1YYL: CD4M33, a scorpion-toxin mimic of CD4

crystal structure of CD4M33, 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 2.75 Å resolution. Released 3 May 2005.

Method: X-ray diffraction
Resolution: 2.75 Å
Organisms: Human immunodeficiency virus 1, Homo sapiens, synthetic construct
Chains: 8
Atoms: 12,370
Mol. weight: 174.81 kDa
Ligands: NAG
Released: 3 May 2005

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

Secondary structure: helices and β-sheets

1YYL contains 53 α-helices and 151 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, 30 β-strands

Element	Residues	Length	Sheet
β-strand	91-94	4	1
α-helix	99-113	15
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	271-274	4	7
α-helix	283	1
β-strand	284-296	13	7
β-strand	330-331	2	8
β-strand	332-333	2	7
β-strand	334	1	9
α-helix	335-353	19
β-strand	358-361	4	7
β-strand	367	1	10
α-helix	369-372	4
β-strand	374-378	5	6
β-strand	381-385	5	6
α-helix	388-390	3
β-strand	393-394	2	7
β-strand	413	1	9
β-strand	416-417	2	8
β-strand	418-421	4	6
β-strand	423-425	3	2
β-strand	432-434	3	2
α-helix	435-438	4
β-strand	445-456	12	7
β-strand	465-470	6	7
α-helix	475-483	9
β-strand	486-490	5	5

Chain H: 9 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	16
α-helix	7-9	3
β-strand	10-12	3	17
β-strand	18-25	8	16
α-helix	29-31	3
β-strand	32-39	8	17
β-strand	46-52	7	17
β-strand	56-59	4	17
β-strand	67-72	6	16
β-strand	77-82	6	16
α-helix	84-86	3
β-strand	88-96	9	17
α-helix	100-100B	3
β-strand	102-103	2	17
β-strand	107-111	5	17
β-strand	117	1	18
α-helix	118-119	2
β-strand	120-124	5	19
β-strand	135-145	11	19
β-strand	146	1	18
β-strand	151-154	4	20
α-helix	155-157	3
β-strand	159	1	20
β-strand	163-165	3	19
α-helix	166-168	3
β-strand	169-170	2	19
β-strand	176-185	10	19
α-helix	186-188	3
β-strand	195-200	6	20
α-helix	201-203	3
β-strand	205-210	6	20

Chain L: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	11
β-strand	10-13	4	12
β-strand	19-25	7	11
β-strand	33-38	6	12
β-strand	45-49	5	12
β-strand	53-54	2	12
α-helix	55	1
β-strand	62-67	6	11
β-strand	70-75	6	11
α-helix	80-82	3
β-strand	85-90	6	12
β-strand	97-98	2	12
β-strand	102-106	5	12
β-strand	111	1	13
α-helix	112-113	2
β-strand	114-118	5	14
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	14
β-strand	140	1	13
β-strand	144-150	7	15
β-strand	154	1	15
β-strand	159-163	5	14
α-helix	165-167	3
β-strand	173-182	10	14
α-helix	183-186	4
β-strand	191-198	8	15
β-strand	205-210	6	15

Chain M: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
α-helix	3-11	9
β-strand	17-20	4	10
β-strand	23-26	4	10

Chain P: 10 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	1091-1094	4	21
α-helix	1095-1097	3
α-helix	1099-1112	14
β-strand	1120-1126	7	22
β-strand	1196-1202	7	22
β-strand	1215	1	23
β-strand	1218	1	24
α-helix	1219-1220	2
β-strand	1223-1228	6	25
β-strand	1236-1239	4	21
β-strand	1242-1245	4	25
β-strand	1247	1	24
α-helix	1248-1250	3
β-strand	1251	1	23
β-strand	1256	1	26
β-strand	1259-1261	3	27
α-helix	1264-1266	3
β-strand	1271-1274	4	27
α-helix	1283	1
β-strand	1284-1287	4	27
β-strand	1293-1296	4	28
β-strand	1330-1334	5	28
α-helix	1335-1353	19
β-strand	1358-1361	4	27
β-strand	1367	1	29
α-helix	1369-1372	4
β-strand	1374-1378	5	26
β-strand	1381-1385	5	26
β-strand	1393	1	27
β-strand	1413-1417	5	28
β-strand	1420-1421	2	26
β-strand	1423-1425	3	22
β-strand	1432-1434	3	22
α-helix	1435-1438	4
β-strand	1445-1448	4	28
β-strand	1449-1456	8	27
β-strand	1465-1470	6	27
α-helix	1475-1483	9
β-strand	1486-1490	5	25

