6UYD: Envelope glycoprotein E2

Structure of Hepatitis C Virus Envelope Glycoprotein E2mc3-v1 redesigned core from genotype 1a bound to broadly neutralizing antibody AR3C. Determined by X-ray diffraction at 1.9 Å resolution. Released 22 Apr 2020.

Method: X-ray diffraction
Resolution: 1.9 Å
Organisms: Hepatitis C virus (isolate H), Homo sapiens
Chains: 6
Atoms: 9,525
Mol. weight: 136.52 kDa
Ligands: NAG
Released: 22 Apr 2020

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

Secondary structure: helices and β-sheets

6UYD contains 55 α-helices and 125 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: 10 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	16
α-helix	7-9	3
β-strand	10-12	3	17
β-strand	18-24	7	16
β-strand	33-39	7	17
β-strand	46-52	7	17
β-strand	56-59	4	17
α-helix	61-63	3
β-strand	67-72	6	16
β-strand	77-82	6	16
α-helix	84-86	3
β-strand	88-95	8	17
β-strand	100-100B	3	18
β-strand	100E-100G	3	18
β-strand	102-103	2	17
β-strand	104	1	16
β-strand	107-111	5	17
α-helix	115-116	2
β-strand	117	1	19
α-helix	118-119	2
β-strand	120-124	5	20
β-strand	135-145	11	20
β-strand	146	1	19
β-strand	151-154	4	21
α-helix	155-157	3
β-strand	159	1	21
β-strand	163-165	3	20
α-helix	166-168	3
β-strand	169-170	2	20
β-strand	176-185	10	20
α-helix	186-188	3
β-strand	194-200	7	21
α-helix	201-203	3
β-strand	205-211	7	21
α-helix	213-215	3

Chain B: 11 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	22
β-strand	10-13	4	17
β-strand	19-25	7	22
β-strand	33-38	6	17
α-helix	43-44	2
β-strand	45-49	5	17
β-strand	53-54	2	17
α-helix	55	1
β-strand	62-67	6	22
β-strand	70-75	6	22
α-helix	80-82	3
β-strand	84-90	7	17
α-helix	96	1
β-strand	97-98	2	17
β-strand	102-106	5	17
α-helix	107	1
β-strand	111	1	23
α-helix	112-113	2
β-strand	114-118	5	24
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	24
β-strand	140	1	23
β-strand	145-150	6	25
β-strand	153-154	2	25
α-helix	155	1
β-strand	159-163	5	24
α-helix	164-167	4
β-strand	173-182	10	24
α-helix	183-187	5
β-strand	191-197	7	25
β-strand	205-210	6	25

Chain E: 7 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	422-424	3
β-strand	427	1	1
β-strand	429-430	2	2
α-helix	437-441	5
α-helix	488-494	6
β-strand	496-498	3	3
α-helix	499-501	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	536-538	3	3
β-strand	551-556	6	1
β-strand	561-564	4	1
β-strand	602	1	4
β-strand	607-609	3	4
α-helix	614-617	4
α-helix	619-621	3
α-helix	624	1
β-strand	625-633	9	4
β-strand	636-644	9	4

Chain F: 8 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	422-424	3
β-strand	427	1	26
β-strand	429-430	2	18
α-helix	437-441	5
α-helix	457-488	3
α-helix	491-494	4
β-strand	496-498	3	27
α-helix	499-501	3
β-strand	502	1	28
β-strand	503	1	26
β-strand	506-509	4	29
β-strand	513-516	4	29
β-strand	519	1	27
β-strand	525	1	27
β-strand	536-538	3	27
β-strand	552-555	4	29
β-strand	556	1	28
β-strand	561-564	4	29
β-strand	602-604	3	30
β-strand	607-609	3	30
α-helix	614-617	4
α-helix	619-621	3
α-helix	624	1
β-strand	625-633	9	30
β-strand	636-644	9	30

