6WO3: Envelope glycoprotein E2

Structure of Hepatitis C Virus Envelope Glycoprotein E2 core from genotype 6a bound to broadly neutralizing antibody U1. Determined by X-ray diffraction at 2.38 Å resolution. Released 19 Aug 2020.

Method: X-ray diffraction
Resolution: 2.38 Å
Organisms: Recombinant Hepatitis C virus HK6a/JFH-1, Homo sapiens
Chains: 3
Atoms: 4,588
Mol. weight: 68.82 kDa
Ligands: NAG
Released: 19 Aug 2020

Explore 6WO3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6WO3 contains 24 α-helices and 61 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	1
β-strand	428	1	2
α-helix	439-442	4
β-strand	496-498	3	3
α-helix	499-501	3
β-strand	502	1	4
β-strand	503-504	2	1
β-strand	506-509	4	5
β-strand	513-516	4	5
β-strand	519	1	3
β-strand	525	1	3
β-strand	536-538	3	3
α-helix	540-542	3
β-strand	551-555	5	5
β-strand	556	1	4
β-strand	561-565	5	5
β-strand	607-609	3	6
α-helix	614-617	4
α-helix	619-621	3
α-helix	624	1
β-strand	625-633	9	6
β-strand	636-644	9	6

Chain H: 10 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	7
α-helix	7-9	3
β-strand	10-12	3	8
β-strand	18-23	6	7
β-strand	33-39	7	8
β-strand	45-51	7	8
β-strand	57-59	3	8
α-helix	61-63	3
β-strand	67-71	5	7
β-strand	75-80	6	7
α-helix	84-86	3
β-strand	88-96	9	8
β-strand	100B	1	2
β-strand	100H-103	5	8
β-strand	107-111	5	8
α-helix	115-116	2
β-strand	117	1	9
α-helix	118-119	2
β-strand	120-124	5	10
α-helix	128-130	3
β-strand	131-132	2	10
β-strand	135-145	11	10
β-strand	146	1	9
β-strand	151-154	4	11
α-helix	155-157	3
β-strand	159	1	11
β-strand	163-165	3	10
α-helix	166-168	3
β-strand	169-170	2	10
β-strand	176-185	10	10
α-helix	186-188	3
β-strand	194-200	7	11
α-helix	201-203	3
β-strand	205-211	7	11

Chain L: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	12
β-strand	10-14	5	13
β-strand	19-25	7	12
β-strand	33-38	6	13
β-strand	45-49	5	13
β-strand	53-54	2	13
α-helix	55	1
β-strand	62-67	6	12
β-strand	70-75	6	12
α-helix	80-82	3
β-strand	84-90	7	13
β-strand	97-98	2	13
β-strand	102-107	6	13
β-strand	111	1	14
α-helix	112-113	2
β-strand	114-118	5	15
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	15
β-strand	140	1	14
β-strand	144-150	7	16
β-strand	153-154	2	16
α-helix	155	1
β-strand	159-163	5	15
α-helix	164-167	4
β-strand	173-182	10	15
α-helix	183-187	5
β-strand	191-198	8	16
β-strand	205-210	6	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Envelope glycoprotein E2	E	protein	189	Recombinant Hepatitis C virus HK6a/JFH-1	B9V0E2
Fab U1 heavy chain	H	protein	230	Homo sapiens
Fab U1 light chain	L	protein	213	Homo sapiens

Sequence of entity 1 (E), FASTA

>6WO3_1 Envelope glycoprotein E2 (chains E)
QLINTNGSWHINRTALNCNDSLQTGFITSLFYAKNVDSSGCPERMAACGSSGCWHYAPRP
CDVVSARTVCGPVYCFTPSPVVVGTTDKLGIPTYNWGENETDVFMLESLRPPTGGWFGCT
WMNSTGFTKTCGAPPGGPTDGGSGPWITPRCLVDYPYRLWHYPCTVNFTLHKVRMFVGGI
EHRFDAACN

Sequence of entity 2 (H), FASTA

>6WO3_2 Fab U1 heavy chain (chains H)
EVQLLEQSGPEVKRPGTSVKMSCKISGGASITQAMSWVRQAPGQGLEWMGGITPIFGTVN
YAQKILGRVTITADEDTVSLELSSLKSEDTAVYYCAREVNLKTWNLAHPNVFDVWGQGTM
LTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPA
VLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCGS

Sequence of entity 3 (L), FASTA

>6WO3_3 Fab U1 light chain (chains L)
LTLTQSPSSLSASVGDRVTITCRASQSISSFLNWYQQKPGKAPKLLIYAASSLQSGVPPR
FSGSGSGTDFTLTISSLQPEDFATYYCQQSYSTPRTFGQGTKLEIKRTVAAPSVFIFPPS
DEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTL
SKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

Primary citation

An alternate conformation of HCV E2 neutralizing face as an additional vaccine target. Tzarum, N., Giang, E., Kadam, R.U. et al. Sci Adv (2020) 6:eabb5642-eabb5642. DOI 10.1126/sciadv.abb5642 · 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…
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…
6BKD 3.25 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…

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