand	802-804	3	24
β-strand	815-819	5	24
α-helix	824-826	3
α-helix	832	1
β-strand	837-842	6	24
β-strand	853-854	2	24
β-strand	859	1	24
β-strand	860	1	25
β-strand	866-867	2	26
α-helix	869-871	3
β-strand	873-877	5	26
β-strand	878	1	25
β-strand	882	1	27
β-strand	892	1	27
β-strand	894-901	8	26
β-strand	907	1	28
β-strand	911	1	26
β-strand	915	1	26
β-strand	919-920	2	26
β-strand	923-926	4	26
α-helix	931-932	2
β-strand	937	1	29
β-strand	943-945	3	30
β-strand	952-954	3	30
α-helix	956-958	3
β-strand	964-966	3	31
β-strand	973-975	3	31
β-strand	987	1	32
β-strand	990	1	32
β-strand	1015-1016	2	33
β-strand	1019-1021	3	29
β-strand	1027-1030	4	29
β-strand	1032-1033	2	33
β-strand	1036	1	34
β-strand	1042	1	34
β-strand	1043	1	35
β-strand	1046-1050	5	29
α-helix	1063-1064	2
β-strand	1065-1067	3	35
β-strand	1074-1076	3	35
β-strand	1080-1081	2	29
α-helix	1087-1090	4
β-strand	1091	1	28
β-strand	1094-1095	2	36
β-strand	1102	1	37
β-strand	1103-1104	2	36
α-helix	1106-1109	4
β-strand	1118	1	38
β-strand	1128-1129	2	39
β-strand	1151	1	40
β-strand	1152-1153	2	39
β-strand	1160	1	40
β-strand	1169-1170	2	41
β-strand	1175	1	42
β-strand	1176-1177	2	41
β-strand	1178-1180	3	38
β-strand	1186	1	43
β-strand	1189	1	43
β-strand	1192-1197	6	38
β-strand	1198	1	42
β-strand	1207-1212	6	38
β-strand	1215-1220	6	38
α-helix	1227	1
β-strand	1228	1	37
β-strand	1232	1	44
β-strand	1239	1	45
β-strand	1246	1	45
α-helix	1250-1252	3
β-strand	1257-1260	4	46
β-strand	1265-1268	4	46
β-strand	1288	1	47
β-strand	1290-1293	4	46
α-helix	1305	1
β-strand	1306	1	47
α-helix	1307	1
β-strand	1311-1315	5	44
β-strand	1317-1322	6	44
β-strand	1327	1	48
β-strand	1333	1	48
β-strand	1335-1342	8	44
β-strand	1346-1352	7	44
β-strand	1359-1366	8	44
α-helix	1375-1377	3
β-strand	1379-1381	3	49
β-strand	1387-1389	3	49
α-helix	1391-1393	3
α-helix	1399	1
β-strand	1400-1401	2	50
α-helix	1402	1
β-strand	1403	1	51
β-strand	1411-1414	4	50
β-strand	1435-1438	4	50
β-strand	1444-1447	4	50
β-strand	1448-1449	2	51
β-strand	1454-1456	3	51
β-strand	1459-1465	7	51
α-helix	1476-1477	2
β-strand	1478-1483	6	51
β-strand	1495-1500	6	51
β-strand	1504-1509	6	51
β-strand	1516	1	49
β-strand	1520-1522	3	52
β-strand	1526-1527	2	53
β-strand	1536-1537	2	53
α-helix	1539-1541	3
β-strand	1547-1550	4	54
β-strand	1556-1559	4	54
β-strand	1576	1	54
β-strand	1590-1592	3	52
β-strand	1597-1599	3	52
β-strand	1617-1621	5	52
β-strand	1622-1623	2	55
β-strand	1637-1639	3	52
β-strand	1644-1647	4	52
β-strand	1650-1651	2	55
β-strand	1662-1665	4	56
β-strand	1668-1671	4	56
α-helix	1673-1675	3
β-strand	1682-1683	2	57
β-strand	1687	1	58
β-strand	1699-1701	3	57
β-strand	1710	1	59
β-strand	1713	1	59
β-strand	1721-1723	3	57
β-strand	1731-1732	2	57
β-strand	1735-1736	2	60
β-strand	1741-1742	2	60
β-strand	1749-1754	6	60
α-helix	1758-1759	2
β-strand	1768-1775	8	60
β-strand	1785-1786	2	60
β-strand	1788	1	58
β-strand	1793-1800	8	60
α-helix	1805-1806	2
β-strand	1834-1837	4	61
β-strand	1842-1845	4	61
β-strand	1862-1867	6	61
β-strand	1876-1877	2	61
β-strand	1885-1886	2	62
β-strand	1891-1896	6	62
α-helix	1910-1913	4
α-helix	1915	1
β-strand	1916-1918	3	63
β-strand	1921-1923	3	63
β-strand	1927	1	64
β-strand	1935-1937	3	64
β-strand	1941	1	63
β-strand	1948-1950	3	64
β-strand	1959-1965	7	62
β-strand	1966	1	65
β-strand	1977-1980	4	62
β-strand	1985-1989	5	62
β-strand	1992	1	65
β-strand	2004-2006	3	66
β-strand	2011-2013	3	66
β-strand	2034	1	67
β-strand	2055-2057	3	67
β-strand	2063-2065	3	67
β-strand	2074-2077	4	68
β-strand	2080-2083	4	68
β-strand	2101	1	68
β-strand	2104-2105	2	69
β-strand	2110-2117	8	69
β-strand	2124-2130	7	69
β-strand	2149-2150	2	70
β-strand	2155-2156	2	70
β-strand	2173-2175	3	71
β-strand	2182-2184	3	71
β-strand	2200-2202	3	72
β-strand	2217-2218	2	72
β-strand	2222-2223	2	73
β-strand	2226	1	74
β-strand	2231	1	74
β-strand	2232-2235	4	73
β-strand	2252-2255	4	73
β-strand	2270-2272	3	73
β-strand	2276-2281	6	73

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cation-independent mannose-6-phosphate receptor	A	protein	2499	Bos taurus	P08169 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6UM1_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

Ligands and cofactors

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

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
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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