6UYG: Envelope glycoprotein E2

Structure of Hepatitis C Virus Envelope Glycoprotein E2c3 core from genotype 6a bound to broadly neutralizing antibody AR3A and non neutralizing antibody E1. Determined by X-ray diffraction at 3.38 Å resolution. Released 22 Apr 2020.

Method: X-ray diffraction
Resolution: 3.38 Å
Organisms: Recombinant Hepatitis C virus HK6a/JFH-1, Homo sapiens, Streptococcus sp.
Chains: 6
Atoms: 7,733
Mol. weight: 124.1 kDa
Ligands: NAG
Released: 22 Apr 2020

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

Secondary structure: helices and β-sheets

6UYG contains 23 α-helices and 104 β-strands across 6 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 A: 4 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	16
β-strand	5-6	2	17
β-strand	10-12	3	18
β-strand	18-19	2	17
β-strand	22-23	2	17
β-strand	32-39	8	18
β-strand	45-51	7	18
β-strand	57-59	3	18
β-strand	67-72	6	17
β-strand	77-82	6	17
α-helix	84-86	3
β-strand	88-96	9	18
β-strand	99	1	4
β-strand	102-103	2	18
β-strand	104	1	16
β-strand	107-111	5	18
α-helix	115-116	2
β-strand	117	1	19
α-helix	118-119	2
β-strand	120-123	4	20
β-strand	136-145	10	20
β-strand	146	1	19
β-strand	151-152	2	21
β-strand	164-165	2	20
α-helix	166-168	3
β-strand	169-170	2	20
β-strand	176-184	9	20
β-strand	198-200	3	21
β-strand	205-206	2	21

Chain B: 5 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	22
β-strand	10-12	3	23
β-strand	19-24	6	22
β-strand	33-38	6	23
β-strand	45-50	6	23
β-strand	53-54	2	23
α-helix	55	1
β-strand	62-67	6	22
β-strand	70-75	6	22
β-strand	84-90	7	23
α-helix	96	1
β-strand	97-98	2	23
β-strand	102-105	4	23
β-strand	114-118	5	24
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	24
β-strand	145-150	6	25
β-strand	153-155	3	25
β-strand	159-163	5	24
β-strand	173-182	10	24
α-helix	183-187	5
β-strand	193-197	5	25
β-strand	205-207	3	25

Chain E: 5 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	422-424	3
β-strand	427	1	1
β-strand	430	1	2
α-helix	439-442	4
β-strand	497-498	2	3
β-strand	502-509	8	1
β-strand	513-516	4	1
β-strand	519	1	3
β-strand	525	1	3
β-strand	536-537	2	3
α-helix	542	1
β-strand	547	1	4
β-strand	551-556	6	1
β-strand	561-563	3	1
β-strand	609	1	5
α-helix	614-617	4
α-helix	619-621	3
β-strand	625-633	9	5
β-strand	636-644	9	5

Chain G: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	6-13	8	10
β-strand	17-25	9	10
α-helix	30-41	12
β-strand	47-51	5	10
β-strand	56-60	5	10

Chain H: 4 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	10-12	3	6
β-strand	18-21	4	7
β-strand	34-39	6	6
β-strand	45-51	7	6
β-strand	57-58	2	6
β-strand	67-68	2	7
β-strand	79-82	4	7
α-helix	84-86	3
β-strand	88-93	6	6
β-strand	100-100A	2	2
β-strand	100F-100G	2	2
β-strand	103	1	6
β-strand	108-111	4	6
β-strand	117	1	8
α-helix	118-119	2
β-strand	120-124	5	9
β-strand	138-145	8	9
β-strand	146	1	8
β-strand	151-154	4	10
β-strand	163-165	3	9
α-helix	166-168	3
β-strand	169-170	2	9
β-strand	176-182	7	9
β-strand	194-200	7	10
α-helix	201-203	3
β-strand	205-211	7	10

