3SE9: HIV-1 Clade AE strain 93TH057 gp120

Crystal structure of broadly and potently neutralizing antibody VRC-PG04 in complex with HIV-1 gp120. Determined by X-ray diffraction at 2.0 Å resolution. Released 10 Aug 2011.

Method: X-ray diffraction
Resolution: 2.0 Å
Organisms: Human immunodeficiency virus 1, Homo sapiens
Chains: 3
Atoms: 6,803
Mol. weight: 90.84 kDa
Ligands: NAG, BU3
Released: 10 Aug 2011

Explore 3SE9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3SE9 contains 27 α-helices and 74 β-strands across 3 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: 10 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	45-47	3	1
β-strand	53-56	4	2
α-helix	65-73	9
β-strand	75-76	2	2
α-helix	77	1
β-strand	84-85	2	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
β-strand	271-273	3	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
α-helix	369-372	4
β-strand	374-378	5	5
β-strand	381-385	5	5
α-helix	388-390	3
β-strand	413-420	8	5
β-strand	423-426	4	4
β-strand	431-434	4	4
α-helix	436-439	4
β-strand	443-456	14	5
β-strand	465-470	6	5
α-helix	476-483	8
β-strand	486-491	6	1

Chain H: 10 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	6
β-strand	5-6	2	7
α-helix	7-9	3
β-strand	10-12	3	8
β-strand	18-23	6	7
α-helix	26-30	5
β-strand	32-39	9	8
β-strand	46-52	7	8
β-strand	56-58	3	8
α-helix	61-66	6
β-strand	67-72	6	7
β-strand	77-82	6	7
α-helix	84-86	3
β-strand	88-96	9	8
β-strand	102-103	2	8
β-strand	104	1	6
β-strand	107-111	5	8
β-strand	117	1	9
α-helix	118-119	2
β-strand	120-124	5	10
α-helix	125-127	3
β-strand	135-145	11	10
β-strand	146	1	9
β-strand	151-154	4	11
α-helix	155-157	3
β-strand	159	1	11
β-strand	163-165	3	10
α-helix	166-168	3
β-strand	169-170	2	10
β-strand	176-185	10	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: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	13
β-strand	10-13	4	14
β-strand	19-25	7	13
β-strand	34-38	5	14
β-strand	45-49	5	14
β-strand	53-54	2	14
α-helix	55	1
β-strand	62-67	6	13
β-strand	70-75	6	13
α-helix	80-82	3
β-strand	85-90	6	14
β-strand	97-98	2	14
β-strand	102-106	5	14
β-strand	111	1	15
α-helix	112-113	2
β-strand	114-118	5	16
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	16
β-strand	140	1	15
β-strand	145-150	6	17
β-strand	153-155	3	17
β-strand	159-163	5	16
α-helix	164-167	4
β-strand	173-182	10	16
α-helix	183-187	5
β-strand	191-197	7	17
β-strand	205-210	6	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HIV-1 Clade AE strain 93TH057 gp120	G	protein	353	Human immunodeficiency virus 1	Q0ED31
Heavy chain of antibody VRC-PG04	H	protein	228	Homo sapiens
Light chain of antibody VRC-PG04	L	protein	208	Homo sapiens

Sequence of entity 1 (G), FASTA

>3SE9_1 HIV-1 Clade AE strain 93TH057 gp120 (chains G)
VWKDADTTLFCASDAKAHETEVHNVWATHACVPTDPNPQEIHLENVTENFNMWKNNMVEQ
MQEDVISLWDQSLQPCVKLTGGSVIKQACPKISFDPIPIHYCTPAGYVILKCNDKNFNGT
GPCKNVSSVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTNNAKTIIVHLNKSVEINC
TRPSNGGSGSGGDIRKAYCEINGTKWNKVLKQVTEKLKEHFNNKTIIFQPPSGGDLEITM
HHFNCRGEFFYCNTTQLFNNTCIGNETMKGCNGTITLPCKIKQIINMWQGTGQAMYAPPI
DGKINCVSNITGILLTRDGGANNTSNETFRPGGGNIKDNWRSELYKYKVVQIE

Sequence of entity 2 (H), FASTA

>3SE9_2 Heavy chain of antibody VRC-PG04 (chains H)
QVQLVQSGSGVKKPGASVRVSCWTSEDIFERTELIHWVRQAPGQGLEWIGWVKTVTGAVN
FGSPDFRQRVSLTRDRDLFTAHMDIRGLTQGDTATYFCARQKFYTGGQGWYFDLWGRGTL
IVVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPA
VLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Sequence of entity 3 (L), FASTA

>3SE9_3 Light chain of antibody VRC-PG04 (chains L)
EIVLTQSPGTLSLSPGETASLSCTAASYGHMTWYQKKPGQPPKLLIFATSKRASGIPDRF
SGSQFGKQYTLTITRMEPEDFARYYCQQLEFFGQGTRLEIRRTVAAPSVFIFPPSDEQLK
SGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADY
EKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	10
BU3	(r,r)-2,3-butanediol	C4 H10 O2	1

Water and common crystallization additives (SO4, GOL, CL, TRS) are not listed.

Primary citation

Focused evolution of HIV-1 neutralizing antibodies revealed by structures and deep sequencing. Wu, X., Zhou, T., Zhu, J. et al. Science (2011) 333:1593-1602. DOI 10.1126/science.1207532 · 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…
4H8W 1.85 Å, Crystal structure of non-neutralizing and ADCC-potent antibody N5-i5 in complex with…
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
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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