5CIN: FAB 4E10 heavy chain

Crystal Structure of non-neutralizing version of 4E10 (DeltaLoop) with epitope bound. Determined by X-ray diffraction at 1.7 Å resolution. Released 23 Sept 2015.

Method: X-ray diffraction
Resolution: 1.7 Å
Organisms: Homo sapiens, Human immunodeficiency virus 1
Chains: 3
Atoms: 4,109
Mol. weight: 49.03 kDa
Released: 23 Sept 2015

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

Secondary structure: helices and β-sheets

5CIN contains 18 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: 7 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
β-strand	56-59	4	2
β-strand	67-72	6	1
β-strand	77-82	6	1
α-helix	84-86	3
β-strand	88-98	11	2
β-strand	100E-103	9	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	195-197	3
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	675-682	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
FAB 4E10 heavy chain	H	protein	224	Homo sapiens
FAB 4E10 light chain	L	protein	212	Homo sapiens
Peptide from MPER region of HIV-1 ENV	P	protein	16	Human immunodeficiency virus 1	P04578 (AlphaFold model)

Sequence of entity 1 (H), FASTA

>5CIN_1 FAB 4E10 HEAVY CHAIN (chains H)
VQLVQSGAEVKRPGSSVTVSCKASGGSFSTYALSWVRQAPGRGLEWMGGVIPLLTITNYA
PRFQGRITITADRSTSTAYLELNSLRPEDTAVYYCAREGTTGSGGKPIGAFAHWGQGTLV
TVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAV
LQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP

Sequence of entity 2 (L), FASTA

>5CIN_2 FAB 4E10 LIGHT CHAIN (chains L)
EIVLTQSPGTQSLSPGERATLSCRASQSVGNNKLAWYQQRPGQAPRLLIYGASSRPSGVA
DRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGQSLSTFGQGTKVEVKRTVAAPSVFIFP
PSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNR

Sequence of entity 3 (P), FASTA

>5CIN_3 Peptide from MPER region of HIV-1 ENV (chains P)
NWFDITNWLWYIKKKK

Primary citation

Structural and Thermodynamic Basis of Epitope Binding by Neutralizing and Nonneutralizing Forms of the Anti-HIV-1 Antibody 4E10. Rujas, E., Gulzar, N., Morante, K. et al. J Virol (2015) 89:11975-11989. DOI 10.1128/JVI.01793-15 · 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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