8YSZ: Complex IR with three IGF-II

Cryo-EM structure of the complex IR with three IGF-II. Determined by electron microscopy at 3.38 Å resolution. Released 26 Mar 2025.

Method: Electron microscopy
Resolution: 3.38 Å
Organism: Homo sapiens
Chains: 4
Atoms: 10,912
Mol. weight: 351 kDa
Released: 26 Mar 2025

Explore 8YSZ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8YSZ contains 52 α-helices and 118 β-strands across 4 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: 24 helices, 73 β-strands

Element	Residues	Length	Sheet
β-strand	33-41	9	2
α-helix	44-47	4
β-strand	53-63	11	2
α-helix	70-73	4
β-strand	83-84	2	2
β-strand	87-91	5	2
β-strand	98	1	3
β-strand	108-109	2	2
β-strand	115	1	2
β-strand	118-123	6	2
β-strand	130	1	3
β-strand	138-139	2	2
β-strand	143-147	5	2
β-strand	153	1	3
α-helix	160-163	4
β-strand	164	1	2
β-strand	171-173	3	2
α-helix	176-178	3
β-strand	198-199	2	4
β-strand	206-207	2	4
β-strand	209	1	5
β-strand	215	1	5
α-helix	216-217	2
β-strand	228	1	6
β-strand	234	1	6
β-strand	239-243	5	7
β-strand	250	1	8
β-strand	252-255	4	7
β-strand	258-260	3	8
β-strand	263-265	3	8
β-strand	273-275	3	8
β-strand	279-281	3	8
α-helix	283-295	13
β-strand	305-307	3	8
β-strand	310-312	3	8
β-strand	322	1	9
β-strand	327	1	8
β-strand	328	1	9
β-strand	339	1	10
α-helix	340-341	2
α-helix	342-344	3
β-strand	345-348	4	11
α-helix	351-355	5
β-strand	363	1	10
β-strand	366-369	4	11
α-helix	378-385	8
β-strand	391	1	10
β-strand	395-398	4	11
β-strand	405	1	12
β-strand	415	1	10
β-strand	421	1	11
β-strand	425-430	6	11
β-strand	437	1	12
β-strand	448	1	10
β-strand	452-456	5	11
α-helix	463-471	9
α-helix	475-477	3
β-strand	483-484	2	11
β-strand	502-507	6	13
β-strand	511-516	6	13
α-helix	517-518	2
α-helix	524-526	3
β-strand	527-534	8	14
β-strand	535-536	2	15
α-helix	543-545	3
α-helix	556	1
β-strand	557-561	5	14
α-helix	562-565	4
α-helix	574-576	3
β-strand	578-581	4	13
α-helix	583-584	2
β-strand	588-590	3	15
β-strand	593-597	5	14
β-strand	609	1	14
β-strand	614-616	3	15
α-helix	617-619	3
β-strand	626-634	9	16
β-strand	637-643	7	16
β-strand	654-660	7	17
α-helix	662-665	4
α-helix	667-669	3
α-helix	678-681	4
β-strand	799-801	3	17
β-strand	806-808	3	16
β-strand	819-825	7	17
β-strand	838-841	4	17
β-strand	863	1	18
β-strand	866	1	18
β-strand	883-884	2	19
β-strand	886-887	2	20
β-strand	897-898	2	20
α-helix	904-907	4
β-strand	919-923	5	21
β-strand	926	1	22
β-strand	927-928	2	19
β-strand	936	1	22
β-strand	940-944	5	21

Chain B: 20 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	338-346	9	23
α-helix	355-357	3
β-strand	361-362	2	23
β-strand	363	1	24
β-strand	364-367	4	23
α-helix	377-385	9
β-strand	390-393	4	24
β-strand	395-397	3	23
β-strand	405	1	25
α-helix	406-409	4
β-strand	414-417	4	24
α-helix	422-424	3
β-strand	425-429	5	23
β-strand	437	1	25
β-strand	446	1	26
β-strand	447-448	2	24
β-strand	452-455	4	23
β-strand	458	1	27
α-helix	463-472	10
β-strand	473	1	26
α-helix	477-479	3
β-strand	489	1	27
β-strand	498	1	28
β-strand	502-507	6	29
β-strand	512-516	5	29
α-helix	517-518	2
α-helix	524-526	3
β-strand	527-536	10	30
β-strand	557-561	5	30
α-helix	562-564	3
α-helix	574-576	3
β-strand	577-580	4	29
α-helix	583-584	2
β-strand	588-597	10	30
α-helix	604-606	3
β-strand	608	1	28
β-strand	609	1	30
α-helix	610-612	3
β-strand	613-616	4	30
α-helix	617-619	3
β-strand	629-634	6	31
β-strand	637-641	5	31
α-helix	643-645	3
β-strand	655-660	6	32
α-helix	721-740	20
β-strand	798-801	4	32
β-strand	806-809	4	31
α-helix	810	1
β-strand	817-823	7	32
β-strand	825	1	33
β-strand	834	1	33
β-strand	838-843	6	32
α-helix	844-846	3
β-strand	857-861	5	34
β-strand	867-871	5	34
β-strand	884	1	35
β-strand	888	1	36
β-strand	896	1	36
β-strand	900	1	35
α-helix	904-906	3
α-helix	934-941	8

Chain C: 6 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	11-21	11
α-helix	25	1
β-strand	26	1	37
α-helix	27	1
α-helix	42-46	5
α-helix	53-56	4
α-helix	57-59	3
β-strand	60	1	37

