5X08: Fab 4E10 Heavy chain

Crystal structure of broadly neutralizing anti-HIV-1 antibody 4E10, mutant Npro, with peptide bound. Determined by X-ray diffraction at 1.49 Å resolution. Released 5 Apr 2017.

Method: X-ray diffraction
Resolution: 1.49 Å
Organisms: Homo sapiens, Human immunodeficiency virus type 1 (MAL ISOLATE)
Chains: 3
Atoms: 3,988
Mol. weight: 50.38 kDa
Released: 5 Apr 2017

Explore 5X08 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5X08 contains 20 α-helices and 44 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: 9 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	1
α-helix	7-9	3
β-strand	10-12	3	2
β-strand	18-25	8	1
β-strand	34-39	6	2
β-strand	45-52	8	2
α-helix	52A-54	3
β-strand	56-59	4	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	88-97	10	2
β-strand	100F-103	8	2
β-strand	107-111	5	2
β-strand	117	1	3
α-helix	118-119	2
β-strand	120-124	5	4
β-strand	137-147	11	4
β-strand	148	1	3
β-strand	153-157	4	5
α-helix	162-164	3
β-strand	166	1	5
β-strand	171-173	3	4
α-helix	174-176	3
β-strand	177-178	2	4
β-strand	185-194	10	4
α-helix	195-198	4
β-strand	207-212	6	5
α-helix	213-215	3
β-strand	217-222	6	5

Chain L: 9 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	6
β-strand	10-13	4	7
β-strand	19-25	7	6
α-helix	27A-28	2
α-helix	29-31	3
β-strand	33-38	6	7
β-strand	45-48	4	7
β-strand	49	1	8
β-strand	53	1	8
β-strand	62-67	6	6
β-strand	70-75	6	6
α-helix	80-82	3
β-strand	85-90	6	7
β-strand	97-98	2	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

Chain P: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	672-674	3
α-helix	675-683	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fab 4E10 Heavy chain	H	protein	230	Homo sapiens
Fab 4E10 Light chain	L	protein	214	Homo sapiens
Envelope glycoprotein gp160	P	protein	16	Human immunodeficiency virus type 1 (MAL ISOLATE)	P04578 (AlphaFold model)

Sequence of entity 1 (H), FASTA

>5X08_1 Fab 4E10 Heavy chain (chains H)
QVQLVQSGAEVKRPGSSVTVSCKASGGSFSTYALSWVRQAPGRGLEWMGGVIPLLTITNY
APRFQGRITITADRSTSTAYLELNSLRPEDTAVYYCAREGTTPPGWGWLGKPIGAFAHWG
QGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVH
TFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK

Sequence of entity 2 (L), FASTA

>5X08_2 Fab 4E10 Light chain (chains L)
EIVLTQSPGTQSLSPGERATLSCRASQSVGNNKLAWYQQRPGQAPRLLIYGASSRPSGVA
DRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGQSLSTFGQGTKVEVKRTVAAPSVFIFP
PSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE

Sequence of entity 3 (P), FASTA

>5X08_3 Envelope glycoprotein gp160 (chains P)
NWFDITNWLWYIKKKK

Primary citation

Functional Contacts between MPER and the Anti-HIV-1 Broadly Neutralizing Antibody 4E10 Extend into the Core of the Membrane. Rujas, E., Insausti, S., Garcia-Porras, M. et al. J Mol Biol (2017) 429:1213-1226. DOI 10.1016/j.jmb.2017.03.008 · 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
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…
6BXQ 1.58 Å, Crystal Structure of HLA-B*57:01 with an HIV peptide RKV

Browse structure collections

About this viewer

MolViewer shows 5X08 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.