4H8W: Non-neutralizing and ADCC-potent antibody N5-i5

Crystal structure of non-neutralizing and ADCC-potent antibody N5-i5 in complex with HIV-1 clade A/E gp120 and sCD4. Determined by X-ray diffraction at 1.85 Å resolution. Released 9 Apr 2014.

Method: X-ray diffraction
Resolution: 1.85 Å
Organism: Homo sapiens
Chains: 4
Atoms: 8,180
Mol. weight: 109.06 kDa
Ligands: MRD, NAG
Released: 9 Apr 2014

Explore 4H8W in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4H8W contains 32 α-helices and 96 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 C: 4 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	6
β-strand	12-14	3	20
β-strand	17	1	21
β-strand	26-30	5	6
β-strand	35-40	6	6
β-strand	43-46	4	6
α-helix	52-54	3
β-strand	55-56	2	20
α-helix	59-64	6
β-strand	66	1	21
β-strand	69-71	3	20
α-helix	76-78	3
β-strand	80-86	7	6
β-strand	89-98	10	6
β-strand	99-102	4	22
β-strand	107	1	23
β-strand	114-119	6	22
β-strand	127-131	5	24
β-strand	137-139	3	24
β-strand	143-146	4	22
α-helix	151-153	3
β-strand	155-163	9	24
β-strand	166-174	9	24
β-strand	175	1	23

Chain G: 11 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	46-47	2	1
β-strand	53-56	4	2
α-helix	65-73	9
β-strand	75-76	2	2
α-helix	77-78	2
β-strand	83-85	3	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	215-218	4	2
β-strand	223-228	6	1
β-strand	236-239	4	3
β-strand	242-245	4	1
β-strand	247	1	2
β-strand	251	1	2
β-strand	256	1	5
β-strand	259-261	3	5
α-helix	264-266	3
β-strand	271-274	4	5
α-helix	283	1
β-strand	284-298	15	5
β-strand	328-334	7	5
α-helix	335-352	18
α-helix	357	1
β-strand	358-361	4	5
β-strand	367	1	6
α-helix	369-372	4
β-strand	374-378	5	5
β-strand	381-385	5	5
α-helix	388-390	3
β-strand	413-421	9	5
β-strand	423-425	3	4
β-strand	432-434	3	4
α-helix	436-439	4
β-strand	443-456	14	5
β-strand	465-470	6	5
α-helix	475-483	9
β-strand	486-490	5	1

Chain H: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	7
β-strand	10-12	3	8
β-strand	18-25	8	7
α-helix	29-31	3
β-strand	34-39	6	8
β-strand	45-51	7	8
β-strand	57-59	3	8
α-helix	61-63	3
β-strand	67-72	6	7
β-strand	77-82	6	7
α-helix	84-86	3
β-strand	88-95	8	8
β-strand	100B-103	4	8
β-strand	107-111	5	8
α-helix	115-116	2
β-strand	117	1	9
α-helix	118-119	2
β-strand	120-124	5	10
β-strand	137-145	9	10
β-strand	146	1	9
β-strand	151-154	4	11
α-helix	155-157	3
β-strand	163-165	3	10
α-helix	166-168	3
β-strand	169-170	2	10
β-strand	176-183	8	10
α-helix	186-188	3
β-strand	189	1	12
β-strand	192	1	12
β-strand	194-200	7	11
α-helix	201-203	3
β-strand	205-211	7	11

Chain L: 8 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	13
β-strand	6	1	14
β-strand	10-13	4	15
β-strand	19-24	6	14
β-strand	33-38	6	15
β-strand	45-48	4	15
β-strand	49	1	16
β-strand	53	1	16
β-strand	62-67	6	14
β-strand	70-75	6	14
α-helix	80-82	3
β-strand	84-91	8	15
α-helix	93-95A	4
β-strand	96-98	3	15
β-strand	99	1	13
β-strand	102-106	5	15
α-helix	109-111	3
β-strand	112	1	17
α-helix	113-114	2
β-strand	115-119	5	18
α-helix	120-122	3
α-helix	123-127	5
β-strand	131-140	10	18
β-strand	141	1	17
β-strand	146-151	6	19
β-strand	154-155	2	19
β-strand	160-162	3	18
α-helix	163-165	3
β-strand	166-167	2	18
β-strand	173-181	9	18
α-helix	183-188	6
β-strand	192-198	7	19
β-strand	201-207	7	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HIV-1 clade a/e 93TH057 (H375S) GP120	G	protein	353	Homo sapiens	Q0ED31
FAB heavy chain of adcc and non-neutralizing anti-HIV-1 antibody N5-I5	H	protein	226	Homo sapiens
FAB light chain of adcc and non-neutralizing anti-HIV-1 antibody N5-I5	L	protein	217	Homo sapiens
T-cell surface glycoprotein CD4	C	protein	185	Homo sapiens	P01730 (AlphaFold model)

