1YYM: F23, a scorpion-toxin mimic of CD4

crystal structure of F23, a scorpion-toxin mimic of CD4, in complex with HIV-1 YU2 gp120 envelope glycoprotein and anti-HIV-1 antibody 17b. Determined by X-ray diffraction at 2.2 Å resolution. Released 3 May 2005.

Method: X-ray diffraction
Resolution: 2.2 Å
Organisms: Human immunodeficiency virus 1, Homo sapiens, synthetic construct
Chains: 8
Atoms: 12,823
Mol. weight: 174.9 kDa
Ligands: NAG, IPA
Released: 3 May 2005

Explore 1YYM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1YYM contains 56 α-helices and 147 β-strands across 8 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 G: 9 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	91-94	4	1
α-helix	95-97	3
α-helix	99-115	17
β-strand	120-126	7	2
β-strand	196-202	7	2
β-strand	215	1	3
β-strand	218	1	4
α-helix	219-220	2
β-strand	223-228	6	5
β-strand	236-239	4	1
β-strand	242-245	4	5
β-strand	247	1	4
β-strand	251	1	3
β-strand	256	1	6
β-strand	259-261	3	7
α-helix	264-266	3
β-strand	271-273	3	7
β-strand	284-297	14	7
β-strand	330-334	5	7
α-helix	335-353	19
β-strand	358-361	4	7
β-strand	367	1	8
α-helix	369-372	4
β-strand	374-378	5	6
β-strand	381-385	5	6
α-helix	389-391	3
β-strand	393-394	2	7
β-strand	413-417	5	7
β-strand	418-420	3	6
β-strand	423-425	3	2
β-strand	432-434	3	2
α-helix	436-438	3
β-strand	444-456	13	7
β-strand	465-470	6	7
α-helix	476-483	8
β-strand	486-490	5	5

Chain H: 10 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	14
α-helix	7-9	3
β-strand	10-12	3	15
β-strand	18-25	8	14
α-helix	29-31	3
β-strand	32-39	8	15
β-strand	46-52	7	15
β-strand	56-59	4	15
α-helix	61-63	3
β-strand	67-72	6	14
β-strand	77-82	6	14
α-helix	84-86	3
β-strand	88-96	9	15
α-helix	100-100B	3
β-strand	102-103	2	15
β-strand	107-111	5	15
β-strand	117	1	16
α-helix	118-119	2
β-strand	120-124	5	17
β-strand	135-145	11	17
β-strand	146	1	16
β-strand	151-154	4	18
α-helix	155-157	3
β-strand	159	1	18
β-strand	163-165	3	17
α-helix	166-168	3
β-strand	169-170	2	17
β-strand	176-185	10	17
α-helix	186-188	3
β-strand	189	1	19
β-strand	192	1	19
β-strand	195-200	6	18
α-helix	201-203	3
β-strand	205-210	6	18

Chain L: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	4-7	4	9
β-strand	10-13	4	10
β-strand	19-25	7	9
β-strand	33-38	6	10
β-strand	45-49	5	10
β-strand	53-54	2	10
α-helix	55	1
β-strand	62-67	6	9
β-strand	70-75	6	9
α-helix	80-82	3
β-strand	85-90	6	10
β-strand	97-98	2	10
β-strand	102-106	5	10
β-strand	111	1	11
α-helix	112-113	2
β-strand	114-118	5	12
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	12
β-strand	140	1	11
β-strand	145-150	6	13
β-strand	153-154	2	13
α-helix	155	1
β-strand	159-163	5	12
α-helix	165-167	3
β-strand	173-182	10	12
α-helix	183-186	4
β-strand	191-197	7	13
β-strand	205-210	6	13

Chain M: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
α-helix	3-11	9
β-strand	17-20	4	8
β-strand	23-26	4	8

