6WX2: VFP16.02 antibody heavy chain

Vaccine-elicited mouse FP-targeting neutralizing antibody vFP16.02 with F60P mutation on light chain in complex with HIV fusion peptide (residue 512-519). Determined by X-ray diffraction at 2.39 Å resolution. Released 17 Mar 2021.

Method: X-ray diffraction
Resolution: 2.39 Å
Organisms: Mus musculus, Human immunodeficiency virus 1
Chains: 6
Atoms: 6,783
Mol. weight: 95.79 kDa
Released: 17 Mar 2021

Explore 6WX2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6WX2 contains 27 α-helices and 90 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.

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

Element	Residues	Length	Sheet
β-strand	3-5	3	1
β-strand	9-12	4	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	33-39	7	2
β-strand	45-51	7	2
β-strand	58-60	3	2
α-helix	62-64	3
β-strand	68-73	6	1
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-99	8	2
β-strand	108	1	2
β-strand	112-116	5	2
α-helix	120-121	2
β-strand	122	1	3
β-strand	125-129	5	4
β-strand	140-150	11	4
β-strand	151	1	3
β-strand	156-159	4	5
α-helix	160-162	3
β-strand	164	1	5
β-strand	168-176	9	4
β-strand	179-189	11	4
β-strand	199-204	6	5
α-helix	205-207	3
β-strand	209-214	6	5

Chain B: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	6
β-strand	10-14	5	7
β-strand	19-25	7	6
β-strand	30	1	8
β-strand	36	1	8
β-strand	38-43	6	7
β-strand	50-53	4	7
β-strand	54	1	9
β-strand	58	1	9
β-strand	67-72	6	6
β-strand	75-80	6	6
α-helix	85-87	3
β-strand	89-95	7	7
α-helix	101	1
β-strand	102-103	2	7
β-strand	107-112	6	7
β-strand	116	1	10
α-helix	117-118	2
β-strand	119-123	5	11
α-helix	124-126	3
α-helix	127-130	4
β-strand	134-144	11	11
β-strand	145	1	10
β-strand	150-155	6	12
β-strand	158-160	3	12
β-strand	164-168	5	11
α-helix	169-172	4
β-strand	178-187	10	11
α-helix	188-192	5
β-strand	196-202	7	12
α-helix	209	1
β-strand	210-215	6	12

Chain L: 7 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	18
β-strand	10-14	5	19
β-strand	19-25	7	18
β-strand	30	1	20
β-strand	36	1	20
β-strand	38-43	6	19
β-strand	49-53	5	19
β-strand	54	1	21
β-strand	58	1	21
β-strand	67-72	6	18
β-strand	75-80	6	18
α-helix	85-87	3
β-strand	89-95	7	19
α-helix	101	1
β-strand	102-103	2	19
β-strand	107-112	6	19
β-strand	116	1	22
α-helix	117-118	2
β-strand	119-123	5	23
α-helix	124-126	3
α-helix	127-130	4
β-strand	134-144	11	23
β-strand	145	1	22
β-strand	150-155	6	24
β-strand	158-160	3	24
β-strand	164-168	5	23
α-helix	169-172	4
β-strand	178-187	10	23
α-helix	188-192	5
β-strand	196-202	7	24
β-strand	210-215	6	24

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
vFP16.02 antibody heavy chain	A, H	protein	217	Mus musculus
vFP16.02 antibody light chain	B, L	protein	218	Mus musculus
fusion peptide	C, F	protein	8	Human immunodeficiency virus 1	Q2N0S7

Sequence of entity 1 (A, H), FASTA

>6WX2_1 vFP16.02 antibody heavy chain (chains A, H)
QVQLLQSGAELVRPGASVTLSCKASGYAFSDYEIHWVKQTPVRGLDWIGAFDPKSGASAS
NQKVKGRAILTADKSSSTAYMELRSLTSEDSAVYYCTRLRYFGYFDVWGTGTTVTVSSAS
TTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLY
TLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVP

Sequence of entity 2 (B, L), FASTA

>6WX2_2 vFP16.02 antibody light chain (chains B, L)
DVLMTQTPLSLPVSLGGQASISCRSSQSVVYSDGDTYLEWYLQKPGQSPKLLIYKVSRRP
SGVPDRFSGSGSGTDFTLKISRVETEDLGVYYCFQGSHVPYTFGGGTKLEIKRTDAAPTV
SIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSM
SSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE

Sequence of entity 3 (C, F), FASTA

>6WX2_3 fusion peptide (chains C, F)
AVGIGAVF

Primary citation

Mutational fitness landscapes reveal genetic and structural improvement pathways for a vaccine-elicited HIV-1 broadly neutralizing antibody. Madan, B., Zhang, B., Xu, K. et al. Proc Natl Acad Sci U S A (2021) 118. DOI 10.1073/pnas.2011653118 · PubMed

Other PDB entries of the same protein (UniProt Q2N0S7), best resolution first:

5I8C 1.54 Å, Crystal Structure of HIV-1 Clade A BG505 Fusion Peptide (residue 512-520) in Complex…
8FR6 2.5 Å, Antibody vFP53.02 in complex with HIV-1 envelope trimer BG505 DS-SOSIP
8G4T 2.81 Å, Vaccine-elicited human antibody 2C09 in complex with HIV-1 envelope trimer BG505 DS-SOSIP
6V8Z 2.9 Å, VRC03 and 10-1074 Bound BG505 F14 HIV-1 SOSIP Envelope Trimer Structure
8G4M 2.95 Å, Vaccine-elicited human antibody 2C06 in complex with HIV-1 envelope trimer BG505 DS-SOSIP
6MPG 3.2 Å, Cryo-EM structure at 3.2 A resolution of HIV-1 fusion peptide-directed antibody,…
6UM7 3.5 Å, Cryo-EM structure of vaccine-elicited HIV-1 neutralizing antibody DH270.mu1 in complex…
9PNN 3.5 Å, Cryo-EM structure of J601-A6 Fab in complex with HIV-1 BG505 DS-SOSIP Env trimer
6CM3 3.54 Å, BG505 SOSIP in complex with sCD4, 17b, 8ANC195
6CDI 3.6 Å, Cryo-EM structure at 3.6 A resolution of vaccine-elicited antibody vFP16.02 in complex…
8DOW 3.69 Å, Cryo-EM structure of HIV-1 Env(CH848 10.17 DS.SOSIP_DT) in complex with DH1030.1 Fab
7LL1 3.73 Å, Cryo-EM structure of BG505 DS-SOSIP in complex with glycan276-dependent broadly…

Browse structure collections

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