5FGB: Anti-HCV E2 Fab HC84-1 light chain

Three dimensional structure of broadly neutralizing human anti - Hepatitis C virus (HCV) glycoprotein E2 Fab fragment HC33.4. Determined by X-ray diffraction at 1.65 Å resolution. Released 20 Jan 2016.

Method: X-ray diffraction
Resolution: 1.65 Å
Organisms: Homo sapiens, Hepatitis C virus genotype 1a (isolate H)
Chains: 6
Atoms: 7,252
Mol. weight: 109.43 kDa
Released: 20 Jan 2016

Explore 5FGB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5FGB contains 33 α-helices and 88 β-strands across 4 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: 9 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	1
β-strand	9-13	5	2
β-strand	18-23	6	1
α-helix	27-29	3
β-strand	33-37	5	2
β-strand	44-47	4	2
β-strand	48	1	3
β-strand	52	1	3
α-helix	53-54	2
β-strand	61-66	6	1
β-strand	69-74	6	1
α-helix	79-81	3
β-strand	83-91	9	2
β-strand	95-98	4	2
β-strand	102-107	6	2
β-strand	111	1	4
α-helix	112-113	2
β-strand	114-118	5	5
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	5
β-strand	140	1	4
β-strand	145-150	6	6
β-strand	153-154	2	6
α-helix	155	1
β-strand	159-163	5	5
α-helix	164-167	4
β-strand	173-182	10	5
α-helix	183-187	5
β-strand	191-197	7	6
β-strand	205-210	6	6

Chain B: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	7
β-strand	9-13	5	8
β-strand	18-23	6	7
β-strand	33-37	5	8
β-strand	44-47	4	8
β-strand	48	1	9
β-strand	52	1	9
α-helix	53-54	2
β-strand	61-66	6	7
β-strand	69-74	6	7
α-helix	79-81	3
β-strand	83-91	9	8
β-strand	95-98	4	8
β-strand	102-107	6	8
β-strand	111	1	10
α-helix	112-113	2
β-strand	114-118	5	11
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	11
β-strand	140	1	10
β-strand	145-150	6	12
β-strand	153-154	2	12
α-helix	155	1
β-strand	159-163	5	11
α-helix	164-167	4
β-strand	173-182	10	11
α-helix	183-187	5
β-strand	191-197	7	12
β-strand	205-210	6	12

Chain C: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	13
β-strand	10-12	3	14
β-strand	18-25	8	13
α-helix	29-31	3
β-strand	33-39	7	14
β-strand	45-51	7	14
β-strand	58-60	3	14
β-strand	68-73	6	13
β-strand	78-83	6	13
α-helix	88-90	3
β-strand	92-101	10	14
β-strand	107-112	6	14
β-strand	116-120	5	14
α-helix	124-125	2
β-strand	126	1	15
α-helix	127-128	2
β-strand	129-133	5	16
β-strand	144-154	11	16
β-strand	155	1	15
β-strand	160-163	4	17
α-helix	164-166	3
β-strand	168	1	17
β-strand	172-174	3	16
α-helix	175-177	3
β-strand	178-179	2	16
β-strand	185-194	10	16
α-helix	195-197	3
β-strand	204-209	6	17
α-helix	210-212	3
β-strand	214-219	6	17

Chain E: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	18
β-strand	10-12	3	19
β-strand	18-25	8	18
α-helix	29-31	3
β-strand	34-39	6	19
β-strand	45-51	7	19
β-strand	58-60	3	19
β-strand	68-73	6	18
β-strand	78-83	6	18
α-helix	88-90	3
β-strand	92-101	10	19
β-strand	107-112	6	19
β-strand	116-120	5	19
α-helix	124-125	2
β-strand	126	1	20
α-helix	127-128	2
β-strand	129-133	5	21
β-strand	144-154	11	21
β-strand	155	1	20
β-strand	160-163	4	22
α-helix	164-166	3
β-strand	168	1	22
β-strand	172-174	3	21
α-helix	175-177	3
β-strand	178-179	2	21
β-strand	185-194	10	21
α-helix	195-197	3
β-strand	204-209	6	22
α-helix	210-212	3
β-strand	214-219	6	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Anti-HCV E2 Fab HC84-1 light chain	A, B	protein	216	Homo sapiens
Anti-HCV E2 Fab HC84-1 heavy chain	C, E	protein	269	Homo sapiens
Genome polyprotein	F, G	protein	21	Hepatitis C virus genotype 1a (isolate H)	P27958 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5FGB_1 Anti-HCV E2 Fab HC84-1 light chain (chains A, B)
RSSYELTQLPSLSVSLGQTASITCSGDNLGDKFVCWYQQKPGQTPVLVMYEDTKRPSGIP
ERFAGSNSGNTATLTITGTQAMDEADYYCQTWDSSTDVVFGGGTKLTVLRTVAAPSVFIF
PPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSST
LTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 2 (C, E), FASTA

>5FGB_2 Anti-HCV E2 Fab HC84-1 heavy chain (chains C, E)
EVQLVQSGGGLVQPGGSLRLSCAASGFTFSSYAMSWVRQAPGKGLEWVSAISGSGGSTYY
ADSVKGRFTISRDNSKNILYLQMNSLKAEDTATYYCARAVVFTDSSAYYYSKYFDYWSQG
TLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTF
PAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKAEPKSCDKLEDDDDKA
GWSHPQFEKGGGSGGGSGGGSWSHPQFEK

Sequence of entity 3 (F, G), FASTA

>5FGB_3 Genome polyprotein (chains F, G)
PGAKQNIQLINTNGSWHINST

Primary citation

Antibody Response to Hypervariable Region 1 Interferes with Broadly Neutralizing Antibodies to Hepatitis C Virus. Keck, Z.Y., Girard-Blanc, C., Wang, W. et al. J Virol (2016) 90:3112-3122. DOI 10.1128/JVI.02458-15 · 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…
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
6UYD 1.9 Å, Structure of Hepatitis C Virus Envelope Glycoprotein E2mc3-v1 redesigned core from…
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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