Chain P: 10 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	1091-1094	4	20
α-helix	1095-1097	3
α-helix	1099-1115	17
β-strand	1120-1126	7	21
β-strand	1196-1202	7	21
β-strand	1215	1	22
β-strand	1218	1	23
α-helix	1219-1220	2
β-strand	1223-1228	6	24
β-strand	1236-1239	4	20
β-strand	1242-1245	4	24
β-strand	1247	1	23
β-strand	1251	1	22
β-strand	1256	1	25
β-strand	1259-1261	3	26
α-helix	1264-1266	3
β-strand	1271-1273	3	26
α-helix	1283	1
β-strand	1284-1296	13	26
β-strand	1330-1334	5	26
α-helix	1335-1353	19
α-helix	1357	1
β-strand	1358-1361	4	26
β-strand	1367	1	27
α-helix	1369-1372	4
β-strand	1374-1378	5	25
β-strand	1381-1385	5	25
α-helix	1388-1390	3
β-strand	1413-1417	5	26
β-strand	1418-1420	3	25
β-strand	1423-1425	3	21
β-strand	1432-1434	3	21
β-strand	1445-1456	12	26
β-strand	1465-1470	6	26
α-helix	1476-1483	8
β-strand	1486-1490	5	24

Chain Q: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	1004-1007	4	28
β-strand	1010-1013	4	29
β-strand	1019-1025	7	28
β-strand	1033-1038	6	29
β-strand	1045-1049	5	29
β-strand	1053-1054	2	29
α-helix	1055	1
β-strand	1062-1067	6	28
β-strand	1070-1075	6	28
α-helix	1080-1082	3
β-strand	1085-1090	6	29
β-strand	1097-1098	2	29
β-strand	1102-1106	5	29
β-strand	1111	1	30
α-helix	1112-1113	2
β-strand	1114-1118	5	31
α-helix	1119-1121	3
α-helix	1122-1127	6
β-strand	1129-1139	11	31
β-strand	1140	1	30
β-strand	1145-1150	6	32
β-strand	1153-1154	2	32
α-helix	1155	1
β-strand	1159-1163	5	31
α-helix	1164-1167	4
β-strand	1173-1182	10	31
α-helix	1183-1186	4
β-strand	1191-1197	7	32
β-strand	1205-1210	6	32

Chain R: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	1003-1006	4	33
β-strand	1010-1012	3	34
β-strand	1018-1025	8	33
α-helix	1029-1031	3
β-strand	1032-1039	8	34
β-strand	1046-1052	7	34
β-strand	1056-1059	4	34
β-strand	1067-1072	6	33
β-strand	1077-1082	6	33
α-helix	1084-1086	3
β-strand	1088-1096	9	34
α-helix	1100-1100B	3
β-strand	1102-1103	2	34
β-strand	1107-1111	5	34
β-strand	1117	1	35
α-helix	1118-1119	2
β-strand	1120-1124	5	36
β-strand	1135-1145	11	36
β-strand	1146	1	35
β-strand	1151-1154	4	37
α-helix	1155-1157	3
β-strand	1159	1	37
β-strand	1164-1165	2	36
α-helix	1166-1168	3
β-strand	1169-1170	2	36
β-strand	1176-1185	10	36
α-helix	1186-1188	3
β-strand	1189	1	38
β-strand	1192	1	38
β-strand	1195-1200	6	37
α-helix	1201-1203	3
β-strand	1205-1210	6	37

Chain S: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
α-helix	1003-1011	9
β-strand	1017-1020	4	27
β-strand	1023-1026	4	27

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Exterior membrane glycoprotein(GP120),Exterior membrane glycoprotein(GP120),Exterior membrane…	G, P	protein	313	Human immunodeficiency virus 1	P35961
antibody 17b light chain	L, Q	protein	214	Homo sapiens
antibody 17b heavy chain	H, R	protein	229	Homo sapiens
F23, scorpion-toxin mimic of CD4	M, S	protein	27	synthetic construct

