4JZW: CD4-mimetic miniprotein M48U1

Crystal structure of CD4-mimetic miniprotein M48U1 in complex with HIV-1 YU2 gp120 in P212121 space group. Determined by X-ray diffraction at 1.78 Å resolution. Released 12 Jun 2013.

Method: X-ray diffraction
Resolution: 1.78 Å
Organism: Human immunodeficiency virus 1
Chains: 4
Atoms: 7,061
Mol. weight: 94.22 kDa
Ligands: IPA, NAG
Released: 12 Jun 2013

Explore 4JZW in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4JZW contains 25 α-helices and 63 β-strands across 4 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: 10 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	45	1
β-strand	46-47	2	1
β-strand	53-56	4	2
α-helix	65-73	9
β-strand	74-76	3	2
α-helix	77	1
β-strand	83-86	4	1
β-strand	91-94	4	3
α-helix	99-115	17
β-strand	120-123	4	4
β-strand	199-202	4	4
β-strand	215	1	5
β-strand	216-218	3	2
β-strand	223-228	6	1
β-strand	236-239	4	3
β-strand	242-245	4	1
β-strand	247	1	2
α-helix	248-250	3
β-strand	251	1	5
β-strand	256	1	6
β-strand	259-261	3	6
β-strand	271-274	4	6
α-helix	283	1
β-strand	284-298	15	6
β-strand	328-334	7	6
α-helix	335-353	19
β-strand	358-361	4	6
β-strand	367	1	7
α-helix	369-372	4
β-strand	374-378	5	6
β-strand	381-385	5	6
β-strand	393	1	6
β-strand	413-421	9	6
β-strand	423-425	3	4
β-strand	432-434	3	4
α-helix	436-439	4
β-strand	443-456	14	6
β-strand	465-470	6	6
α-helix	475-483	9
β-strand	486-490	5	1

Chain G: 13 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	45	1
β-strand	46-47	2	8
β-strand	53-56	4	9
α-helix	65-73	9
β-strand	74-76	3	9
α-helix	77	1
β-strand	84-85	2	8
β-strand	91-94	4	10
α-helix	99-115	17
β-strand	120-123	4	11
β-strand	199-202	4	11
β-strand	215-218	4	9
β-strand	223-228	6	8
β-strand	236-239	4	10
β-strand	242-245	4	8
β-strand	247	1	9
α-helix	248-250	3
β-strand	251	1	9
β-strand	256	1	12
β-strand	259-261	3	12
α-helix	264-266	3
β-strand	271-274	4	12
α-helix	283	1
β-strand	284-298	15	12
β-strand	328-334	7	12
α-helix	335-353	19
α-helix	357	1
β-strand	358-361	4	12
β-strand	367	1	13
α-helix	369-372	4
β-strand	374-378	5	12
β-strand	381-385	5	12
α-helix	388-391	4
β-strand	393	1	12
β-strand	413-421	9	12
β-strand	423-425	3	11
β-strand	432-434	3	11
α-helix	436-439	4
β-strand	443-456	14	12
β-strand	465-470	6	12
α-helix	475-483	9
β-strand	486-490	5	8

Chain M: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
α-helix	3-12	10
β-strand	17-20	4	13
β-strand	23-26	4	13

Chain R: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
α-helix	3-11	9
β-strand	17-20	4	7
β-strand	23-26	4	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HIV-1 YU2 gp120 glycoprotein	A, G	protein	376	Human immunodeficiency virus 1	P35961
CD4-mimetic miniprotein M48U1	M, R	protein	28

Sequence of entity 1 (A, G), FASTA

>4JZW_1 HIV-1 YU2 gp120 glycoprotein (chains A, G)
MPMGSLQPLATLYLLGMLVASVLAVWKEATTTLFCASDAKAYDTEVHNVWATHACVPTDP
NPQEVKLENVTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTGGSVITQACPKVSFEP
IPIHYCAPAGFAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVI
RSENFTNNAKTIIVQLNESVVINCTRPNNGGSGSGGDIRQAHCNLSKTQWENTLEQIAIK
LKEQFGNNKTIIFNPSSGGDPEIVTHSFNCGGEFFYCNSTQLFTWNDTRKLNNTGRNITL
PCRIKQIINMWQEVGKAMYAPPIRGQIRCSSNITGLLLTRDGGKDTNGTEIFRPGGGDMR
DNWRSELYKYKVVKIE

Sequence of entity 2 (M, R), FASTA

>4JZW_2 CD4-MIMETIC MINIPROTEIN M48U1 (chains M, R)
XNLHFCQLRCKSLGLLGRCAPTXCACVX

Ligands and cofactors

ID	Name	Formula	Copies
IPA	Isopropyl alcohol	C3 H8 O	8
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	18

Water and common crystallization additives (EDO, SO4) are not listed.

Primary citation

Structural Basis for Highly Effective HIV-1 Neutralization by CD4-Mimetic Miniproteins Revealed by 1.5 A Cocrystal Structure of gp120 and M48U1. Acharya, P., Luongo, T.S., Louder, M.K. et al. Structure (2013) 21:1018-1029. DOI 10.1016/j.str.2013.04.015 · 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…
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…
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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