Chain L: 4 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	11
β-strand	10-13	4	12
β-strand	19-25	7	11
β-strand	33-38	6	12
β-strand	45-49	5	12
β-strand	53-54	2	12
α-helix	55	1
β-strand	62-67	6	11
β-strand	70-75	6	11
α-helix	80-82	3
β-strand	85-90	6	12
β-strand	97-98	2	12
β-strand	103-106	4	12
β-strand	111	1	13
β-strand	117-118	2	14
α-helix	122-125	4
β-strand	131-139	9	14
β-strand	140	1	13
β-strand	145-146	2	15
β-strand	159-160	2	14
β-strand	163	1	14
α-helix	164-167	4
β-strand	173-180	8	14
β-strand	196-197	2	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Envelope glycoprotein E2	E	protein	189	Recombinant Hepatitis C virus HK6a/JFH-1	B9V0E2
Fab AR3A heavy chain	H	protein	232	Homo sapiens
Fab AR3A light chain	L	protein	214	Homo sapiens
Fab E1 heavy chain	A	protein	227	Homo sapiens
Fab E1 light chain	B	protein	219	Homo sapiens
Immunoglobulin G-binding protein G	G	protein	61	Streptococcus sp.	P19909 (AlphaFold model)

Sequence of entity 1 (E), FASTA

>6UYG_1 Envelope glycoprotein E2 (chains E)
QLINTNGSWHINRTALNCNDSLQTGFITSLFYAKNVDSSGCPERMAACGSSGCWHYAPRP
CDVVSARTVCGPVYCFTPSPVVVGTTDKLGIPTYNWGENETDVFMLESLRPPTGGWFGCT
WMNSTGFTKTCGAPPGGPTDGGSGPWITPRCLVDYPYRLWHYPCTVNFTLHKVRMFVGGI
EHRFDAACN

Sequence of entity 2 (H), FASTA

>6UYG_2 Fab AR3A heavy chain (chains H)
VQLLEQSGAEVKTPGSSVRVSCRPPGGNFNSYSINWVRQAPGHGLEWVGTFIPMFGTSKY
AQKFQGRVTITADGSSGTAYMDLNSLRSDDTAFYYCVRPETPRYCSGGFCYGEFDNWGQG
TLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTF
PAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCGS

Sequence of entity 3 (L), FASTA

>6UYG_3 Fab AR3A light chain (chains L)
ELTLTQSPGTLSLSPGKRATLSCRASQSVSGSYLAWYQQKPGQAPRLLIYGASNRATGIP
HRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGSSPTFGQGTRVDIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 4 (A), FASTA

>6UYG_4 Fab E1 heavy chain (chains A)
EVQLLEQSGAELKKPGSSVKVSCKPSDGTFRAYTLSWVRQAPGQTLEWMGRIMPTVGITN
YAQKFQGRVTISADMSTATAYMELSSLRSDDTAIYYCAKGPYVGLGEGFSEWGQGTLVTV
SSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQ
SSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCGS

Sequence of entity 5 (B), FASTA

>6UYG_5 Fab E1 light chain (chains B)
ELVLTQSPLSLPVTLGQPASISCRSTQSLVYSDGNTYLNWFHQRAGQPPRRLIYKVSNRD
SGVPERFSGSGSGTDFTLKISRVEAEDVGIYYCMQGAHWPPTFGGGTKVEINRTVAAPSV
FIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSL
SSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 6 (G), FASTA

>6UYG_6 Immunoglobulin G-binding protein G (chains G)
MTPAVTTYKLVINGKTLKGETTTKAVDAETAEKAFKQYANDNGVDGVWTYDDATKTFTVT
E

Ligands and cofactors

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

Primary citation

Proof of concept for rational design of hepatitis C virus E2 core nanoparticle vaccines. He, L., Tzarum, N., Lin, X. et al. Sci Adv (2020) 6:eaaz6225-eaaz6225. DOI 10.1126/sciadv.aaz6225 · 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…
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…

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