4HPY: RV144-elicited antibody CH59

Crystal structure of RV144-elicited antibody CH59 in complex with V2 peptide. Determined by X-ray diffraction at 1.5 Å resolution. Released 6 Feb 2013.

Method: X-ray diffraction
Resolution: 1.5 Å
Organisms: Homo sapiens, Human immunodeficiency virus 1
Chains: 3
Atoms: 3,877
Mol. weight: 49.46 kDa
Released: 6 Feb 2013

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

Secondary structure: helices and β-sheets

4HPY contains 19 α-helices and 49 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 H: 11 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	11-12	2	2
β-strand	18-25	8	1
β-strand	34-39	6	3
β-strand	45-51	7	3
β-strand	57-59	3	3
β-strand	67-72	6	1
α-helix	73-75	3
β-strand	77-82	6	1
α-helix	84-86	3
β-strand	88-94	7	3
α-helix	95-96	2
α-helix	97-99	3
β-strand	102-103	2	3
β-strand	107-109	3	3
β-strand	110-111	2	2
β-strand	117	1	4
α-helix	118-119	2
β-strand	120-124	5	5
α-helix	128-130	3
β-strand	131-132	2	5
β-strand	135-145	11	5
β-strand	146	1	4
β-strand	151-154	4	6
α-helix	155-157	3
β-strand	159	1	6
β-strand	163-165	3	5
α-helix	166-168	3
β-strand	169-170	2	5
α-helix	171	1
β-strand	176-185	10	5
α-helix	186-188	3
β-strand	195-200	6	6
α-helix	201-203	3
β-strand	205-210	6	6

Chain L: 7 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	7
β-strand	9-13	4	8
α-helix	18	1
β-strand	19-24	6	7
β-strand	31	1	9
β-strand	34-38	5	8
β-strand	45-48	4	8
β-strand	49	1	10
β-strand	53	1	10
β-strand	62-67	6	7
β-strand	70-75	6	7
α-helix	80-82	3
β-strand	84-91	8	8
β-strand	96-98	3	8
β-strand	102-106	5	8
β-strand	111	1	11
α-helix	112-113	2
β-strand	114-118	5	12
α-helix	119-121	3
α-helix	122-125	4
β-strand	130-139	10	12
β-strand	140	1	11
β-strand	145-150	6	13
β-strand	153-155	3	13
β-strand	159-161	3	12
α-helix	162-164	3
β-strand	165-166	2	12
β-strand	172-180	9	12
α-helix	182-187	6
β-strand	191-197	7	13
β-strand	200-206	7	13

Chain P: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	170	1	9
α-helix	174-176	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
CH59 Fab heavy chain	H	protein	225	Homo sapiens	Q6N089 (AlphaFold model)
CH59 Fab light chain	L	protein	215	Homo sapiens	Q8N5F4 (AlphaFold model)
Envelope glycoprotein gp160	P	protein	19	Human immunodeficiency virus 1	G9HS63

Sequence of entity 1 (H), FASTA

>4HPY_1 CH59 Fab heavy chain (chains H)
EVQLVESGGGLVQPGRSLRLSCAASGFTFDDGAMHWVRQAPGKGLEWVSGISWNSNIIAY
ADSVKGRFTISRDNAKNSLYLEMNSLRVEDTALYYCAKDSPRGELPLNYWGQGTLVTVSS
ASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSS
GLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDK

Sequence of entity 2 (L), FASTA

>4HPY_2 CH59 Fab light chain (chains L)
DSYELTQPPSVSVSPGQTARITCSGDALPKNYAYWYQQKSGQAPVLVIYEDSKRPSGIPE
RFSGSSSGTMATLTISGAQVEDEADYYCYSTDSSGNHRVFGGGTKLTVLGQPKAAPSVTL
FPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSY
LSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Sequence of entity 3 (P), FASTA

>4HPY_3 Envelope glycoprotein gp160 (chains P)
ELRDKKQKVHALFYKLDIV

Primary citation

Vaccine Induction of Antibodies against a Structurally Heterogeneous Site of Immune Pressure within HIV-1 Envelope Protein Variable Regions 1 and 2. Liao, H.X., Bonsignori, M., Alam, S.M. et al. Immunity (2013) 38:176-186. DOI 10.1016/j.immuni.2012.11.011 · PubMed

Other PDB entries of the same protein (UniProt Q6N089 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5EWI 1.6 Å, Crystal Structure of the Human Fab VRC38.01, an HIV-1 V1V2-Directed Neutralizing…
4NUJ 1.83 Å, Crystal structure of HIV-1 broadly neutralizing antibody PGT152
3QCU 1.98 Å, Crystal structure of the LT3015 antibody Fab fragment in complex with lysophosphatidic…
5VKK 2.01 Å, Crystal structure of Fab fragment of anti-CD22 Epratuzumab
3QCT 2.15 Å, Crystal structure of the humanized apo LT3015 anti-lysophosphatidic acid antibody Fab…
3MNV 2.4 Å, Crystal structure of the non-neutralizing HIV antibody 13H11 Fab fragment
3QCV 2.51 Å, Crystal structure of the LT3015 antibody Fab fragment in complex with lysophosphatidic…
5XRQ 2.6 Å, Crystal structure of human monoclonal antibody H3v-47
2OQJ 2.8 Å, Crystal structure analysis of Fab 2G12 in complex with peptide 2G12.1
6V8Z 2.9 Å, VRC03 and 10-1074 Bound BG505 F14 HIV-1 SOSIP Envelope Trimer Structure
5UG0 3.4 Å, Human antibody H2897 in complex with influenza hemagglutinin H1 Solomon Islands/03/2006
5WKO 3.49 Å, Crystal structure of antibody 27F3 recognizing the HA from A/California/04/2009 (H1N1)…

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