6WO4: Fab HC11 heavy chain

Structure of Hepatitis C Virus Envelope Glycoprotein E2 core from genotype 6a bound to broadly neutralizing antibody HC11. Determined by X-ray diffraction at 2.35 Å resolution. Released 19 Aug 2020.

Method: X-ray diffraction
Resolution: 2.35 Å
Organisms: Homo sapiens, Recombinant Hepatitis C virus HK6a/JFH-1
Chains: 3
Atoms: 4,732
Mol. weight: 71.59 kDa
Ligands: NAG
Released: 19 Aug 2020

Explore 6WO4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6WO4 contains 27 α-helices and 58 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: 9 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	422-424	3
β-strand	426-427	2	7
β-strand	429-430	2	2
α-helix	439-442	4
α-helix	446-448	3
β-strand	496-498	3	8
α-helix	499-501	3
β-strand	502-510	9	7
β-strand	512-516	5	7
β-strand	519	1	8
β-strand	525	1	8
β-strand	536-538	3	8
α-helix	540-542	3
β-strand	551-556	6	7
β-strand	561-565	5	7
α-helix	566-568	3
β-strand	604	1	9
β-strand	607-609	3	9
α-helix	614-617	4
α-helix	619-621	3
α-helix	624	1
β-strand	625-633	9	9
β-strand	636-644	9	9

Chain H: 10 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	1
α-helix	7-9	3
β-strand	10-12	3	2
β-strand	18-25	8	1
β-strand	34-39	6	2
β-strand	46-51	6	2
α-helix	52A-54	3
β-strand	57-59	3	2
α-helix	61-63	3
β-strand	67-72	6	1
β-strand	77-82	6	1
α-helix	84-86	3
β-strand	88-100A	14	2
β-strand	100D-103	9	2
β-strand	107-111	5	2
β-strand	117	1	3
α-helix	118-119	2
β-strand	120-124	5	4
α-helix	125-126	2
β-strand	127	1	5
β-strand	135-145	11	4
β-strand	146	1	3
β-strand	151-154	4	6
α-helix	155-157	3
β-strand	159	1	6
β-strand	163-165	3	4
α-helix	166-168	3
β-strand	169-170	2	4
β-strand	176-185	10	4
α-helix	186-188	3
β-strand	195-200	6	6
α-helix	201-203	3
β-strand	205-210	6	6
β-strand	214	1	5

Chain L: 8 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	10
β-strand	10-13	4	11
β-strand	19-29	11	10
α-helix	30-31	3
β-strand	33-38	6	11
β-strand	45-49	5	11
β-strand	53-54	2	11
α-helix	55	1
β-strand	62-75	14	10
α-helix	80-82	3
β-strand	85-90	6	11
β-strand	97-98	2	11
β-strand	102-106	5	11
β-strand	111	1	12
α-helix	112-113	2
β-strand	114-118	5	13
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	13
β-strand	140	1	12
β-strand	145-150	6	14
β-strand	153-155	3	14
β-strand	159-163	5	13
α-helix	164-167	4
β-strand	173-182	10	13
α-helix	183-188	6
β-strand	191-197	7	14
β-strand	205-210	6	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fab HC11 heavy chain	H	protein	231	Homo sapiens
Envelope glycoprotein E2	E	protein	189	Recombinant Hepatitis C virus HK6a/JFH-1	B9V0E2
Fab HC11 light chain	L	protein	235	Homo sapiens

Sequence of entity 1 (H), FASTA

>6WO4_1 Fab HC11 heavy chain (chains H)
EVQLVESGAEVKKPGSSVKVSCKASGATFSSFIFSWVRQAPGQGPEWMGGIIPMFGTAKY
APRLQGRVTITADESTSTAYMDLSSLRFEDTAVYYCAMEVPGFCRGGSCSGYMDVWGKGT
LVTVSPASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFP
AVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCGS

Sequence of entity 2 (E), FASTA

>6WO4_2 Envelope glycoprotein E2 (chains E)
QLINTNGSWHINRTALNCNDSLQTGFITSLFYAKNVDSSGCPERMAACGSSGCWHYAPRP
CDVVSARTVCGPVYCFTPSPVVVGTTDKLGIPTYNWGENETDVFMLESLRPPTGGWFGCT
WMNSTGFTKTCGAPPGGPTDGGSGPWITPRCLVDYPYRLWHYPCTVNFTLHKVRMFVGGI
EHRFDAACN

Sequence of entity 3 (L), FASTA

>6WO4_3 Fab HC11 light chain (chains L)
GVPTQVLGLLLLWLTDARCQAAVLTQSPGTLSLSPGERATLSCRASHSVSSSNLAWYQQK
PGQAPRLLMYGASRRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGSSPITFG
QGTRLDIKGTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNS
QESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

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

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…
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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