Sequence of entity 1 (G), FASTA

>4H8W_1 HIV-1 CLADE A/E 93TH057 (H375S) GP120 (chains G)
VWKDADTTLFCASDAKAHETEVHNVWATHACVPTDPNPQEIHLENVTENFNMWKNNMVEQ
MQEDVISLWDQSLQPCVKLTGGSVIKQACPKISFDPIPIHYCTPAGYVILKCNDKNFNGT
GPCKNVSSVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTNNAKTIIVHLNKSVEINC
TRPSNGGSGSGGDIRKAYCEINGTKWNKVLKQVTEKLKEHFNNKTIIFQPPSGGDLEITM
HSFNCRGEFFYCNTTQLFNNTCIGNETMKGCNGTITLPCKIKQIINMWQGTGQAMYAPPI
DGKINCVSNITGILLTRDGGANNTSNETFRPGGGNIKDNWRSELYKYKVVQIE

Sequence of entity 2 (H), FASTA

>4H8W_2 FAB HEAVY CHAIN OF ADCC AND NON-NEUTRALIZING ANTI-HIV-1 ANTIBODY N5-I5 (chains H)
EVQLVESGGGLVQPGGSLRLSCAASGFTFSTYAMSWVRQAPGKGLEWVSSINNSGRNTFS
ADSVKGRFTISRDNSKNTLFLVMNSLRAEDTAVYYCAKDLRLGGGSDYWGQGTLVTVSSA
STKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSG
LYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTH

Sequence of entity 3 (L), FASTA

>4H8W_3 FAB LIGHT CHAIN OF ADCC AND NON-NEUTRALIZING ANTI-HIV-1 ANTIBODY N5-I5 (chains L)
QSALTQPASVSGSPGQSITISCTGTSSDVGSYNFVSWYQQHPGKAPKLMIYEVSERPSGI
SNRFSGSKSGNTASLTISGLQAEDEADYYCSSYAGSTTFRVFGGGTKLTVRGQPKAAPSV
TLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAAS
SYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Sequence of entity 4 (C), FASTA

>4H8W_4 T-cell surface glycoprotein CD4 (chains C)
KKVVLGKKGDTVELTCTASQKKSIQFHWKNSNQIKILGNQGSFLTKGPSKLNDRADSRRS
LWDQGNFPLIIKNLKIEDSDTYICEVEDQKEEVQLLVFGLTANSDTHLLQGQSLTLTLES
PPGSSPSVQCRSPRGKNIQGGKTLSVSQLELQDSGTWTCTVLQNQKKVEFKIDIVVLAFQ
KASNT

Ligands and cofactors

ID	Name	Formula	Copies
MRD	(4R)-2-methylpentane-2,4-diol	C6 H14 O2	3
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	10

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

Primary citation

Structural Definition of an Antibody-Dependent Cellular Cytotoxicity Response Implicated in Reduced Risk for HIV-1 Infection. Acharya, P., Tolbert, W.D., Gohain, N. et al. J Virol (2014) 88:12895-12906. DOI 10.1128/JVI.02194-14 · PubMed

Other PDB entries of the same protein (UniProt Q0ED31), best resolution first:

4XVT 1.69 Å, Crystal structure of HIV-1 93TH057 coreE gp120 with antibody…
4DKP 1.8 Å, Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with AWS-I-50
4DKR 1.8 Å, Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with AWS-I-169
4YDL 1.8 Å, Crystal structure of broadly and potently neutralizing antibody C38-VRC18.02 in complex…
4DKQ 1.89 Å, Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with DMJ-I-228
3SE8 1.9 Å, Crystal structure of broadly and potently neutralizing antibody VRC03 in complex with…
3TGT 1.9 Å, Crystal structure of unliganded HIV-1 clade A/E strain 93TH057 gp120 core
4DKO 1.98 Å, Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with TS-II-224
3SE9 2.0 Å, Crystal structure of broadly and potently neutralizing antibody VRC-PG04 in complex with…
4YDK 2.05 Å, Crystal structure of broadly and potently neutralizing antibody C38-VRC16.01 in complex…
4OLZ 2.1 Å, Crystal structure of antibody VRC07-G54W in complex with clade A/E 93TH057 HIV-1 gp120…
4OM1 2.13 Å, Crystal structure of antibody VRC07-I30Q, G54W, S58N in complex with clade A/E 93TH057…

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