4AL8: Dengue virus DIII

Structure of Dengue virus DIII in complex with Fab 2H12. Determined by X-ray diffraction at 1.66 Å resolution. Released 6 Jun 2012.

Method: X-ray diffraction
Resolution: 1.66 Å
Organisms: DENGUE VIRUS, HOMO SAPIENS
Chains: 3
Atoms: 4,662
Mol. weight: 58.02 kDa
Released: 6 Jun 2012

Explore 4AL8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4AL8 contains 22 α-helices and 54 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 C: 4 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	299-300	2
β-strand	301	1	1
α-helix	302	1
β-strand	306-308	3	2
β-strand	313-314	2	2
β-strand	320-326	7	2
β-strand	333-334	2	1
α-helix	335-336	2
β-strand	337-340	4	3
β-strand	346-347	2	3
β-strand	351	1	2
β-strand	357-358	2	1
β-strand	365-369	5	2
α-helix	371-372	2
β-strand	374-380	7	3
β-strand	387-393	7	3

Chain H: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	4
β-strand	9-12	4	5
β-strand	18-25	8	4
α-helix	29-31	3
β-strand	33-39	7	5
β-strand	46-51	6	5
β-strand	58-60	3	5
α-helix	62-64	3
β-strand	68-73	6	4
α-helix	74-76	3
β-strand	78-83	6	4
α-helix	88-90	3
β-strand	92-99	8	5
β-strand	107	1	5
β-strand	111-115	5	5
α-helix	118-120	3
β-strand	121	1	6
α-helix	122-123	2
β-strand	124-128	5	7
β-strand	139-149	11	7
β-strand	150	1	6
β-strand	155-158	4	8
α-helix	159-161	3
β-strand	163	1	8
β-strand	168-175	8	7
β-strand	178-188	11	7
α-helix	189-191	3
β-strand	198-203	6	8
α-helix	204-206	3
β-strand	208-213	6	8

Chain L: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	9
β-strand	10-13	4	5
β-strand	19-25	7	9
β-strand	33-38	6	5
β-strand	45-49	5	5
β-strand	53-54	2	5
α-helix	55	1
β-strand	62-65	4	9
β-strand	70-75	6	9
α-helix	80-82	3
β-strand	85-90	6	5
α-helix	96	1
β-strand	97-98	2	5
β-strand	102-106	5	5
β-strand	111	1	10
α-helix	112-113	2
β-strand	114-118	5	11
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	11
β-strand	140	1	10
β-strand	145-150	6	12
β-strand	153-155	3	12
β-strand	159-163	5	11
α-helix	164-167	4
β-strand	173-182	10	11
α-helix	183-186	4
β-strand	191-197	7	12
α-helix	204	1
β-strand	205-210	6	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Envelope protein	C	protein	101	DENGUE VIRUS	P17763 (AlphaFold model)
FAB 2H12 heavy chain	H	protein	217	HOMO SAPIENS
FAB 2H12 light chain	L	protein	213	HOMO SAPIENS

Sequence of entity 1 (C), FASTA

>4AL8_1 ENVELOPE PROTEIN (chains C)
KGMSYVMCTGSFKLEKEVAETQHGTVLVQVKYEGTDAPCKIPFSSQDEKGVTQNGRLITA
NPIVTDKEKPVNIEAEPPFGESYIVVGAGEKALKLSWFKKG

Sequence of entity 2 (H), FASTA

>4AL8_2 FAB 2H12 HEAVY CHAIN (chains H)
DVQLVEPGAELVQPGASVKMSCKASGYTFSSYWINWEKQRPGKGLEWIGNIYPGSGTVNY
DDKFKSKATLTIDTSSNTAYMQLSSLTSEDSAVYYCTRGGSHAMDYWGQGTSVTVSSAKT
TPPSVYPLAPGCGDTTGSSVTLGCLVKGYFPESVTVTWNSGSLSSSVHTFPALLQSGLYT
MSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLEPR

Sequence of entity 3 (L), FASTA

>4AL8_3 FAB 2H12 LIGHT CHAIN (chains L)
DIVMTQSQKFMSTSVGDRVSITCKASQNVRTSVAWYQQKPGQSPKALIYLASNRHTGVPD
RFTGSGSGTDFTLTISNVQSEDLADYFCLQHWTYPYTFGGGTKLEIKRADAAPTVSIFPP
SSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLT
LTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE

Primary citation

Structural Analysis of a Dengue Cross-Reactive Antibody Complexed with Envelope Domain III Reveals the Molecular Basis of Cross-Reactivity. Midgley, C.M., Flanagan, A., Tran, H.B. et al. J Immunol (2012) 188:4971. DOI 10.4049/JIMMUNOL.1200227 · PubMed

Other PDB entries of the same protein (UniProt P17763 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4LCY 1.6 Å, Crystal structure of HLA-b46 at 1.6 angstrom resolution
4GSX 1.9 Å, High resolution structure of dengue virus serotype 1 sE containing stem
3LKW 2.0 Å, Crystal Structure of Dengue Virus 1 NS2B/NS3 protease active site mutant
3L6P 2.2 Å, Crystal Structure of Dengue Virus 1 NS2B/NS3 protease
4GT0 2.57 Å, Structure of dengue virus serotype 1 sE containing stem to residue 421
4OIG 2.69 Å, Dengue Virus Non-structural Protein NS1
8VPR 2.7 Å, Crystal structure of mouse Importin alpha in complex with Dengue 1 NS5 central NLS peptide
5WKF 2.95 Å, D30 TCR in complex with HLA-A*11:01-GTS1
5VIC 3.0 Å, Crystal structure of anti-Zika antibody Z004 bound to DENV-1 Envelope protein DIII
5WJL 3.15 Å, Crystal Structure of HLA-A*11:01 with GTS1 peptide
7DWT 19.0 Å, Cryo-EM structure of Dengue virus serotype 1 strain WestPac 74 in complex with human…
7DWU 19.0 Å, Cryo-EM structure of Dengue virus serotype 1 strain WestPac 74 in complex with human…

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