2I60: [Phe23]M47, a scorpion-toxin mimic of CD4

Crystal structure of [Phe23]M47, 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 2.4 Å resolution. Released 10 Oct 2006.

Method: X-ray diffraction
Resolution: 2.4 Å
Organisms: Human immunodeficiency virus 1, Homo sapiens, synthetic construct
Chains: 8
Atoms: 12,434
Mol. weight: 174.94 kDa
Ligands: NAG, IPA
Released: 10 Oct 2006

Explore 2I60 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2I60 contains 59 α-helices and 146 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: 11 helices, 27 β-strands

Element	Residues	Length	Sheet
α-helix	84-86	3
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
α-helix	248-250	3
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	388-390	3
β-strand	393-394	2	7
β-strand	413-417	5	7
β-strand	418-421	4	6
β-strand	423-425	3	2
β-strand	432-434	3	2
α-helix	436-438	3
β-strand	445-456	12	7
β-strand	465-470	6	7
α-helix	476-483	8
β-strand	486-490	5	5

Chain H: 11 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	14
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
α-helix	52A-54	3
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
α-helix	114-116	3
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	164-165	2	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	195-200	6	18
α-helix	201-203	3
β-strand	205-210	6	18

Chain L: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
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	122-127	6
β-strand	129-139	11	12
β-strand	140	1	11
β-strand	144-150	7	13
β-strand	153-154	2	13
β-strand	159-163	5	12
α-helix	165-167	3
β-strand	173-182	10	12
α-helix	183-186	4
β-strand	191-198	8	13
β-strand	205-210	6	13

Chains M and S: 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, 28 β-strands

Element	Residues	Length	Sheet
α-helix	88-90	3
β-strand	91-94	4	19
α-helix	99-112	14
β-strand	120-125	6	20
β-strand	197-202	6	20
β-strand	215	1	21
β-strand	218	1	22
α-helix	219-220	2
β-strand	223-228	6	23
β-strand	236-239	4	19
β-strand	242-245	4	23
β-strand	247	1	22
α-helix	248-250	3
β-strand	251	1	21
β-strand	256	1	24
β-strand	257	1	25
β-strand	259-261	3	26
α-helix	264-266	3
β-strand	271-273	3	26
β-strand	284-296	13	26
β-strand	330-334	5	26
α-helix	335-353	19
β-strand	358-361	4	26
β-strand	367	1	27
α-helix	369-372	4
β-strand	374-378	5	24
β-strand	381-385	5	24
α-helix	388-390	3
β-strand	413-417	5	26
β-strand	418-421	4	24
β-strand	423-425	3	20
β-strand	432-434	3	20
α-helix	435-438	4
β-strand	445-457	13	26
β-strand	465-470	6	26
β-strand	472	1	25
α-helix	476-483	8
β-strand	486-490	5	23

Chain Q: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	28
β-strand	10-13	4	29
β-strand	19-25	7	28
β-strand	33-38	6	29
β-strand	45-49	5	29
β-strand	53-54	2	29
α-helix	55	1
β-strand	62-67	6	28
β-strand	70-75	6	28
α-helix	80-82	3
β-strand	85-90	6	29
β-strand	97-98	2	29
β-strand	102-106	5	29
β-strand	111	1	30
α-helix	112-113	2
β-strand	114-118	5	31
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	31
β-strand	140	1	30
β-strand	144-150	7	32
β-strand	154	1	32
β-strand	159-163	5	31
α-helix	164-167	4
β-strand	173-182	10	31
α-helix	183-187	5
β-strand	191-198	8	32
β-strand	205-210	6	32

Chain R: 11 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	33
β-strand	10-12	3	34
β-strand	18-25	8	33
α-helix	29-31	3
β-strand	32-39	8	34
β-strand	46-52	7	34
α-helix	52A-54	3
β-strand	56-59	4	34
α-helix	61-63	3
β-strand	67-72	6	33
β-strand	77-82	6	33
α-helix	84-86	3
β-strand	88-96	9	34
α-helix	100-100B	3
β-strand	102-103	2	34
β-strand	104	1	33
β-strand	107-111	5	34
α-helix	114-116	3
β-strand	117	1	35
α-helix	118-119	2
β-strand	120-124	5	36
β-strand	135-145	11	36
β-strand	146	1	35
β-strand	151-154	4	37
α-helix	155-157	3
β-strand	159	1	37
β-strand	163-165	3	36
α-helix	166-168	3
β-strand	169-170	2	36
β-strand	176-185	10	36
α-helix	186-188	3
β-strand	194-200	7	37
α-helix	201-203	3
β-strand	205-211	7	37

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Exterior membrane GLYCOPROTEIN(GP120)	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
[PHE23]M47, scorpion-toxin mimic of CD4	M, S	protein	27	synthetic construct

Sequence of entity 1 (G, P), FASTA

>2I60_1 EXTERIOR MEMBRANE GLYCOPROTEIN(GP120) (chains G, P)
GARSEVKLENVTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVGAGSCNTSVIT
QACPKVSFEPIPIHYCAPAGFAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQLLLN
GSLAEEEIVIRSENFTNNAKTIIVQLNESVVINCTGAGHCNLSKTQWENTLEQIAIKLKE
QFGNNKTIIFNPSSGGDPEIVTHSFNCGGEFFYCNSTQLFTWNDTRKLNNTGRNITLPCR
IKQIINMWQEVGKAMYAPPIRGQIRCSSNITGLLLTRDGGKDTNGTEIFRPGGGDMRDNW
RSELYKYKVVKIE

Sequence of entity 2 (L, Q), FASTA

>2I60_2 ANTIBODY 17B LIGHT CHAIN (chains L, Q)
DIVMTQSPATLSVSPGERATLSCRASESVSSDLAWYQQKPGQAPRLLIYGASTRATGVPA
RFSGSGSGAEFTLTISSLQSEDFAVYYCQQYNNWPPRYTFGQGTRLEIKRTVAAPSVFIF
PPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSST
LTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG

Sequence of entity 3 (H, R), FASTA

>2I60_3 ANTIBODY 17B HEAVY CHAIN (chains H, R)
EVQLVESGAEVKKPGSSVKVSCKASGDTFIRYSFTWVRQAPGQGLEWMGRIITILDVAHY
APHLQGRVTITADKSTSTVYLELRNLRSDDTAVYFCAGVYEGEADEGEYDNNGFLKHWGQ
GTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHT
FPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK

Sequence of entity 4 (M, S), FASTA

>2I60_4 [PHE23]M47, SCORPION-TOXIN MIMIC OF CD4 (chains M, S)
XNLHFCQLRCKSLGLLGRCAPTFCACX

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

Primary citation

Combinatorial optimization of a CD4-mimetic miniprotein and cocrystal structures with HIV-1 gp120 envelope glycoprotein. Stricher, F., Huang, C.C., Descours, A. et al. J Mol Biol (2008) 382:510-524. DOI 10.1016/j.jmb.2008.06.069 · 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…
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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