4RX4: HIV-1 Clade A Q842.d12 gp120

Crystal structure of VH1-46 germline-derived CD4-binding site-directed antibody 8ANC134 in complex with HIV-1 clade A Q842.d12 gp120. Determined by X-ray diffraction at 3.45 Å resolution. Released 1 Jul 2015.

Method: X-ray diffraction
Resolution: 3.45 Å
Organisms: Human immunodeficiency virus 1, Homo sapiens
Chains: 6
Atoms: 11,975
Mol. weight: 178.98 kDa
Ligands: NAG
Released: 1 Jul 2015

Explore 4RX4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4RX4 contains 49 α-helices and 144 β-strands across 6 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: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	26
β-strand	11-12	2	27
β-strand	18-23	6	26
α-helix	26-31	6
β-strand	33-39	7	28
β-strand	45-51	7	28
β-strand	57-59	3	28
β-strand	67-72	6	26
β-strand	77-82	6	26
α-helix	84-86	3
β-strand	88-95	8	28
β-strand	102-103	2	28
β-strand	107-109	3	28
β-strand	110-111	2	27
α-helix	114-115	2
β-strand	117	1	29
α-helix	118-119	2
β-strand	120-124	5	30
α-helix	125-127	3
β-strand	136-145	10	30
β-strand	146	1	29
β-strand	151-154	4	31
β-strand	163-165	3	30
α-helix	166-168	3
β-strand	169-170	2	30
β-strand	176-184	9	30
β-strand	195-200	6	31
α-helix	201-203	3
β-strand	205-210	6	31

Chain D: 8 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	32
β-strand	10-13	4	33
α-helix	18	1
β-strand	19-30	11	32
β-strand	34-38	5	33
β-strand	45-48	4	33
β-strand	54	1	33
β-strand	62-75	14	32
α-helix	80-82	3
β-strand	85-89	5	33
α-helix	96-97	2
β-strand	98	1	33
α-helix	99	1
β-strand	102-106	5	33
β-strand	111	1	34
β-strand	114-118	5	35
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	35
β-strand	140	1	34
β-strand	144-150	7	36
β-strand	153-155	3	36
β-strand	159-163	5	35
α-helix	164-167	4
β-strand	173-182	10	35
α-helix	183-186	4
β-strand	191-198	8	36
β-strand	205-210	6	36

Chain E: 9 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	46-47	2	20
β-strand	53-55	3	21
α-helix	65-73	9
β-strand	75	1	21
α-helix	76-78	3
β-strand	83-85	3	20
β-strand	91-94	4	22
α-helix	95-97	3
α-helix	99-115	17
β-strand	120-122	3	23
β-strand	215	1	24
β-strand	216-218	3	21
β-strand	224-228	5	20
β-strand	236-239	4	22
β-strand	242-245	4	20
β-strand	247	1	21
α-helix	248-250	3
β-strand	251	1	24
β-strand	256	1	25
β-strand	259-261	3	25
β-strand	271-273	3	25
β-strand	284-298	15	25
β-strand	328-333	6	25
α-helix	335-350	16
β-strand	359-361	3	25
α-helix	369-372	4
β-strand	374-378	5	25
β-strand	381-385	5	25
β-strand	393	1	25
β-strand	414-420	7	25
β-strand	423-425	3	23
β-strand	432-434	3	23
α-helix	436-439	4
β-strand	443-456	14	25
β-strand	466-470	5	25
α-helix	476-483	8
β-strand	486-490	5	20

Chain G: 9 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	47	1	1
β-strand	53-55	3	2
α-helix	65-73	9
β-strand	74-75	2	2
α-helix	76-78	3
β-strand	83-85	3	1
β-strand	89	1	3
β-strand	91-94	4	4
α-helix	95-97	3
α-helix	99-115	17
β-strand	119	1	5
β-strand	215	1	6
β-strand	216-218	3	2
β-strand	223-228	6	1
β-strand	236-239	4	4
β-strand	241	1	3
β-strand	242-245	4	1
β-strand	247	1	2
α-helix	248-250	3
β-strand	251	1	6
β-strand	256	1	7
β-strand	259-261	3	7
β-strand	271-273	3	7
β-strand	284-298	15	7
β-strand	328-333	6	7
α-helix	335-352	18
β-strand	359-361	3	7
α-helix	369-372	4
β-strand	374-378	5	7
β-strand	381-385	5	7
β-strand	393-394	2	7
β-strand	414-420	7	7
β-strand	423-425	3	5
β-strand	432-434	3	5
α-helix	436-439	4
β-strand	443-456	14	7
β-strand	466-470	5	7
α-helix	476-483	8
β-strand	486-490	5	1

