5EOC: Fab C2

Crystal structure of Fab C2 in complex with a Cyclic variant of Hepatitis C Virus E2 epitope I. Determined by X-ray diffraction at 1.98 Å resolution. Released 10 Feb 2016.

Method: X-ray diffraction
Resolution: 1.98 Å
Organisms: Mus musculus, Hepatitis C virus
Chains: 6
Atoms: 7,216
Mol. weight: 97.54 kDa
Released: 10 Feb 2016

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

Secondary structure: helices and β-sheets

5EOC contains 33 α-helices and 92 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 H: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	1
β-strand	9-12	4	2
β-strand	18-25	8	1
β-strand	34-39	6	2
β-strand	46-51	6	2
β-strand	58-60	3	2
α-helix	62-64	3
β-strand	68-73	6	1
α-helix	74-76	3
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-99	8	2
β-strand	106-109	4	2
β-strand	113-117	5	2
β-strand	123	1	3
α-helix	124-125	2
β-strand	126-130	5	4
β-strand	139-149	11	4
β-strand	150	1	3
β-strand	155-158	4	5
α-helix	159-161	3
β-strand	163	1	5
β-strand	167-169	3	4
α-helix	170-172	3
β-strand	173-174	2	4
β-strand	179-188	10	4
α-helix	189-191	3
β-strand	198-203	6	5
α-helix	204-206	3
β-strand	208-213	6	5

Chain J: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	12
β-strand	9-12	4	13
β-strand	18-25	8	12
β-strand	34-39	6	13
β-strand	46-52	7	13
β-strand	57-60	4	13
α-helix	62-64	3
β-strand	68-73	6	12
β-strand	78-83	6	12
α-helix	88-90	3
β-strand	92-99	8	13
β-strand	106-109	4	13
β-strand	113-117	5	13
α-helix	121-122	2
β-strand	123	1	14
α-helix	124-125	2
β-strand	126-130	5	15
β-strand	139-149	11	15
β-strand	150	1	14
β-strand	155-158	4	16
α-helix	159-161	3
β-strand	167-169	3	15
α-helix	170-172	3
β-strand	173-175	3	15
β-strand	178-188	11	15
α-helix	189-191	3
β-strand	198-203	6	16
α-helix	204-206	3
β-strand	208-213	6	16

Chain L: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	4-7	4	6
β-strand	10-14	5	7
β-strand	19-25	7	6
β-strand	30-31	2	8
β-strand	34-35	2	8
β-strand	37-42	6	7
β-strand	49-53	5	7
β-strand	57-58	2	7
α-helix	59	1
β-strand	66-71	6	6
β-strand	74-79	6	6
α-helix	84-86	3
β-strand	88-94	7	7
β-strand	102	1	7
β-strand	106-111	6	7
β-strand	115	1	9
α-helix	116-117	2
β-strand	118-122	5	10
α-helix	123-125	3
α-helix	126-129	4
β-strand	133-143	11	10
β-strand	144	1	9
β-strand	149-154	6	11
β-strand	157-159	3	11
β-strand	163-167	5	10
α-helix	168-171	4
β-strand	177-186	10	10
α-helix	187-192	6
β-strand	195-201	7	11
α-helix	208	1
β-strand	209-214	6	11

Chain M: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	4-7	4	17
β-strand	10-14	5	18
β-strand	20-25	6	17
β-strand	30	1	18
β-strand	35-42	8	18
β-strand	49-54	6	18
β-strand	58	1	18
β-strand	67-70	4	17
β-strand	74-78	5	17
α-helix	84-86	3
β-strand	88-94	7	18
α-helix	100	1
β-strand	101-102	2	18
β-strand	106-111	6	18
β-strand	115	1	19
β-strand	118-122	5	20
α-helix	123-125	3
α-helix	126-129	4
β-strand	133-143	11	20
β-strand	144	1	19
β-strand	149-154	6	21
β-strand	157-159	3	21
β-strand	163-167	5	20
α-helix	168-171	4
β-strand	177-186	10	20
α-helix	187-191	5
β-strand	195-201	7	21
α-helix	208	1
β-strand	209-214	6	21

Chain P: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	412-414	3	22
β-strand	420-422	3	22

Chain Q: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	412-415	4	23
β-strand	419-422	4	23

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fab fragment (Heavy chain)	H	protein	217	Mus musculus
Fab fragment (Light chain)	L, M	protein	216	Mus musculus
Fab fragment (Heavy chain)	J	protein	217	Mus musculus
Ala-cys-gln-leu-ile-asn-thr-asn-gly-ser-trp-his-ile-cys	P, Q	protein	14	Hepatitis C virus	P27958 (AlphaFold model)

Sequence of entity 1 (H), FASTA

>5EOC_1 Fab fragment (Heavy chain) (chains H)
EVQLQQPGAELVRPGGSVKLSCKASGYSFTTYWMNWVKQRPGQGLEWIGMIQPSDSETRL
NQKFKDKATLTLDRSSSTVYMQLSSPTSDDSAVYYCARTGRGDAWLTYWGQGTSVTVSSA
KTTPPSVYPLAPGSAANSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYT
LSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR

Sequence of entity 2 (L, M), FASTA

>5EOC_2 Fab fragment (Light chain) (chains L, M)
NIVLTQSPVSLAVSLGQRATISCRASKSVSTSGYSYMHWYQQKPGQPPRLLLYLGSNLES
GVPARFSGSGSGTDFTLNIHPVEEEDAATYYCQHIRELTRSFGGGTKLEIKRADAAPTVS
IFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMS
STLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN

Sequence of entity 3 (J), FASTA

>5EOC_3 Fab fragment (Heavy chain) (chains J)
EVQLQQPGAELVRPGGSVKLSCKASGYSFTTYWMMWVKQRPGQGLEWIGMIQPSDSETRL
NQKFKDKATLTLDRSSSTVYMQLSSPTSDDSAVYYCARTGRGDAWLTYWGQGTSVTVSSA
KTTPPSVYPLAPGSAANSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYT
LSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR

Sequence of entity 4 (P, Q), FASTA

>5EOC_4 ALA-CYS-GLN-LEU-ILE-ASN-THR-ASN-GLY-SER-TRP-HIS-ILE-CYS (chains P, Q)
ACQLINTNGSWHIC

Primary citation

Generation and Characterization of Monoclonal Antibodies against a Cyclic Variant of Hepatitis C Virus E2 Epitope 412-422. Sandomenico, A., Leonardi, A., Berisio, R. et al. J Virol (2016) 90:3745-3759. DOI 10.1128/JVI.02397-15 · 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…
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
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…
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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