6CDM: VFP7.04 heavy chain

Structure of vaccine-elicited HIV-1 neutralizing antibody vFP7.04 in complex with HIV-1 fusion peptide residue 512-519. Determined by X-ray diffraction at 2.41 Å resolution. Released 16 May 2018.

Method: X-ray diffraction
Resolution: 2.41 Å
Organisms: Mus musculus, Human immunodeficiency virus 1
Chains: 6
Atoms: 7,075
Mol. weight: 96.97 kDa
Released: 16 May 2018

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

Secondary structure: helices and β-sheets

6CDM contains 38 α-helices and 94 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.

Chain A: 10 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	1
α-helix	7	1
β-strand	10-12	3	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	33-40	8	2
β-strand	44-51	8	2
β-strand	57-59	3	2
α-helix	61-63	3
β-strand	64	1	1
β-strand	67-72	6	1
β-strand	77-82	6	1
α-helix	84-86	3
β-strand	88-95	8	2
β-strand	103	1	2
β-strand	107-111	5	2
α-helix	115-116	2
β-strand	117	1	3
α-helix	118-119	2
β-strand	120-124	5	4
α-helix	128-130	3
β-strand	131-132	2	4
β-strand	135-145	11	4
β-strand	146	1	3
β-strand	151-154	4	5
α-helix	155-157	3
β-strand	159	1	5
β-strand	163-165	3	4
α-helix	166-168	3
β-strand	169-170	2	4
β-strand	176-185	10	4
β-strand	194-200	7	5
α-helix	201-203	3
β-strand	205-211	7	5

Chain B: 9 helices, 23 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	27C	1	8
β-strand	31	1	8
β-strand	33-38	6	7
β-strand	45-49	5	7
β-strand	53-54	2	7
α-helix	55	1
β-strand	62-67	6	6
β-strand	70-75	6	6
α-helix	80-82	3
β-strand	84-90	7	7
α-helix	96	1
β-strand	97-98	2	7
β-strand	102-107	6	7
β-strand	111	1	9
α-helix	112-113	2
β-strand	114-118	5	10
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	10
β-strand	140	1	9
β-strand	145-150	6	11
β-strand	153-154	2	11
α-helix	155	1
β-strand	159-163	5	10
α-helix	164-167	4
β-strand	173-182	10	10
α-helix	183-186	4
β-strand	191-197	7	11
β-strand	205-210	6	11

Chain D: 10 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	12
α-helix	7-9	3
β-strand	10-12	3	13
β-strand	18-25	8	12
α-helix	29-31	3
β-strand	33-40	8	13
β-strand	44-51	8	13
β-strand	57-59	3	13
α-helix	61-63	3
β-strand	64	1	12
β-strand	67-72	6	12
β-strand	77-82	6	12
α-helix	84-86	3
β-strand	88-95	8	13
β-strand	103	1	13
β-strand	107-111	5	13
α-helix	115-116	2
β-strand	117	1	14
α-helix	118-119	2
β-strand	120-124	5	15
α-helix	128-130	3
β-strand	131-132	2	15
β-strand	135-145	11	15
β-strand	146	1	14
β-strand	151-154	4	16
α-helix	155-157	3
β-strand	159	1	16
β-strand	163-165	3	15
α-helix	166-168	3
β-strand	169-170	2	15
β-strand	176-185	10	15
β-strand	194-200	7	16
α-helix	201-203	3
β-strand	205-211	7	16

Chain E: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	17
β-strand	10-14	5	18
β-strand	19-25	7	17
β-strand	27C	1	19
β-strand	31	1	19
β-strand	33-38	6	18
β-strand	45-49	5	18
β-strand	53-54	2	18
α-helix	55	1
β-strand	62-67	6	17
β-strand	70-75	6	17
α-helix	80-82	3
β-strand	84-90	7	18
α-helix	96	1
β-strand	97-98	2	18
β-strand	102-107	6	18
β-strand	111	1	20
α-helix	112-113	2
β-strand	114-118	5	21
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	21
β-strand	140	1	20
β-strand	145-150	6	22
β-strand	153-154	2	22
α-helix	155	1
β-strand	159-163	5	21
α-helix	164-167	4
β-strand	173-182	10	21
α-helix	183-186	4
β-strand	191-197	7	22
β-strand	205-210	6	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
vFP7.04 heavy chain	A, D	protein	221	Mus musculus
vFP7.04 light chain	B, E	protein	219	Mus musculus
HIV fusion peptide (512-519)	C, F	protein	8	Human immunodeficiency virus 1	Q2N0S5

Sequence of entity 1 (A, D), FASTA

>6CDM_1 vFP7.04 heavy chain (chains A, D)
QVQLQQSGAELVRPGASVTLSCKASGYTFTDYEMHWVKQTPVHGLEWIGAIVPETGFTAY
TQKFKGKAMLTADKSSSTAYMELRSLTSEDSAVYFCSRLRLYWYFDVWGTGTTVTVSSAS
TKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGL
YSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Sequence of entity 2 (B, E), FASTA

>6CDM_2 vFP7.04 light chain (chains B, E)
GVLMTQTPLSLPVRLGDQASISCRSSQSIVYSNGNTYLEWYLQRPGQSPKLLIYKVSNRF
SGVPDRVSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPYTFGGGTKLEIKRTVAAPSV
FIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSL
SSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (C, F), FASTA

>6CDM_3 HIV fusion peptide (512-519) (chains C, F)
AVGIGAVF

Primary citation

Epitope-based vaccine design yields fusion peptide-directed antibodies that neutralize diverse strains of HIV-1. Xu, K., Acharya, P., Kong, R. et al. Nat Med (2018) 24:857-867. DOI 10.1038/s41591-018-0042-6 · PubMed

Other PDB entries of the same protein (UniProt Q2N0S5), best resolution first:

6CDO 2.1 Å, Structure of vaccine-elicited HIV-1 neutralizing antibody vFP16.02 in complex with HIV-1…
6CDP 2.46 Å, Vaccine-elicited HIV-1 neutralizing antibody vFP20.01 in complex with HIV-1 fusion…
9P6E 2.7 Å, N49P7-FR Fab in complex with BG505 MD39 SOSIP and RM20A3 Fab
9P6G 2.7 Å, eN49P7-FRv1-23 Fab in complex with BG505 MD39 SOSIP and RM20A3 Fab
8TTW 2.96 Å, Cryo-EM structure of BG505 SOSIP.664 HIV-1 Env trimer in complex with temsavir, 8ANC195,…
9Y9V 2.98 Å, The cryoem structure of rhesus macaque 1A8 and PGT121 fabs in complex with BG505…
9Q0W 3.0 Å, Cryo-EM Structure of HIV-1 BG505DS-SOSIP.664 Env Trimer Bound to DFPH-a.01_10R59P_LC Fab
9Q3S 3.01 Å, Cryo-EM structure of PGT121 Fab and Rhesus macaque Ab4 Fab in complex with HIV-1 Env…
5U7M 3.02 Å, Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer Bound to Small Molecule…
5U7O 3.03 Å, Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer Bound to Small Molecule…
4TVP 3.1 Å, Crystal Structure of the HIV-1 BG505 SOSIP.664 Env Trimer Ectodomain, Comprising…
8TKC 3.1 Å, cryo-EM structure of HIV-1 BG505DS-SOSIP.664 env trimer bound to DJ85-b.01 FAB

Browse structure collections

About this viewer

MolViewer shows 6CDM directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.