6UYF: Fab AR3B heavy chain

Structure of Hepatitis C Virus Envelope Glycoprotein E2mc3-v1 redesigned core from genotype 6a bound to broadly neutralizing antibody AR3B. Determined by X-ray diffraction at 2.06 Å resolution. Released 22 Apr 2020.

Method: X-ray diffraction
Resolution: 2.06 Å
Organisms: Homo sapiens, Recombinant Hepatitis C virus HK6a/JFH-1
Chains: 3
Atoms: 4,901
Mol. weight: 68.89 kDa
Ligands: NAG
Released: 22 Apr 2020

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

Secondary structure: helices and β-sheets

6UYF contains 23 α-helices and 63 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, 18 β-strands

Element	Residues	Length	Sheet
α-helix	422-424	3
β-strand	427	1	11
β-strand	429-430	2	3
α-helix	439-442	4
α-helix	491-494	4
β-strand	496-498	3	12
α-helix	499-501	3
β-strand	502	1	13
β-strand	503	1	11
β-strand	506-509	4	14
β-strand	513-516	4	14
β-strand	519	1	12
β-strand	525	1	12
β-strand	536-538	3	12
β-strand	551-555	5	14
β-strand	556	1	13
β-strand	561-564	4	14
β-strand	599	1	15
β-strand	602-604	3	15
β-strand	607-609	3	15
α-helix	614-617	4
α-helix	619-621	3
β-strand	625-633	9	15
β-strand	636-644	9	15

Chain H: 7 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	1
β-strand	10-12	3	2
β-strand	18-24	7	1
β-strand	34-39	6	2
β-strand	45-52	8	2
β-strand	56-59	4	2
β-strand	67-72	6	1
β-strand	77-82	6	1
α-helix	84-86	3
β-strand	88-95	8	2
α-helix	96	1
β-strand	100A-100C	3	3
β-strand	100F-100H	3	3
β-strand	100K-103	4	2
β-strand	104	1	1
β-strand	107-111	5	2
β-strand	117	1	4
α-helix	118-119	2
β-strand	120-124	5	5
β-strand	136-145	10	5
β-strand	146	1	4
β-strand	151-154	4	6
α-helix	155-157	3
β-strand	159	1	6
β-strand	163-165	3	5
α-helix	166-168	3
β-strand	169-170	2	5
β-strand	176-184	9	5
α-helix	186-188	3
β-strand	195-200	6	6
α-helix	201-203	3
β-strand	205-210	6	6

Chain L: 10 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	7
β-strand	10-13	4	2
β-strand	19-29	11	7
α-helix	30A-32	3
β-strand	33-38	6	2
β-strand	45-49	5	2
β-strand	53-54	2	2
α-helix	55	1
β-strand	62-75	14	7
α-helix	80-82	3
β-strand	85-90	6	2
α-helix	96	1
β-strand	97-98	2	2
β-strand	102-106	5	2
β-strand	111	1	8
α-helix	112-113	2
β-strand	114-118	5	9
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	9
β-strand	140	1	8
β-strand	145-150	6	10
β-strand	153-154	2	10
α-helix	155	1
β-strand	159-163	5	9
α-helix	164-167	4
β-strand	173-182	10	9
α-helix	183-186	4
β-strand	191-197	7	10
β-strand	205-210	6	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fab AR3B heavy chain	H	protein	230	Homo sapiens
Fab AR3B light chain	L	protein	215	Homo sapiens
Envelope glycoprotein E2	E	protein	177	Recombinant Hepatitis C virus HK6a/JFH-1	B9V0E2

Sequence of entity 1 (H), FASTA

>6UYF_1 Fab AR3B heavy chain (chains H)
LLEQSGPEVKKPGSSVKVSCKDSGDTFNEPVTWVRQAPGQGLEWIGGIIPAFGVTKYAQK
FQGRVIISADASTATAYLELSSLRSEDTAVYYCAKVGLRGIVMVGGLAMNWLDPWGQGTQ
VTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPA
VLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCGS

Sequence of entity 2 (L), FASTA

>6UYF_2 Fab AR3B light chain (chains L)
EIELTQSPGTLSLSPGERATLSCRASQSVSSSYLAWYQQKPGQAPRLLIYGASSRATGIP
DRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGSSPQTFGQGTKVEIKRTVAAPSVFIFP
PSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (E), FASTA

>6UYF_3 Envelope glycoprotein E2 (chains E)
QLINTNGSWHINRTALNCNDSLQTGFITSLFYAKNVDSSGCQNWDEPHYPRPCDVVSART
VCGPVYCFTPSPVVVGTTDKLGIPTYNWGENETDVFMLESLGGWFGCTWMNSTGFTKTCG
APPGGPTDGGSGPWITPRCLVDYPYRLWHYPCTVNFTLHKVRMFVGGIEHRFDAACN

Ligands and cofactors

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

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:

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…
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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