7EKK: PDB entry 7EKK

Anti-HIV-1 broadly neutralizing antibody delta-loop 4E10 modified with pyrene acetamide. Determined by X-ray diffraction at 1.7 Å resolution. Released 11 Aug 2021.

Method: X-ray diffraction
Resolution: 1.7 Å
Organisms: Homo sapiens, Human immunodeficiency virus 1
Chains: 3
Atoms: 3,998
Mol. weight: 49.16 kDa
Released: 11 Aug 2021

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

Secondary structure: helices and β-sheets

7EKK contains 19 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: 8 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
α-helix	61-63	3
β-strand	67-72	6	1
β-strand	77-82	6	1
α-helix	84-86	3
β-strand	88-98	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	195-198	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	122-125	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 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
Heavy chain of the Fab region of Delta-loop variant of anti-HIV-1 broadly neutralizing antibody…	H	protein	224	Homo sapiens
Light chain of the Fab region of Delta-loop variant of anti-HIV-1 broadly neutralizing antibody…	L	protein	212	Homo sapiens
MPER region of the envelope glycoprotein gp41 from HIV-1	P	protein	16	Human immunodeficiency virus 1	P04578 (AlphaFold model)

Sequence of entity 1 (H), FASTA

>7EKK_1 Heavy chain of the Fab region of Delta-loop variant of anti-HIV-1 broadly neutralizing antibody 4E10 modified with pyrene acetamide (chains H)
VQLVQSGAEVKRPGSSVTVSCKASGGSFSTYALSWVRQAPGRGLEWMGGVIPLLTITNYA
PRFQGRITITADRSTSTAYLELNSLRPEDTAVYYCAREGTTGCGGKPIGAFAHWGQGTLV
TVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAV
LQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP

Sequence of entity 2 (L), FASTA

>7EKK_2 Light chain of the Fab region of Delta-loop variant of anti-HIV-1 broadly neutralizing antibody 4E10 modified with pyrene acetamide (chains L)
EIVLTQSPGTQSLSPGERATLSCRASQSVGNNKLAWYQQRPGQAPRLLIYGASSRPSGVA
DRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGQSLSTFGQGTKVEVKRTVAAPSVFIFP
PSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNR

Sequence of entity 3 (P), FASTA

>7EKK_3 MPER region of the envelope glycoprotein gp41 from HIV-1 (chains P)
NWFDITNWLWYIKKKK

Primary citation

Focal accumulation of aromaticity at the CDRH3 loop mitigates 4E10 polyreactivity without altering its HIV neutralization profile. Rujas, E., Leaman, D.P., Insausti, S. et al. iScience (2021) 24:102987-102987. DOI 10.1016/j.isci.2021.102987 · 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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