Chain H: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	8
β-strand	11-12	2	9
β-strand	18-24	7	8
α-helix	26-31	6
β-strand	33-39	7	10
β-strand	45-51	7	10
β-strand	57-59	3	10
β-strand	67-72	6	8
β-strand	77-82	6	8
α-helix	84-86	3
β-strand	88-95	8	10
β-strand	100F	1	11
β-strand	102-103	2	10
β-strand	107-109	3	10
β-strand	110-111	2	9
α-helix	114-116	3
β-strand	117	1	12
α-helix	118-119	2
β-strand	120-124	5	13
α-helix	125-127	3
β-strand	136-145	10	13
β-strand	146	1	12
β-strand	151-154	4	14
α-helix	155-157	3
β-strand	163-165	3	13
α-helix	166-168	3
β-strand	169-170	2	13
β-strand	176-184	9	13
β-strand	195-200	6	14
α-helix	201-203	3
β-strand	205-210	6	14

Chain L: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	15
β-strand	10-13	4	16
α-helix	18	1
β-strand	19-30	11	15
β-strand	34-38	5	16
β-strand	45-48	4	16
β-strand	50	1	11
β-strand	54	1	16
β-strand	62-75	14	15
α-helix	80-82	3
β-strand	85-89	5	16
α-helix	96-97	2
β-strand	98	1	16
α-helix	99	1
β-strand	102-106	5	16
β-strand	111	1	17
β-strand	114-118	5	18
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	18
β-strand	140	1	17
β-strand	145-150	6	19
β-strand	153-155	3	19
β-strand	159-163	5	18
α-helix	164-167	4
β-strand	173-182	10	18
α-helix	183-187	5
β-strand	191-197	7	19
β-strand	205-210	6	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HIV-1 Clade A Q842.d12 gp120	E, G	protein	354	Human immunodeficiency virus 1	Q8JDI3
8ANC134 Heavy chain	A, H	protein	229	Homo sapiens
8ANC134 Light Chain	D, L	protein	213	Homo sapiens

Sequence of entity 1 (E, G), FASTA

>4RX4_1 HIV-1 Clade A Q842.d12 gp120 (chains E, G)
VWKEAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQ
MHTDIISLWDQSLKPCVKLTGGSAITQACPKVTFEPIPIHYCAPAGFAILKCKDEEFNGI
GPCKNVSTVQCTHGIKPVVSTQLLLNGSLAEKEVKIRCENITNNAKTIIVQLVNPVKINC
TRPNNGGSGSGGDIRQAHCNVNRTEWNNTLHQVVEQLRKHFNKTINFANSTGGDLEITTH
SFNCGGEFFYCNTTNLFNSTWNHTASMNSTESNDTIILPCRIKQIINMWQRVGQAMYAPP
IRGVIRCESNITGLILTRDGGNTNSTRETFRPGGGDMRDNWRSELYKYKVVKIE

Sequence of entity 2 (A, H), FASTA

>4RX4_2 8ANC134 Heavy chain (chains A, H)
QGQLVQSGGGVKKPGTSVTISCLASEYTFNEFVIHWIRQAPGQGPVWLGLIKRSGRLMTS
YKFQDRLSLRRDRSTGTVFMELRGLRLDDTAVYYCARDGLGEVAPAYLYGIDAWGQGSTV
IVTSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAV
LQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKAEPKSCDK

Sequence of entity 3 (D, L), FASTA

>4RX4_3 8ANC134 Light Chain (chains D, L)
EIVLTQSPATLSLSPGERATLSCRASQGLNFVVWYQQKGGQAPRLLIHGPTDRAPGVPDR
FSARGSGTEFSLVISSVEPDDFALYYCQEYSSTPYNFGPGTRVERKRTVAAPSVFIFPPS
DEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTL
SKADYEKHKVYACEVTHQGLRSPVTKSFNRGEC

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	11

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

Primary citation

Structural Repertoire of HIV-1-Neutralizing Antibodies Targeting the CD4 Supersite in 14 Donors. Zhou, T., Lynch, R.M., Chen, L. et al. Cell (2015) 161:1280-1292. DOI 10.1016/j.cell.2015.05.007 · PubMed

Other PDB entries of the same protein (UniProt Q8JDI3), best resolution first:

4XMP 1.78 Å, Crystal structure of broadly and potently neutralizing antibody VRC08 in complex with…
4XNY 2.3 Å, Crystal structure of broadly and potently neutralizing antibody VRC08C in complex with…

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