6BKD: Polyprotein

Structure of Hepatitis C Virus Envelope Glycoprotein E2 core from genotype 6a bound to broadly neutralizing antibody AR3D. Determined by X-ray diffraction at 3.25 Å resolution. Released 26 Dec 2018.

Method: X-ray diffraction
Resolution: 3.25 Å
Organisms: Recombinant Hepatitis C virus HK6a/JFH-1, Homo sapiens
Chains: 3
Atoms: 4,440
Mol. weight: 68.64 kDa
Released: 26 Dec 2018

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

Secondary structure: helices and β-sheets

6BKD contains 20 α-helices and 53 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: 7 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	422-424	3
β-strand	427	1	1
α-helix	439-442	4
α-helix	492-494	3
β-strand	496-498	3	2
α-helix	499-501	3
β-strand	502-509	8	3
β-strand	513-516	4	3
β-strand	519	1	2
β-strand	525	1	2
β-strand	536-538	3	2
α-helix	540-542	3
β-strand	551-556	6	3
β-strand	561-565	5	3
β-strand	607-609	3	4
α-helix	614-617	4
α-helix	619-621	3
β-strand	625-632	8	4
β-strand	637-644	8	4

Chain H: 5 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	5
β-strand	10-12	3	6
β-strand	18-20	3	5
β-strand	22-24	3	5
β-strand	32-39	8	6
β-strand	45-52	8	6
β-strand	56-59	4	6
β-strand	67-72	6	5
β-strand	77-82	6	5
β-strand	88-97	10	6
α-helix	98-100A	4
α-helix	100I-100J	2
β-strand	103	1	6
β-strand	107-111	5	6
α-helix	115-116	2
α-helix	118-119	2
β-strand	120-124	5	7
β-strand	135-145	11	7
β-strand	150-154	5	8
β-strand	163-165	3	7
α-helix	166-168	3
β-strand	169-170	2	7
β-strand	176-185	10	7
β-strand	194-200	7	8
β-strand	205-211	7	8

Chain L: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	9
β-strand	10-13	4	10
β-strand	19-25	7	9
α-helix	28-30	3
β-strand	33-38	6	10
β-strand	45-48	4	10
β-strand	54	1	10
β-strand	62-65	4	9
β-strand	71-75	5	9
β-strand	85-90	6	10
β-strand	97-98	2	10
α-helix	100-101	2
β-strand	102-106	5	10
β-strand	111	1	11
α-helix	112-113	2
β-strand	114-118	5	12
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	12
β-strand	140	1	11
β-strand	146-150	5	13
β-strand	153-154	2	13
β-strand	161-163	3	12
α-helix	165-167	3
β-strand	173-182	10	12
α-helix	183-187	5
β-strand	191-196	6	13
α-helix	204	1
β-strand	205-210	6	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Polyprotein	E	protein	189	Recombinant Hepatitis C virus HK6a/JFH-1	B9V0E2
Fab AR3D heavy chain	H	protein	234	Homo sapiens	S6B2A6 (AlphaFold model)
Fab AR3D light chain	L	protein	212	Homo sapiens	Q6PIL8 (AlphaFold model)

Sequence of entity 1 (E), FASTA

>6BKD_1 Polyprotein (chains E)
QLINTNGSWHINRTALNCNDSLQTGFITSLFYAKNVDSSGCPERMAACGSSGCWHYAPRP
CDVVSARTVCGPVYCFTPSPVVVGTTDKLGIPTYNWGENETDVFMLESLRPPTGGWFGCT
WMNSTGFTKTCGAPPGGPTDGGSGPWITPRCLVDYPYRLWHYPCTVNFTLHKVRMFVGGI
EHRFDAACN

Sequence of entity 2 (H), FASTA

>6BKD_2 Fab AR3D heavy chain (chains H)
LLEQSGAEVKKPGSSVKVSCKASGDTFRSYVITWARQAPGQGLEWMGAIIPFFGTTNLAQ
KFQGRVTITADESTKTVYMDLSSLRSDDTAVYYCAKAGDLSVGGVLAGGVPHLRHFDPWG
QGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVH
TFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCGS

Sequence of entity 3 (L), FASTA

>6BKD_3 Fab AR3D light chain (chains L)
ELTQSPGTLSLSPGERATLSCRAGQTVASNSLAWYQHKPGQAPRLLIYGASIRASGIPDR
FSGSGSGTDFTLTISRLEPEDFAVYYCQQYGLSSTFGQGTRLEIKRTVAAPSVFIFPPSD
EQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLS
KADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

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 B9V0E2), best resolution first:

6UYF 2.06 Å, Structure of Hepatitis C Virus Envelope Glycoprotein E2mc3-v1 redesigned core from…
6WO4 2.35 Å, Structure of Hepatitis C Virus Envelope Glycoprotein E2 core from genotype 6a bound to…
6WO3 2.38 Å, Structure of Hepatitis C Virus Envelope Glycoprotein E2 core from genotype 6a bound to…
6BKC 2.6 Å, Structure of Hepatitis C Virus Envelope Glycoprotein E2 core from genotype 6a bound to…
7JTG 2.6 Å, Structure of Hepatitis C Virus Envelope Glycoprotein E2 core from genotype 6a bound to…
6BKB 2.8 Å, Structure of Hepatitis C Virus Envelope Glycoprotein E2 core from genotype 6a bound to…
9MNS 2.89 Å, Structure of Hepatitis C virus envelope glycoprotein E2 core from genotype 6a bound to…
7JTF 3.35 Å, Structure of Hepatitis C Virus Envelope Glycoprotein E2 core from genotype 6a bound to…
6UYG 3.38 Å, Structure of Hepatitis C Virus Envelope Glycoprotein E2c3 core from genotype 6a bound to…

Browse structure collections

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