6FLC: 2C8 Fab

2C8 Fab bound to EDIII of DenV 2. Determined by X-ray diffraction at 2.0 Å resolution. Released 24 Oct 2018.

Method: X-ray diffraction
Resolution: 2.0 Å
Organisms: Mus musculus, Dengue virus 2
Chains: 6
Atoms: 8,758
Mol. weight: 119.7 kDa
Released: 24 Oct 2018

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

Secondary structure: helices and β-sheets

6FLC contains 44 α-helices and 112 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 A: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-14	5	2
β-strand	19-25	7	1
β-strand	33-38	6	2
β-strand	45-49	5	2
β-strand	53-54	2	2
α-helix	55	1
β-strand	62-66	5	1
β-strand	70-75	6	1
α-helix	80-82	3
β-strand	84-90	7	2
α-helix	97	1
β-strand	98	1	2
α-helix	99	1
β-strand	102-107	6	2
β-strand	111	1	3
β-strand	114-118	5	4
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	4
β-strand	140	1	3
β-strand	145-150	6	5
β-strand	153-155	3	5
β-strand	159-163	5	4
α-helix	164-167	4
β-strand	173-182	10	4
α-helix	183-186	4
β-strand	191-197	7	5
α-helix	204	1
β-strand	205-210	6	5

Chains B and H: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	6
β-strand	11-12	2	7
β-strand	18-25	8	6
α-helix	29-31	3
β-strand	34-39	6	8
β-strand	46-51	6	8
α-helix	54-56	3
β-strand	60-62	3	8
β-strand	70-75	6	6
β-strand	80-85	6	6
α-helix	90-92	3
β-strand	94-103	10	8
β-strand	106-111	6	8
β-strand	115-117	3	8
β-strand	118-119	2	7
α-helix	122-124	3
β-strand	125	1	9
α-helix	126-127	2
β-strand	128-132	5	10
β-strand	143-153	11	10
β-strand	154	1	9
β-strand	159-162	4	11
α-helix	163-165	3
β-strand	167	1	11
β-strand	171-173	3	10
α-helix	174-176	3
β-strand	177-179	3	10
β-strand	182-192	11	10
β-strand	202-207	6	11
α-helix	208-210	3
β-strand	212-217	6	11

Chain G: 5 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	300-301	2	12
α-helix	302	1
β-strand	306-308	3	13
α-helix	311-312	2
β-strand	313-314	2	13
α-helix	315	1
β-strand	320-326	7	13
β-strand	333-334	2	12
β-strand	337-340	4	14
β-strand	347	1	14
β-strand	350-351	2	13
β-strand	357-358	2	12
β-strand	365-370	6	13
α-helix	371-372	2
β-strand	374-380	7	14
α-helix	382	1
β-strand	387-393	7	14

Chain I: 5 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	300-301	2	21
α-helix	302	1
β-strand	306-308	3	22
α-helix	311-312	2
β-strand	313-314	2	22
α-helix	315	1
β-strand	320-326	7	22
β-strand	333-334	2	21
β-strand	337-340	4	23
β-strand	347	1	23
β-strand	350-351	2	22
β-strand	357-358	2	21
β-strand	365-370	6	22
α-helix	371-372	2
β-strand	375-380	6	23
α-helix	382	1
β-strand	387-392	6	23

Chain L: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	24
β-strand	10-13	4	25
β-strand	19-25	7	24
β-strand	33-38	6	25
β-strand	45-49	5	25
β-strand	53-54	2	25
α-helix	55	1
β-strand	62-66	5	24
β-strand	70-75	6	24
α-helix	80-82	3
β-strand	84-90	7	25
α-helix	97	1
β-strand	98	1	25
α-helix	99	1
β-strand	102-106	5	25
β-strand	111	1	26
β-strand	114-118	5	27
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	27
β-strand	140	1	26
β-strand	145-150	6	28
β-strand	153-155	3	28
β-strand	159-163	5	27
α-helix	164-167	4
β-strand	173-182	10	27
α-helix	183-186	4
β-strand	191-197	7	28
α-helix	204	1
β-strand	205-210	6	28

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Light chain of 2C8 Fab	A, L	protein	214	Mus musculus
Heavy chain of 2C8 Fab	B, H	protein	231	Mus musculus
Domain III of Dengue virus 2	G, I	protein	98	Dengue virus 2	P14340

Sequence of entity 1 (A, L), FASTA

>6FLC_1 Light chain of 2C8 Fab (chains A, L)
DIQMTQSPASLSVSVGETVTITCRATKNIYNNLAWYQQKQGRSPQLLVYAATNLADGVPS
RFSGSGSGTQFSLRINSLQSEDFGNYYCQHFWHTPWTFGGGTKLEIKRADAAPTVSIFPP
SSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLT
LTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 2 (B, H), FASTA

>6FLC_2 Heavy chain of 2C8 Fab (chains B, H)
EVKLVESGGGLVQPGGSLSLSCAASGFTFTDYYMTWVRQPPGKALEWLALIRNKASGYTT
EYSASVKGRFTISRDNSQSILYLQMNALRAEDSATYYCTRAKWDGHYFDYWGQGTTLTVS
SAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQS
DLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPRGPTIKPCPPC

Sequence of entity 3 (G, I), FASTA

>6FLC_3 Domain III of Dengue virus 2 (chains G, I)
MSYSMCTGKFKVVKEIAETQHGTIVIRVQYEGDGSPCKIPFEIMDLEKRHVLGRLITVNP
IVTEKDSPVNIEAEPPFGDSYIIIGVEPGQLKLNWFKK

Primary citation

Characterization of a potent and highly unusual minimally enhancing antibody directed against dengue virus. Renner, M., Flanagan, A., Dejnirattisai, W. et al. Nat Immunol (2018) 19:1248-1256. DOI 10.1038/s41590-018-0227-7 · PubMed

Other PDB entries of the same protein (UniProt P14340), best resolution first:

6IZY 2.11 Å, The RNA-dependent RNA polymerase domain of dengue 2 NS5
6FLB 2.2 Å, 3H5 Fab bound to EDIII of DenV 2 Xtal form 2
6IZX 2.43 Å, The RNA-dependent RNA polymerase domain of dengue 2 NS5, bound with RK-0404678
6FLA 2.9 Å, 3H5 Fab bound to EDIII of DenV 2 Xtal form 1
7V3F 3.1 Å, DENV2_NGC_Fab_C10 28degree (1Fab:3E)
7V3G 3.3 Å, DENV2_NGC_Fab_C10 28degrees (2Fab:3E)
7CTH 3.5 Å, Cryo-EM structure of dengue virus serotype 2 in complex with the scFv fragment of the…
3J27 3.6 Å, CryoEM structure of Dengue virus
3J2P 3.6 Å, CryoEM structure of Dengue virus envelope protein heterotetramer
7V3H 3.6 Å, DENV2_NGC_Fab_C10 28degrees (3Fab:3E)
9DTT 3.6 Å, Cryo-EM structure of DENV2 NS5 in complex with Stem Loop A (SLA)
4CBF 4.1 Å, Near-atomic resolution cryo-EM structure of Dengue serotype 4 virus

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