4YDV: Antibody 7B2 that captures HIV-1 virions

Structure of the antibody 7B2 that captures HIV-1 virions. Determined by X-ray diffraction at 2.7 Å resolution. Released 12 Aug 2015.

Method: X-ray diffraction
Resolution: 2.7 Å
Organisms: Human immunodeficiency virus 1, Homo sapiens
Chains: 6
Atoms: 6,805
Mol. weight: 115.16 kDa
Released: 12 Aug 2015

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

Secondary structure: helices and β-sheets

4YDV contains 27 α-helices and 88 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.

Chains A and L: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	11
β-strand	10-13	4	12
β-strand	19-25	7	11
β-strand	33-38	6	12
β-strand	45-49	5	12
β-strand	53-54	2	12
α-helix	55	1
β-strand	62-67	6	11
β-strand	70-75	6	11
α-helix	80-82	3
β-strand	85-90	6	12
β-strand	97-98	2	12
β-strand	102-106	5	12
β-strand	111	1	13
β-strand	114-118	5	14
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	14
β-strand	140	1	13
β-strand	145-150	6	15
β-strand	153-154	2	15
β-strand	159-163	5	14
α-helix	164-167	4
β-strand	173-182	10	14
α-helix	183-187	5
β-strand	192-197	6	15
β-strand	205-209	5	15

Chain B: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	16
β-strand	10-12	3	1
β-strand	18-25	8	16
α-helix	29-31	3
β-strand	33-39	7	1
β-strand	45-51	7	1
β-strand	57-59	3	1
β-strand	67-72A	6	16
α-helix	72B-72	3
β-strand	74-79	6	16
α-helix	84-86	3
β-strand	88-100	13	1
β-strand	100C-103	10	1
β-strand	107-111	5	1
β-strand	117	1	17
α-helix	118-119	2
β-strand	120-124	5	18
β-strand	135-145	11	18
β-strand	146	1	17
β-strand	151-154	4	19
β-strand	159	1	19
β-strand	163-165	3	18
α-helix	166-168	3
β-strand	169-170	2	18
β-strand	176-185	10	18
α-helix	186-189	4
β-strand	194-200	7	19
α-helix	201-203	3
β-strand	205-211	7	19

Chain H: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	7
β-strand	10-12	3	1
β-strand	18-25	8	7
α-helix	29-31	3
β-strand	33-39	7	1
β-strand	45-51	7	1
β-strand	57-59	3	1
β-strand	67-72	6	7
α-helix	72A-72C	3
β-strand	74-79	6	7
α-helix	84-86	3
β-strand	88-100	13	1
β-strand	100C-103	10	1
β-strand	107-111	5	1
β-strand	117	1	8
α-helix	118-119	2
β-strand	120-124	5	9
β-strand	135-145	11	9
β-strand	146	1	8
β-strand	151-154	4	10
β-strand	159	1	10
β-strand	163-165	3	9
α-helix	166-168	3
β-strand	169-170	2	9
β-strand	176-185	10	9
α-helix	186-189	4
β-strand	194-200	7	10
α-helix	201-203	3
β-strand	205-211	7	10

Chain P: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	597-599	3	1

Chain Q: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	597-599	3	1
α-helix	602-605	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HIV GP41 peptide GP41(596-606)	P, Q	protein	13	Human immunodeficiency virus 1	P04578 (AlphaFold model)
HIV ANTIBODY 7B2 LIGHT CHAIN,Ig kappa chain C region	A, L	protein	265	Homo sapiens	P01834 (AlphaFold model)
HIV ANTIBODY 7B2 HEAVY CHAIN,IgG H chain	B, H	protein	252	Homo sapiens	S6B291 (AlphaFold model)

Sequence of entity 1 (P, Q), FASTA

>4YDV_1 HIV GP41 PEPTIDE GP41(596-606) (chains P, Q)
XWGCSGKLICTTX

Sequence of entity 2 (A, L), FASTA

>4YDV_2 HIV ANTIBODY 7B2 LIGHT CHAIN,Ig kappa chain C region (chains A, L)
METDTLLLWVLLLWVPGSTGDDIQMTQSPASLAVPLLLWISGAYGDIVLAQSPDSLAVSP
GERATIHCKSSQTLLYSSNNRHSIAWYQQRPGQPPKLLLYWASMRLSGVPDRFSGSGSGT
DFTLTINNLQAEDVAIYYCHQYSSHPPTFGHGTRVELRRTVAAPSVFIFPPSDEQLKSGT
ASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKH
KVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (B, H), FASTA

>4YDV_3 HIV ANTIBODY 7B2 HEAVY CHAIN,IgG H chain (chains B, H)
METDTLLLWVLLLWVPGSTGDQVQLVQSGGGVFKPGGSLRLSCEASGFTFTEYYMTWVRQ
APGKGLEWLAYISKNGEYSKYSPSSNGRFTISRDNAKNSVFLQLDRLSADDTAVYYCARA
DGLTYFSELLQYIFDLWGQGARVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYF
PEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTK
VDKRVEPKSCDK

Primary citation

Human Non-neutralizing HIV-1 Envelope Monoclonal Antibodies Limit the Number of Founder Viruses during SHIV Mucosal Infection in Rhesus Macaques. Santra, S., Tomaras, G.D., Warrier, R. et al. PLoS Pathog (2015) 11:e1005042-e1005042. DOI 10.1371/journal.ppat.1005042 · PubMed

Other PDB entries of the same protein (UniProt P04578 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8F3A 1.2 Å, HIV-1 gp41 coiled-coil pocket IQN17
6UCF 1.29 Å, N123-VRC34_pI4 HIV neutralizing antibody in complex with HIV fusion peptide residue…
6PSA 1.3 Å, PIE12 D-peptide against HIV entry (in complex with IQN17 Q577R resistance mutant)
6UCE 1.38 Å, N123-VRC34_pI3 HIV neutralizing antibody in complex with HIV fusion peptide residue…
9ARN 1.41 Å, Structure and interactions of HIV-1 gp41 CHR-NHR reverse hairpin constructs reveal…
1DF4 1.45 Å, Interactions between HIV-1 GP41 core and detergents and their implications for membrane…
6BXP 1.45 Å, Crystal Structure of HLA-B*57:01 with a modified HIV peptide RKV-Kyn
7EKB 1.45 Å, Crystal structure of 4E10 modified with pyrene acetamide
5X08 1.49 Å, Crystal structure of broadly neutralizing anti-HIV-1 antibody 4E10, mutant Npro, with…
6JQK 1.5 Å, Structure of C34M/N36
5TKK 1.55 Å, Structure of mouse vaccination-elicited HIV neutralizing antibody vFP5.01 in complex…
6PDR 1.55 Å, Vaccine-elicited murine FP-targeting antibody vFP25.18 in complex with HIV fusion…

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