7N05: F240 antibody fragment

Crystal structure of the F240 antibody fragment bound to the HIV-1 gp41 immunodominant region. Determined by X-ray diffraction at 1.7 Å resolution. Released 30 Mar 2022.

Method: X-ray diffraction
Resolution: 1.7 Å
Organisms: Homo sapiens, HIV-1 06TG.HT008
Chains: 3
Atoms: 3,941
Mol. weight: 52.88 kDa
Released: 30 Mar 2022

Explore 7N05 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7N05 contains 19 α-helices and 45 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 E: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	597-599	3	2
α-helix	604-606	3

Chain H: 10 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	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	67-72	6	1
β-strand	77-82	6	1
α-helix	84-86	3
β-strand	88-100	13	2
β-strand	100C-103	9	2
β-strand	107-111	5	2
α-helix	114-116	3
β-strand	117	1	3
α-helix	118-119	2
β-strand	120-124	5	4
α-helix	125-127	3
β-strand	135-145	11	4
β-strand	146	1	3
β-strand	151-154	4	5
α-helix	155-157	3
β-strand	163-165	3	4
α-helix	166-168	3
β-strand	169-170	2	4
β-strand	176-185	10	4
α-helix	186-188	3
β-strand	195-200	6	5
α-helix	201-203	3
β-strand	205-210	6	5

Chain L: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	6
β-strand	10-13	4	7
β-strand	19-25	7	6
β-strand	27C-27D	2	8
β-strand	30-31	2	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
β-strand	98	1	7
β-strand	102-106	5	7
β-strand	111	1	9
α-helix	112-113	2
β-strand	114-118	5	10
α-helix	119-121	3
α-helix	122-126	5
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

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fab F240 heavy chain	H	protein	246	Homo sapiens
Fab F240 light chain	L	protein	220	Homo sapiens
HIV-1 gp41 immunodominant region	E	protein	16	HIV-1 06TG.HT008	P04578 (AlphaFold model)

Sequence of entity 1 (H), FASTA

>7N05_1 Fab F240 heavy chain (chains H)
QVQLVQSGGGVVKPGASLRLACSASGFTFTDYYMSWIRQTPGKGLQWLAYITKDGSEKKY
ADSLQGRFAVSRDNANNLVFLQLNTVEDDDTGVYYCARDDGYYDRSGYYGVFDLWGQGIR
VTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPA
VLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCGRLVPRGSHHHH
HHHHHH

Sequence of entity 2 (L), FASTA

>7N05_2 Fab F240 light chain (chains L)
EFLLTQSPDSLAVTLGETATITCRSSRNILHSLNNKNYLAWYQQRPGQAPKLLVIWASMR
VSGVADRFSGSGSGTDFALTISSLQPEDAAVYYCQHYYTTHRTFGQGTRVEIRRTVAAPS
VFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYS
LSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (E), FASTA

>7N05_3 HIV-1 gp41 immunodominant region (chains E)
XWGSSGKLISTTAVPW

Primary citation

Conformational plasticity of the HIV-1 gp41 immunodominant region is recognized by multiple non-neutralizing antibodies. Cook, J.D., Khondker, A., Lee, J.E. Commun Biol (2022) 5:291-291. DOI 10.1038/s42003-022-03235-w · 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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