Sequence of entity 1 (G, P), FASTA

>1YYM_1 Exterior membrane glycoprotein(GP120),Exterior membrane glycoprotein(GP120),Exterior membrane glycoprotein(GP120) (chains G, P)
GARSEVKLENVTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVGAGSCNTSVIT
QACPKVSFEPIPIHYCAPAGFAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQLLLN
GSLAEEEIVIRSENFTNNAKTIIVQLNESVVINCTGAGHCNLSKTQWENTLEQIAIKLKE
QFGNNKTIIFNPSSGGDPEIVTHSFNCGGEFFYCNSTQLFTWNDTRKLNNTGRNITLPCR
IKQIINMWQEVGKAMYAPPIRGQIRCSSNITGLLLTRDGGKDTNGTEIFRPGGGDMRDNW
RSELYKYKVVKIE

Sequence of entity 2 (L, Q), FASTA

>1YYM_2 antibody 17b light chain (chains L, Q)
DIVMTQSPATLSVSPGERATLSCRASESVSSDLAWYQQKPGQAPRLLIYGASTRATGVPA
RFSGSGSGAEFTLTISSLQSEDFAVYYCQQYNNWPPRYTFGQGTRLEIKRTVAAPSVFIF
PPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSST
LTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG

Sequence of entity 3 (H, R), FASTA

>1YYM_3 antibody 17b heavy chain (chains H, R)
EVQLVESGAEVKKPGSSVKVSCKASGDTFIRYSFTWVRQAPGQGLEWMGRIITILDVAHY
APHLQGRVTITADKSTSTVYLELRNLRSDDTAVYFCAGVYEGEADEGEYDNNGFLKHWGQ
GTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHT
FPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK

Sequence of entity 4 (M, S), FASTA

>1YYM_4 F23, scorpion-toxin mimic of CD4 (chains M, S)
XNLHFCQLRCKSLGLLGKCAGSFCACX

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	16
IPA	Isopropyl alcohol	C3 H8 O	2

Water and common crystallization additives (EDO) are not listed.

Primary citation

Scorpion-toxin mimics of CD4 in complex with human immunodeficiency virus gp120 crystal structures, molecular mimicry, and neutralization breadth. Huang, C.C., Stricher, F., Martin, L. et al. Structure (2005) 13:755-768. DOI 10.1016/j.str.2005.03.006 · PubMed

Other PDB entries of the same protein (UniProt P35961), best resolution first:

4JZZ 1.49 Å, Crystal structure of CD4-mimetic miniprotein M48U1 in complex with HIV-1 YU2 gp120 in…
4JZW 1.78 Å, Crystal structure of CD4-mimetic miniprotein M48U1 in complex with HIV-1 YU2 gp120 in…
4KA2 1.79 Å, Crystal structure of CD4-mimetic miniprotein M48U12 in complex with HIV-1 YU2 gp120
4RWY 2.13 Å, Crystal structure of VH1-46 germline-derived CD4-binding site-directed antibody 8ANC131…
4K0A 2.13 Å, Crystal structure of CD4-mimetic miniprotein M48U7 in complex with HIV-1 YU2 gp120
4LAJ 2.14 Å, Crystal structure of HIV-1 YU2 envelope gp120 glycoprotein in complex with CD4-mimetic…
2NY7 2.3 Å, HIV-1 gp120 Envelope Glycoprotein Complexed with the Broadly Neutralizing…
2I60 2.4 Å, Crystal structure of [Phe23]M47, a scorpion-toxin mimic of CD4, in complex with HIV-1…
4DVR 2.5 Å, Crystal structure of YU2 gp120 core in complex with Fab 48d and NBD-557
4JO3 2.6 Å, Crystal structure of rabbit mAb R20 Fab in complex with V3 C-terminus of HIV-1 Consensus…
1YYL 2.75 Å, crystal structure of CD4M33, a scorpion-toxin mimic of CD4, in complex with HIV-1 YU2…
1G9N 2.9 Å, HIV-1 YU2 GP120 envelope glycoprotein complexed with CD4 and induced neutralizing…

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