6VWI: PDB entry 6VWI

Head region of the closed conformation of the human type 1 insulin-like growth factor receptor ectodomain in complex with human insulin-like growth factor II. Determined by electron microscopy at 3.7 Å resolution. Released 13 May 2020.

Method: Electron microscopy
Resolution: 3.7 Å
Organisms: Homo sapiens, Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 3
Atoms: 6,469
Mol. weight: 226.24 kDa
Ligands: NAG
Released: 13 May 2020

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

Secondary structure: helices and β-sheets

6VWI contains 30 α-helices and 69 β-strands across 3 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: 13 helices, 45 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	1
β-strand	7-9	3	2
α-helix	13-21	9
β-strand	24-25	2	1
β-strand	29-32	4	2
α-helix	40-42	3
β-strand	50-51	2	1
β-strand	55-58	4	2
β-strand	65	1	3
α-helix	66-68	3
β-strand	75-76	2	1
β-strand	82	1	2
β-strand	85-90	6	2
β-strand	97	1	3
β-strand	105-106	2	1
β-strand	110-114	5	2
α-helix	127-130	4
α-helix	134-136	3
β-strand	138-140	3	2
α-helix	145-147	3
β-strand	164-165	2	4
β-strand	172-173	2	4
β-strand	175-177	3	5
β-strand	180-181	2	5
α-helix	187-189	3
β-strand	194-195	2	6
β-strand	199-200	2	6
β-strand	205-209	5	7
α-helix	215-217	3
β-strand	218-221	4	7
β-strand	224-226	3	8
β-strand	229-231	3	8
α-helix	234-235	2
β-strand	239-241	3	8
β-strand	245-247	3	8
α-helix	249-252	4
β-strand	267-269	3	8
β-strand	272-274	3	8
β-strand	282-283	2	9
β-strand	290	1	8
β-strand	291-292	2	9
β-strand	301-302	2	10
β-strand	308-311	4	11
α-helix	314-318	5
β-strand	325-326	2	10
β-strand	329-332	4	11
α-helix	341-348	8
β-strand	353-354	2	10
β-strand	358-361	4	11
β-strand	368	1	12
β-strand	377-378	2	10
β-strand	388	1	13
β-strand	390-393	4	11
β-strand	400	1	12
β-strand	410-411	2	10
β-strand	415	1	13
β-strand	419	1	11
α-helix	426-435	10

Chain B: 13 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	301-311	11	14
α-helix	314-317	4
α-helix	318-320	3
β-strand	325-332	8	14
α-helix	340-348	9
β-strand	353-354	2	14
β-strand	358-361	4	14
β-strand	368	1	15
β-strand	377-378	2	14
β-strand	388-393	6	14
β-strand	400	1	15
β-strand	404	1	16
β-strand	407	1	16
β-strand	410-411	2	14
β-strand	415-419	5	14
α-helix	426-435	10
α-helix	444-446	3
β-strand	447	1	14
β-strand	461-463	3	17
β-strand	465-470	6	18
β-strand	474-479	6	18
α-helix	487-489	3
β-strand	490-499	10	17
β-strand	520-524	5	17
α-helix	533-534	2
β-strand	535-539	5	18
α-helix	541-542	2
β-strand	546-555	10	17
α-helix	561-563	3
β-strand	567-569	3	17
α-helix	570-571	2
β-strand	572-575	4	17
α-helix	576-577	2
α-helix	678-681	4
α-helix	684-700	17