Chain Q: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	1004-1007	4	30
β-strand	1010-1013	4	31
β-strand	1019-1025	7	30
β-strand	1033-1038	6	31
β-strand	1045-1049	5	31
β-strand	1053-1054	2	31
α-helix	1055	1
β-strand	1062-1067	6	30
β-strand	1070-1075	6	30
α-helix	1080-1082	3
β-strand	1085-1090	6	31
β-strand	1097-1098	2	31
β-strand	1102-1106	5	31
β-strand	1111	1	32
β-strand	1114-1118	5	33
α-helix	1119-1121	3
α-helix	1122-1127	6
β-strand	1130-1139	10	33
β-strand	1140	1	32
β-strand	1145-1150	6	34
β-strand	1153-1154	2	34
β-strand	1159-1163	5	33
α-helix	1165-1167	3
β-strand	1173-1181	9	33
α-helix	1183-1187	5
β-strand	1191-1197	7	34
β-strand	1205-1210	6	34

Chain R: 9 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	1003-1006	4	35
β-strand	1010-1012	3	36
β-strand	1017-1025	9	35
α-helix	1029-1031	3
β-strand	1032-1038	7	37
β-strand	1046-1052	7	37
α-helix	1052A-1054	3
β-strand	1056-1059	4	37
β-strand	1067-1072	6	35
β-strand	1077-1082A	7	35
α-helix	1084-1086	3
β-strand	1088-1090	3	36
β-strand	1091-1096	6	37
α-helix	1100-1100B	3
β-strand	1102-1103	2	37
β-strand	1107-1111	5	36
β-strand	1117	1	38
α-helix	1118-1119	2
β-strand	1120-1124	5	39
β-strand	1130	1	39
β-strand	1135-1145	11	39
β-strand	1146	1	38
β-strand	1151-1154	4	40
α-helix	1155-1157	3
β-strand	1159	1	40
β-strand	1163-1165	3	39
α-helix	1166-1168	3
β-strand	1169-1170	2	39
β-strand	1176-1185	10	39
α-helix	1186-1188	3
β-strand	1194-1200	7	40
α-helix	1201-1203	3
β-strand	1205-1211	7	40

Chain S: 2 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	1003-1009	7
α-helix	1010-1013	4
β-strand	1017-1020	4	29
β-strand	1023-1026	4	29

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
CD4M33, scorpion-toxin mimic of CD4	M, S	protein	27	synthetic construct

Sequence of entity 1 (G, P), FASTA

>1YYL_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

>1YYL_2 antibody 17b light chain (chains L, Q)
DIVMTQSPATLSVSPGERATLSCRASESVSSDLAWYQQKPGQAPRLLIYGASTRATGVPA
RFSGSGSGAEFTLTISSLQSEDFAVYYCQQYNNWPPRYTFGQGTRLEIKRTVAAPSVFIF
PPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSST
LTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG

Sequence of entity 3 (H, R), FASTA

>1YYL_3 antibody 17b heavy chain (chains H, R)
EVQLVESGAEVKKPGSSVKVSCKASGDTFIRYSFTWVRQAPGQGLEWMGRIITILDVAHY
APHLQGRVTITADKSTSTVYLELRNLRSDDTAVYFCAGVYEGEADEGEYDNNGFLKHWGQ
GTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHT
FPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK

Sequence of entity 4 (M, S), FASTA

>1YYL_4 CD4M33, 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

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…
1YYM 2.2 Å, crystal structure of F23, a scorpion-toxin mimic of CD4, in complex with HIV-1 YU2 gp120…
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…
1G9N 2.9 Å, HIV-1 YU2 GP120 envelope glycoprotein complexed with CD4 and induced neutralizing…

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