Chain H: 9 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	5
α-helix	7-9	3
β-strand	10-12	3	6
β-strand	18-24	7	5
β-strand	33-39	7	6
β-strand	46-52	7	6
β-strand	56-59	4	6
α-helix	61-63	3
β-strand	67-72	6	5
β-strand	77-82	6	5
α-helix	84-86	3
β-strand	88-95	8	6
β-strand	100-100B	3	2
β-strand	100E-100G	3	2
β-strand	102-103	2	6
β-strand	104	1	5
β-strand	107-111	5	6
α-helix	115-116	2
β-strand	117	1	7
α-helix	118-119	2
β-strand	120-124	5	8
β-strand	135-145	11	8
β-strand	146	1	7
β-strand	151-154	4	9
α-helix	155-157	3
β-strand	159	1	9
β-strand	164-165	2	8
α-helix	166-168	3
β-strand	169-170	2	8
β-strand	176-185	10	8
α-helix	186-188	3
β-strand	189	1	10
β-strand	192	1	10
β-strand	195-200	6	9
α-helix	201-203	3
β-strand	205-210	6	9

Chain L: 10 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	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	84-90	7	12
α-helix	96	1
β-strand	97-98	2	12
β-strand	102-106	5	12
α-helix	107	1
β-strand	111	1	13
α-helix	112-113	2
β-strand	114-118	5	14
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	14
β-strand	140	1	13
β-strand	145-150	6	15
β-strand	153-154	2	15
α-helix	155	1
β-strand	159-163	5	14
α-helix	164-167	4
β-strand	173-182	10	14
α-helix	183-187	5
β-strand	191-197	7	15
β-strand	205-210	6	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Envelope glycoprotein E2	E, F	protein	177	Hepatitis C virus (isolate H)	P27958 (AlphaFold model)
Fab AR3C heavy chain	A, H	protein	233	Homo sapiens
Fab AR3C light chain	B, L	protein	214	Homo sapiens

Sequence of entity 1 (E, F), FASTA

>6UYD_1 Envelope glycoprotein E2 (chains E, F)
QLINTNGSWHINSTALNCNESLNTGWLAGLFYQHKFDSSGCQNWDEPHYPRPCGIVPAKS
VCGPVYCFTPSPVVVGTTDRSGAPTYSWGANDTDVFVLNNTGNWFGCTWMNSTGFTKVCG
APPGGPTDGGSGPWITPRCMVDYPYRLWHYPCTINYTIFKVRMYVGGVEHRLEAACN

Sequence of entity 2 (A, H), FASTA

>6UYD_2 Fab AR3C heavy chain (chains A, H)
EVQLLEQSGAEVKKPGSSVKVSCETSGGTFDNYALNWVRQAPGQGLEWIGGVVPLFGTTR
NAQKFQGRVTISDDKSTGTGHMELRSLRSEDTAVYYCVRSVTPRYCGGGFCYGEFDYWGQ
GTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHT
FPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCGS

Sequence of entity 3 (B, L), FASTA

>6UYD_3 Fab AR3C light chain (chains B, L)
EIELTQSPATLSVSPGERATLSCRASQSVSSNLAWYQQKPGQAPRLLIYGASTRATGIPA
RFSGSGSGTEFTLTVSRLEPEDSAVYFCQQYYRSPLTFGGGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4

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 P27958 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6BZY 1.6 Å, Structure of the Hepatitis C virus envelope glycoprotein E2 antigenic region 412-423…
5FGB 1.65 Å, Three dimensional structure of broadly neutralizing human anti - Hepatitis C virus (HCV)…
6BQJ 1.69 Å, Crystal structure of hepatis C virus protease (NS3) complexed with tripeptidic acyl…
2XI3 1.7 Å, HCV-H77 NS5B Polymerase Complexed With GTP
4N0Y 1.75 Å, Structure of the Hepatitis C Envelope Glycoprotein E1 antigenic region 314-324 bound to…
2XI2 1.8 Å, HCV-H77 NS5B Apo Polymerase
5FGC 1.9 Å, Three dimensional structure of broadly neutralizing human anti - Hepatitis C virus (HCV)…
6BQK 1.97 Å, Crystal structure of hepatis C virus protease (NS3) complexed with tripeptidic acyl…
5EOC 1.98 Å, Crystal structure of Fab C2 in complex with a Cyclic variant of Hepatitis C Virus E2…
2O8M 2.0 Å, Crystal structure of the S139A mutant of Hepatitis C Virus NS3/4A protease
4XVJ 2.0 Å, Structure of the hepatitis C virus envelope glycoprotein E2 antigenic 2 region 412-423…
4Z0X 2.0 Å, Structure of Hepatitis C Virus Envelope glycoprotein E2 antigenic region 434-446 bound…

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