Chain I: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	11-21	11
β-strand	26	1	19
α-helix	42-43	2
α-helix	44-48	5
α-helix	50-51	2
β-strand	60	1	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Leucine-zippered human type 1 insulin-like growth factor receptor ectodomain	A, B	protein	952	Homo sapiens, Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P03069 (AlphaFold model), P08069 (AlphaFold model)
Insulin-like growth factor II	I	protein	67	Homo sapiens	P01344 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6VWI_1 Leucine-zippered human type 1 insulin-like growth factor receptor ectodomain (chains A, B)
EICGPGIDIRNDYQQLKRLENCTVIEGYLHILLISKAEDYRSYRFPKLTVITEYLLLFRV
AGLESLGDLFPNLTVIRGWKLFYNYALVIFEMTNLKDIGLYNLRNITRGAIRIEKNADLC
YLSTVDWSLILDAVSNNYIVGNKPPKECGDLCPGTMEEKPMCEKTTINNEYNYRCWTTNR
CQKMCPSTCGKRACTENNECCHPECLGSCSAPDNDTACVACRHYYYAGVCVPACPPNTYR
FEGWRCVDRDFCANILSAESSDSEGFVIHDGECMQECPSGFIRNGSQSMYCIPCEGPCPK
VCEEEKKTKTIDSVTSAQMLQGCTIFKGNLLINIRRGNNIASELENFMGLIEVVTGYVKI
RHSHALVSLSFLKNLRLILGEEQLEGNYSFYVLDNQNLQQLWDWDHRNLTIKAGKMYFAF
NPKLCVSEIYRMEEVTGTKGRQSKGDINTRNNGERASCESDVLHFTSTTTSKNRIIITWH
RYRPPDYRDLISFTVYYKEAPFKNVTEYDGQDACGSNSWNMVDVDLPPNKDVEPGILLHG
LKPWTQYAVYVKAVTLTMVENDHIRGAKSEILYIRTNASVPSIPLDVLSASNSSSQLIVK
WNPPSLPNGNLSYYIVRWQRQPQDGYLYRHNYCSKDKIPIRKYADGTIDIEEVTENPKTE
VCGGEKGPCCACPKTEAEKQAEKEEAEYRKVFENFLHNSIFVPRPERKRRDVMQVANTTM
SSRSRNTTAADTYNITDPEELETEYPFFESRVDNKERTVISNLRPFTLYRIDIHSCNHEA
EKLGCSASNFVFARTMPAEGADDIPGPVTWEPRPENSIFLKWPEPENPNGLILMYEIKYG
SQVEDQRECVSRQEYRKYGGAKLNRLNPGNYTARIQATSLSGNGSWTDPVFFYVQAKTGY
ENFIHRMKQLEDKVEELLSKNYHLENEVARLKKLVGERSSSEQKLISEEDLN

Sequence of entity 2 (I), FASTA

>6VWI_2 Insulin-like growth factor II (chains I)
AYRPSETLCGGELVDTLQFVCGDRGFYFSRPASRVSRRSRGIVEECCFRSCDLALLETYC
ATPAKSE

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4

Primary citation

How IGF-II Binds to the Human Type 1 Insulin-like Growth Factor Receptor. Xu, Y., Kirk, N.S., Venugopal, H. et al. Structure (2020) 28:786-798.e6. DOI 10.1016/j.str.2020.05.002 · PubMed

Other PDB entries of the same protein (UniProt P03069 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3AZD 0.98 Å, Crystal structure of tropomyosin N-terminal fragment at 0.98A resolution
2WQ1 1.08 Å, GCN4 leucine zipper mutant with three IxxNTxx motifs coordinating bromide
2WQ0 1.12 Å, GCN4 leucine zipper mutant with three IxxNTxx motifs coordinating chloride
4OWI 1.2 Å, peptide structure
2WQ3 1.22 Å, GCN4 leucine zipper mutant with three IxxNTxx motifs coordinating chloride and nitrate
2HY6 1.25 Å, A seven-helix coiled coil
2WPZ 1.25 Å, GCN4 leucine zipper mutant with two VxxNxxx motifs coordinating chloride
6PSA 1.3 Å, PIE12 D-peptide against HIV entry (in complex with IQN17 Q577R resistance mutant)
2IPZ 1.35 Å, A Parallel Coiled-Coil Tetramer with Offset Helices
2YNY 1.35 Å, Salmonella enterica SadA 255-302 fused to GCN4 adaptors (SadAK1)
5APU 1.35 Å, Sequence IANKEDKAD inserted between GCN4 adaptors - Structure A9b black
2WQ2 1.36 Å, GCN4 leucine zipper mutant with three IxxNTxx motifs coordinating iodide

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