6VWG: PDB entry 6VWG

Head region of the open 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 3.21 Å resolution. Released 13 May 2020.

Method: Electron microscopy
Resolution: 3.21 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 6VWG in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6VWG contains 35 α-helices and 68 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: 20 helices, 44 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	1
β-strand	7-9	3	2
α-helix	13-19	7
β-strand	24-25	2	1
β-strand	29-32	4	2
β-strand	50-51	2	1
β-strand	55-58	4	2
β-strand	65	1	3
α-helix	66-69	4
β-strand	75-76	2	1
β-strand	85-90	6	2
β-strand	97	1	3
β-strand	105-106	2	1
β-strand	110-114	5	2
β-strand	120	1	3
α-helix	127-130	4
α-helix	134-136	3
β-strand	138	1	2
α-helix	145-148	4
α-helix	162-163	2
β-strand	164-167	4	4
β-strand	170-173	4	4
β-strand	175	1	5
β-strand	181	1	5
α-helix	187-189	3
β-strand	194	1	6
α-helix	196-198	3
α-helix	199	1
β-strand	200	1	6
α-helix	201-202	2
β-strand	206-209	4	7
α-helix	215-217	3
β-strand	218-220	3	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	249-254	6
β-strand	267-269	3	8
β-strand	272-274	3	8
α-helix	277-278	2
β-strand	282	1	9
β-strand	292	1	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	340-347	8
β-strand	353-354	2	10
β-strand	358-361	4	11
β-strand	368	1	12
β-strand	377-378	2	10
α-helix	383-384	2
β-strand	388-393	6	11
β-strand	400	1	12
α-helix	404-406	3
β-strand	415-419	5	11
β-strand	421	1	13
α-helix	426-430	5
α-helix	432-436	5
β-strand	447	1	11
β-strand	452	1	13

Chain B: 10 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	308-311	4	14
α-helix	314-320	7
β-strand	325-326	2	15
β-strand	329-332	4	14
α-helix	340-347	8
β-strand	353-354	2	15
β-strand	358-361	4	14
β-strand	368	1	16
β-strand	377-378	2	15
β-strand	388-393	6	14
β-strand	400	1	16
β-strand	411	1	15
β-strand	415-419	5	14
α-helix	426-428	3
α-helix	430-435	6
β-strand	447	1	14
β-strand	461	1	17
β-strand	465-470	6	18
β-strand	475-479	5	18
α-helix	487-489	3
β-strand	490-499	10	19
β-strand	520-524	5	19
α-helix	525-527	3
α-helix	533-534	2
β-strand	535-538	4	18
β-strand	546-555	10	19
α-helix	559-562	4
β-strand	567	1	17
β-strand	568	1	19
α-helix	569-571	3
β-strand	572-575	4	19
α-helix	678-700	23

Chain I: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	11-21	11
α-helix	22-24	3
β-strand	26	1	20
α-helix	42-46	5
α-helix	53-56	4
α-helix	57-59	3
β-strand	60	1	20

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

>6VWG_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

>6VWG_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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