6BKB: Fab AR3A heavy chain

Structure of Hepatitis C Virus Envelope Glycoprotein E2 core from genotype 6a bound to broadly neutralizing antibody AR3A. Determined by X-ray diffraction at 2.8 Å resolution. Released 26 Dec 2018.

Method: X-ray diffraction
Resolution: 2.8 Å
Organisms: Homo sapiens, Recombinant Hepatitis C virus HK6a/JFH-1
Chains: 3
Atoms: 4,584
Mol. weight: 69.67 kDa
Ligands: NAG
Released: 26 Dec 2018

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

Secondary structure: helices and β-sheets

6BKB contains 20 α-helices and 62 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: 6 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	426-427	2	8
β-strand	430	1	4
α-helix	439-441	3
β-strand	496-498	3	9
α-helix	499-501	3
β-strand	502	1	10
β-strand	503-504	2	8
β-strand	506-509	4	11
β-strand	513-516	4	11
β-strand	519	1	9
β-strand	525	1	9
β-strand	536-538	3	9
α-helix	540-542	3
β-strand	551-555	5	11
β-strand	556	1	10
β-strand	561-565	5	11
β-strand	607-609	3	12
α-helix	614-617	4
α-helix	619-621	3
α-helix	624	1
β-strand	625-633	9	12
β-strand	636-644	9	12

Chain H: 6 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	3	1
β-strand	4	1	1
β-strand	5-6	2	2
α-helix	7-9	3
β-strand	10-12	3	3
β-strand	18-23	6	2
β-strand	34-39	6	3
β-strand	46-52	7	3
β-strand	56-58	3	3
β-strand	67-70	4	2
β-strand	78-82	5	2
α-helix	84-86	3
β-strand	88-93	6	3
β-strand	98-100A	4	4
β-strand	100F-100H	3	4
β-strand	103	1	3
β-strand	104	1	1
β-strand	108-111	4	3
β-strand	117	1	5
β-strand	120-124	5	6
β-strand	135-145	11	6
β-strand	146	1	5
β-strand	151-154	4	7
α-helix	155-157	3
β-strand	163-165	3	6
α-helix	166-168	3
β-strand	169-170	2	6
β-strand	176-185	10	6
α-helix	186-188	3
β-strand	194-200	7	7
β-strand	205-211	7	7

Chain L: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	13
β-strand	10-13	4	14
β-strand	19-25	7	13
β-strand	33-38	6	14
β-strand	45-49	5	14
β-strand	53-54	2	14
α-helix	55	1
β-strand	62-67	6	13
β-strand	70-75	6	13
α-helix	80-82	3
β-strand	85-90	6	14
β-strand	97-98	2	14
α-helix	99-101	3
β-strand	102-106	5	14
β-strand	111	1	15
α-helix	112-113	2
β-strand	114-118	5	16
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	16
β-strand	140	1	15
β-strand	144-150	7	17
β-strand	153-154	2	17
β-strand	159-163	5	16
α-helix	164-167	4
β-strand	173-182	10	16
α-helix	183-188	6
β-strand	191-198	8	17
β-strand	205-210	6	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fab AR3A heavy chain	H	protein	232	Homo sapiens	P0DOX5 (AlphaFold model)
Polyprotein	E	protein	189	Recombinant Hepatitis C virus HK6a/JFH-1	B9V0E2
Fab AR3A light chain	L	protein	214	Homo sapiens	Q6PIL8 (AlphaFold model)

Sequence of entity 1 (H), FASTA

>6BKB_1 Fab AR3A heavy chain (chains H)
VQLLEQSGAEVKTPGSSVRVSCRPPGGNFNSYSINWVRQAPGHGLEWVGTFIPMFGTSKY
AQKFQGRVTITADGSSGTAYMDLNSLRSDDTAFYYCVRPETPRYCSGGFCYGEFDNWGQG
TLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTF
PAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCGS

Sequence of entity 2 (E), FASTA

>6BKB_2 Polyprotein (chains E)
QLINTNGSWHINRTALNCNDSLQTGFITSLFYAKNVDSSGCPERMAACGSSGCWHYAPRP
CDVVSARTVCGPVYCFTPSPVVVGTTDKLGIPTYNWGENETDVFMLESLRPPTGGWFGCT
WMNSTGFTKTCGAPPGGPTDGGSGPWITPRCLVDYPYRLWHYPCTVNFTLHKVRMFVGGI
EHRFDAACN

Sequence of entity 3 (L), FASTA

>6BKB_3 Fab AR3A light chain (chains L)
ELTLTQSPGTLSLSPGKRATLSCRASQSVSGSYLAWYQQKPGQAPRLLIYGASNRATGIP
HRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGSSPTFGQGTRVDIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3

Primary citation

Genetic and structural insights into broad neutralization of hepatitis C virus by human VH1-69 antibodies. Tzarum, N., Giang, E., Kong, L. et al. Sci Adv (2019) 5:eaav1882-eaav1882. DOI 10.1126/sciadv.aav1882 · PubMed

Other PDB entries of the same protein (UniProt P0DOX5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6YT7 1.55 Å, Glycosylated knob/dummy-hole fc fragment
6YTB 1.65 Å, Glycosylated knob/dummy-hole/dummy fc fragment
6ARP 1.7 Å, Structure of a mutant Cetuximab Fab fragment
1N0X 1.8 Å, Crystal Structure of a Broadly Neutralizing Anti-HIV-1 Antibody in Complex with a…
6UOE 1.8 Å, 3-25 Fab germline-reversion variant bound to an HCMV gB-derived peptide
8ECV 1.81 Å, Bovine Fab 2F12
6G1E 1.88 Å, BEAT Fc with improved heterodimerization (Q3A-D84.4Q)
5W5L 1.9 Å, Crystal structure of human IgG1-Sigma Fc fragment
6UBI 1.9 Å, N123-VRC34.05 HIV neutralizing antibody in complex with HIV fusion peptide residue 512-519
6DKJ 1.95 Å, human GIPR ECD and Fab complex
6MSY 2.0 Å, Anti-HIV-1 Fab Fab 2G12 + Man4 re-refinement
6UGW 2.0 Å, Crystal structure of the Fc fragment of PF06438179/GP1111 an infliximab biosimilar in a…

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