4Q0X: Non-neutralizing antibody

Crystal structure of non-neutralizing antibody in complex with Epitope II of HCV E2. Determined by X-ray diffraction at 2.9 Å resolution. Released 9 Jul 2014.

Method: X-ray diffraction
Resolution: 2.9 Å
Organisms: Mus musculus, Hepatitis C virus
Chains: 3
Atoms: 3,421
Mol. weight: 50.58 kDa
Released: 9 Jul 2014

Explore 4Q0X in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4Q0X contains 11 α-helices and 43 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: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	437-441	5

Chain H: 5 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	1
β-strand	10-12	3	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	34-40	7	2
β-strand	44-52	9	2
β-strand	57-60	4	2
α-helix	62-64	3
β-strand	68-73	6	1
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-100	9	2
β-strand	104-109	6	2
β-strand	113-117	5	2
β-strand	123	1	3
β-strand	126-130	5	4
β-strand	141-151	11	4
β-strand	152	1	3
β-strand	157-160	4	5
α-helix	161-163	3
β-strand	169-171	3	4
α-helix	172-174	3
β-strand	175-176	2	4
β-strand	181-190	10	4
β-strand	200-205	6	5
β-strand	210-215	6	5

Chain L: 5 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	6
β-strand	10-13	4	7
β-strand	19-25	7	6
β-strand	38-43	6	7
β-strand	49-54	6	7
β-strand	58-59	2	7
α-helix	60	1
β-strand	67-72	6	6
β-strand	75-80	6	6
β-strand	89-95	7	7
β-strand	102-103	2	7
β-strand	104	1	6
β-strand	107-111	5	7
β-strand	116	1	8
β-strand	119-123	5	9
α-helix	124-126	3
α-helix	127-130	4
β-strand	134-144	11	9
β-strand	145	1	8
β-strand	150-155	6	10
β-strand	158-160	3	10
β-strand	164-168	5	9
α-helix	169-172	4
β-strand	178-187	10	9
α-helix	188-191	4
β-strand	196-202	7	10
β-strand	210-215	6	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
mAb 12 heavy chain	H	protein	219	Mus musculus	Q99LC4 (AlphaFold model)
mAb 12 light chain	L	protein	218	Mus musculus	A2NHM3 (AlphaFold model)
Envelope glycoprotein E2	E	protein	26	Hepatitis C virus	P27958 (AlphaFold model)

Sequence of entity 1 (H), FASTA

>4Q0X_1 mAb 12 heavy chain (chains H)
QVQLRQSGPELVKPGASVRISCKASGYTFTSYYIHWVKQRPGQGLEWIGWIYPGNVNTKY
NEKFKGKATLTADKSSSTAYMQLSSLTSEDSAVYFCARDDYDGAWFAYWGQGTLVTVSAA
KTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDL
YTLSSSVTVPSSTWPSQTVTCNVAHPASSTKVDKKIVPR

Sequence of entity 2 (L), FASTA

>4Q0X_2 mAb 12 light chain (chains L)
DVLMTQTPLSLPVSLGDQASISCRSSQSIVHNNGNTYLDWSLQKPGQSPKLLIYKVSNRF
SGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPPTFGGGTKLEIKRADAAPTV
SIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSM
SSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE

Sequence of entity 3 (E), FASTA

>4Q0X_3 Envelope glycoprotein E2 (chains E)
HINSTALNCNESLNTGWLAGLFYQHK

Primary citation

Discrete conformations of epitope II on the hepatitis C virus E2 protein for antibody-mediated neutralization and nonneutralization. Deng, L., Ma, L., Virata-Theimer, M.L. et al. Proc Natl Acad Sci U S A (2014) 111:10690-10695. DOI 10.1073/pnas.1411317111 · PubMed

Other PDB entries of the same protein (UniProt Q99LC4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6C5K 1.75 Å, S25-23 Fab in complex with Chlamydiaceae LPS (Crystal form 2)
6C5I 1.89 Å, Unliganded S25-5 Fab
6C5H 1.99 Å, S25-5 Fab in complex with Chlamydiaceae-specific LPS antigen
6C5J 2.29 Å, S25-23 Fab in complex with Chlamydiaceae LPS (Crystal form 1)
1GIG 2.3 Å, Refined three-dimensional structure of the FAB fragment of a murine IgG1, lambda antibody
3HKF 2.5 Å, Murine unglycosylated IgG Fc fragment
1JHK 2.51 Å, Crystal structure of the anti-estradiol antibody 57-2
2A1W 2.7 Å, Anti-cocaine antibody 7.5.21, crystal form I
5MP3 2.75 Å, Crystal structure of DC8E8 Fab in the complex with a 30-mer tau peptide at pH 6.5
1JNL 3.0 Å, Crystal Structure of Fab-Estradiol Complexes
1JNN 3.2 Å, Crystal Structure of Fab-Estradiol Complexes
1AFV 3.7 Å, HIV-1 capsid protein (P24) complex with FAB25.3

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