Chain D: 2 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	12-21	10
β-strand	26	1	1
α-helix	53-56	4
β-strand	60	1	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Insulin-like growth factor II	C, D	protein	180	Homo sapiens	P01344 (AlphaFold model)
Isoform Short of Insulin receptor	A, B	protein	1370	Homo sapiens	P06213 (AlphaFold model)

Sequence of entity 1 (C, D), FASTA

>8YSZ_1 Insulin-like growth factor II (chains C, D)
MGIPMGKSMLVLLTFLAFASCCIAAYRPSETLCGGELVDTLQFVCGDRGFYFSRPASRVS
RRSRGIVEECCFRSCDLALLETYCATPAKSERDVSTPPTVLPDNFPRYPVGKFFQYDTWK
QSTQRLRRGLPALLRARRGHVLAKELEAFREAKRHRPLIALPTQDPAHGGAPPEMASNRK

Sequence of entity 2 (A, B), FASTA

>8YSZ_2 Isoform Short of Insulin receptor (chains A, B)
MATGGRRGAAAAPLLVAVAALLLGAAGHLYPGEVCPGMDIRNNLTRLHELENCSVIEGHL
QILLMFKTRPEDFRDLSFPKLIMITDYLLLFRVYGLESLKDLFPNLTVIRGSRLFFNYAL
VIFEMVHLKELGLYNLMNITRGSVRIEKNNELCYLATIDWSRILDSVEDNYIVLNKDDNE
ECGDICPGTAKGKTNCPATVINGQFVERCWTHSHCQKVCPTICKSHGCTAEGLCCHSECL
GNCSQPDDPTKCVACRNFYLDGRCVETCPPPYYHFQDWRCVNFSFCQDLHHKCKNSRRQG
CHQYVIHNNKCIPECPSGYTMNSSNLLCTPCLGPCPKVCHLLEGEKTIDSVTSAQELRGC
TVINGSLIINIRGGNNLAAELEANLGLIEEISGYLKIRRSYALVSLSFFRKLRLIRGETL
EIGNYSFYALDNQNLRQLWDWSKHNLTITQGKLFFHYNPKLCLSEIHKMEEVSGTKGRQE
RNDIALKTNGDQASCENELLKFSYIRTSFDKILLRWEPYWPPDFRDLLGFMLFYKEAPYQ
NVTEFDGQDACGSNSWTVVDIDPPLRSNDPKSQNHPGWLMRGLKPWTQYAIFVKTLVTFS
DERRTYGAKSDIIYVQTDATNPSVPLDPISVSNSSSQIILKWKPPSDPNGNITHYLVFWE
RQAEDSELFELDYCLKGLKLPSRTWSPPFESEDSQKHNQSEYEDSAGECCSCPKTDSQIL
KELEESSFRKTFEDYLHNVVFVPRPSRKRRSLGDVGNVTVAVPTVAAFPNTSSTSVPTSP
EEHRPFEKVVNKESLVISGLRHFTGYRIELQACNQDTPEERCSVAAYVSARTMPEAKADD
IVGPVTHEIFENNVVHLMWQEPKEPNGLIVLYEVSYRRYGDEELHLCVSRKHFALERGCR
LRGLSPGNYSVRIRATSLAGNGSWTEPTYFYVTDYLDVPSNIAKIIIGPLIFVFLFSVVI
GSIYLFLRKRQPDGPLGPLYASSNPEYLSASDVFPCSVYVPDEWEVSREKITLLRELGQG
SFGMVYEGNARDIIKGEAETRVAVKTVNESASLRERIEFLNEASVMKGFTCHHVVRLLGV
VSKGQPTLVVMELMAHGDLKSYLRSLRPEAENNPGRPPPTLQEMIQMAAEIADGMAYLNA
KKFVHRDLAARNCMVAHDFTVKIGDFGMTRDIYETDYYRKGGKGLLPVRWMAPESLKDGV
FTTSSDMWSFGVVLWEITSLAEQPYQGLSNEQVLKFVMDGGYLDQPDNCPERVTDLMRMC
WQFNPKMRPTFLEIVNLLKDDLHPSFPEVSFFHSEENKAPESEELEMEFEDMENVPLDRS
SHCQREEAGGRDGGSSLGFKRSYEEHIPYTHMNGGKKNGRILTLPRSNPS

Primary citation

Cryo-EM structure of the complex IR with three IGF-II. Xi, Z. To be published.

Other PDB entries of the same protein (UniProt P01344 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3KR3 2.2 Å, Crystal structure of IGF-II antibody complex
3E4Z 2.28 Å, Crystal structure of human insulin degrading enzyme in complex with insulin-like growth…
6VWG 3.21 Å, Head region of the open conformation of the human type 1 insulin-like growth factor…
8U4C 3.6 Å, Cryo-EM structure of long form insulin receptor (IR-B) with four IGF2 bound, symmetric…
8VJB 3.6 Å, Cryo-EM structure of short form insulin receptor (IR-A) with four IGF2 bound, symmetric…
6VWI 3.7 Å, Head region of the closed conformation of the human type 1 insulin-like growth factor…
8VJC 3.8 Å, Cryo-EM structure of short form insulin receptor (IR-A) with three IGF2 bound,…
2V5P 4.1 Å, Complex structure of human IGF2R domains 11-13 bound to igf-II
8U4E 4.2 Å, Cryo-EM structure of long form insulin receptor (IR-B) with three IGF2 bound, asymmetric…
6UM2 4.32 Å, Structure of M-6-P/IGFII Receptor and IGFII complex
1IGL Solution structure of human insulin-like growth factor II relationship to receptor and…
2L29 Complex structure of E4 mutant human IGF2R domain 11 bound to IGF-II

Browse structure collections

About this viewer

MolViewer shows 8YSZ directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.