6P8I: N-terminal 5 domains of IGFIIR

N-terminal 5 domains of IGFIIR. Determined by X-ray diffraction at 2.54 Å resolution. Released 24 Jun 2020.

Method: X-ray diffraction
Resolution: 2.54 Å
Organism: Homo sapiens
Chains: 1
Atoms: 5,293
Mol. weight: 82.25 kDa
Released: 24 Jun 2020

Explore 6P8I in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6P8I contains 22 α-helices and 66 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: 22 helices, 66 β-strands

Element	Residues	Length	Sheet
α-helix	11-13	3
β-strand	18-22	5	1
β-strand	27-31	5	1
β-strand	46	1	2
β-strand	48-52	5	1
β-strand	57-60	4	1
β-strand	63	1	2
β-strand	67-70	4	3
β-strand	73-81	9	3
β-strand	90-99	10	3
β-strand	107-111	5	3
β-strand	115-122	8	3
α-helix	123-125	3
α-helix	129-131	3
β-strand	136	1	4
β-strand	140-141	2	5
β-strand	149-150	2	5
α-helix	152-154	3
β-strand	159	1	6
β-strand	161-162	2	7
α-helix	163	1
β-strand	164	1	8
β-strand	170-174	5	7
β-strand	178	1	4
β-strand	181	1	6
α-helix	189-192	4
α-helix	194	1
β-strand	199-203	5	7
β-strand	208-211	4	7
β-strand	212	1	8
α-helix	216-217	2
β-strand	218-219	2	8
β-strand	225-230	6	8
α-helix	243-245	3
β-strand	246-252	7	8
β-strand	264-267	4	8
α-helix	269-271	3
β-strand	272-278	7	8
α-helix	280-282	3
α-helix	284-286	3
β-strand	287-290	4	9
β-strand	294-295	2	10
β-strand	304-305	2	10
α-helix	307-309	3
β-strand	317-320	4	11
β-strand	324-328	5	11
β-strand	346-350	5	11
β-strand	357-361	5	11
β-strand	366-371	6	9
β-strand	374-379	6	9
β-strand	384	1	12
α-helix	389	1
β-strand	390	1	12
α-helix	391	1
β-strand	392-399	8	9
β-strand	412-417	6	9
β-strand	420-427	8	9
α-helix	428-430	3
β-strand	441-444	4	13
β-strand	447-450	4	13
β-strand	464-465	2	14
β-strand	480-481	2	14
α-helix	486-488	3
β-strand	521-522	2	15
β-strand	527-531	5	15
β-strand	545-551	7	15
β-strand	561-564	4	15
β-strand	572-578	7	15
α-helix	579-581	3
α-helix	583-584	2
β-strand	587-588	2	16
β-strand	593-595	3	17
β-strand	602-604	3	17
α-helix	606-608	3
β-strand	615-618	4	18
β-strand	622-626	5	18
β-strand	641-647	7	18
β-strand	653-658	6	18
β-strand	662	1	17
β-strand	664-666	3	16
β-strand	669-674	6	16
β-strand	679	1	19
β-strand	687	1	19
β-strand	690-696	7	16
β-strand	705-708	4	16
α-helix	709	1
β-strand	715-721	7	16
α-helix	722-724	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cation-independent mannose-6-phosphate receptor	A	protein	735	Homo sapiens	P11717 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6P8I_1 Cation-independent mannose-6-phosphate receptor (chains A)
AAGSTQAQAAPFPELCSYTWEAVDTKNNVLYKINICGSVDIVQCGPSSAVCMHDLKTRTY
HSVGDSVLRSATRSLLEFNTTVSCDQQGTNHRVQSSIAFLCGKTLGTPEFVTATECVHYF
EWRTTAACKKDIFKANKEVPCYVFDEELRKHDLNPLIKLSGAYLVDDSDPDTSLFINVCR
DIDTLRDPGSQLRACPPGTAACLVRGHQAFDVGQPRDGLKLVRKDRLVLSYVREEAGKLD
FCDGHSPAVTITFVCPSERREGTIPKLTAKSNCRYEIEWITEYACHRDYLESKTCSLSGE
QQDVSIDLTPLAQSGGSSYISDGKEYLFYLNVCGETEIQFCNKKQAAVCQVKKSDTSQVK
AAGRYHNQTLRYSDGDLTLIYFGGDECSSGFQRMSVINFECNKTAGNDGKGTPVFTGEVD
CTYFFTWDTEYACVKEKEDLLCGATDGKKRYDLSALVRHAEPEQNWEAVDGSQTETEKKH
FFINICHRVLQEGKARGCPEDAAVCAVDKNGSKNLGKFISSPMKEKGNIQLSYSDGDDCG
HGKKIKTNITLVCKPGDLESAPVLRTSGEGGCFYEFEWHTAAACVLSKTEGENCTVFDSQ
AGFSFDLSPLTKKNGAYKVETKKYDFYINVCGPVSVSPCQPDSGACQVAKSDEKTWNLGL
SNAKLSYYDGMIQLNYRGGTPYNNERHTPRATLITFLCDRDAGVGFPEYQEEDNSTYNFR
WYTSYACPEEALVPL

Primary citation

Allosteric regulation of lysosomal enzyme recognition by the cation-independent mannose 6-phosphate receptor. Olson, L.J., Misra, S.K., Ishihara, M. et al. Commun Biol (2020) 3:498-498. DOI 10.1038/s42003-020-01211-w · 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
6Z31 2.56 Å, Human cation-independent mannose 6-phosphate/ IGF2 receptor domain 8

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