6WER: DENV2 NS1

DENV2 NS1 in complex with neutralizing 2B7 Fab fragment. Determined by X-ray diffraction at 3.96 Å resolution. Released 23 Dec 2020.

Method: X-ray diffraction
Resolution: 3.96 Å
Organisms: Dengue virus 2, Mus musculus
Chains: 6
Atoms: 11,710
Mol. weight: 195.5 kDa
Ligands: NAG
Released: 23 Dec 2020

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

Secondary structure: helices and β-sheets

6WER contains 52 α-helices and 146 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: 13 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	1
β-strand	12-17	6	1
β-strand	18-22	5	2
β-strand	32-36	5	3
α-helix	39-51	13
β-strand	56-57	2	4
α-helix	62-81	20
β-strand	86-90	5	4
β-strand	102	1	4
β-strand	131-135	5	4
α-helix	145-147	3
β-strand	148-149	2	4
β-strand	153-157	5	3
β-strand	165-171	7	3
β-strand	178	1	5
α-helix	179-180	2
β-strand	185-189	5	6
β-strand	192-196	5	6
β-strand	200-207	8	6
β-strand	209-217	9	6
β-strand	224	1	5
α-helix	225-226	2
α-helix	227-229	3
β-strand	231	1	7
α-helix	238-240	3
α-helix	245-247	3
α-helix	268-270	3
β-strand	273-277	5	6
α-helix	279-280	2
β-strand	284-287	4	8
α-helix	292-294	3
β-strand	298	1	9
β-strand	299	1	6
β-strand	301	1	10
β-strand	307	1	10
β-strand	310-313	4	8
α-helix	320	1
β-strand	321-325	5	6
β-strand	328-331	4	6
β-strand	335-337	3	8
α-helix	342-344	3
β-strand	347	1	9

Chain B: 15 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	1
β-strand	12-17	6	1
β-strand	18-22	5	2
β-strand	33-36	4	11
α-helix	39-51	13
β-strand	56-57	2	12
α-helix	62-81	20
β-strand	86-90	5	12
β-strand	102	1	12
β-strand	131-135	5	12
α-helix	145-147	3
β-strand	148-149	2	12
β-strand	153-158	6	11
β-strand	166-171	6	11
β-strand	178	1	13
α-helix	179-180	2
α-helix	181-183	3
β-strand	185-189	5	6
β-strand	192-196	5	6
β-strand	200-207	8	6
β-strand	209-217	9	6
β-strand	224	1	13
α-helix	225-226	2
α-helix	227-229	3
β-strand	231	1	7
α-helix	238-240	3
α-helix	245-247	3
α-helix	253-255	3
α-helix	268-270	3
β-strand	273-277	5	6
α-helix	279-280	2
β-strand	284-287	4	14
α-helix	292-294	3
β-strand	298	1	15
β-strand	299	1	6
β-strand	301	1	16
β-strand	307	1	16
β-strand	310-313	4	14
α-helix	320	1
β-strand	321-325	5	6
β-strand	328-331	4	6
β-strand	335-337	3	14
α-helix	342-344	3
β-strand	347	1	15

Chains C and E: 3 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	17
β-strand	10-12	3	18
β-strand	19-25	7	17
β-strand	33-39	7	18
β-strand	45-51	7	18
β-strand	57-59	3	18
α-helix	61-63	3
β-strand	68-72	5	17
β-strand	77-81	5	17
α-helix	87-89	3
β-strand	91-98	8	18
β-strand	109	1	18
β-strand	113-117	5	18
β-strand	123	1	19
α-helix	124-125	2
β-strand	126-130	5	20
β-strand	142-151	10	20
β-strand	152	1	19
β-strand	157-160	4	21
β-strand	168-171	4	20
β-strand	175-177	3	20
β-strand	180-189	10	20
β-strand	200-205	6	21
β-strand	210-215	6	21

Chains D and F: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	4-7	4	22
β-strand	10-14	5	23
β-strand	19-25	7	22
β-strand	30-31	2	24
β-strand	34-35	2	24
β-strand	37-42	6	23
β-strand	49-53	5	23
β-strand	57-58	2	23
α-helix	59	1
β-strand	66-71	6	22
β-strand	74-79	6	22
α-helix	84-86	3
β-strand	89-94	6	23
α-helix	100	1
β-strand	101-102	2	23
β-strand	106-111	6	23
β-strand	115	1	25
β-strand	118-122	5	26
α-helix	123-125	3
α-helix	126-130	5
β-strand	133-143	11	26
β-strand	144	1	25
β-strand	149-154	6	27
β-strand	157-159	3	27
β-strand	163-167	5	26
α-helix	168-171	4
β-strand	177-186	10	26
α-helix	187-192	6
β-strand	195-201	7	27
α-helix	208	1
β-strand	209-214	6	27

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Non-structural protein 1	A, B	protein	376	Dengue virus 2	P29990
2B7 Fab heavy chain	C, E	protein	268	Mus musculus
2B7 Fab light chain	D, F	protein	238	Mus musculus

Sequence of entity 1 (A, B), FASTA

>6WER_1 Non-structural protein 1 (chains A, B)
AHHHHHHSSGVDLGTENLYFQSNADSGCVVSWKNKELKCGSGIFITDNVHTWTEQYKFQP
ESPSKLASAIQKAHEEGICGIRSVTRLENLMWKQITPELNHILSENEVKLTIMTGDIKGI
MQAGKRSLRPQPTELKYSWKTWGKAKMLSTESHNQTFLIDGPETAECPNTNRAWNSLEVE
DYGFGVFTTNIWLKLKEKQDVFCDSKLMSAAIKDNRAVHADMGYWIESALNDTWKIEKAS
FIEVKNCHWPKSHTLWSNGVLESEMIIPKNLAGPVSQHNYRPGYHTQITGPWHLGKLEMD
FDFCDGTTVVVTEDCGNRGPSLRTTTASGKLITEWCCRSCTLPPLRYRGEDGCWYGMEIR
PLKEKEENLVNSLVTA

Sequence of entity 2 (C, E), FASTA

>6WER_2 2B7 Fab heavy chain (chains C, E)
MEWSWIFLFLLSGTAGVHSEVQLQQSGPELVKPGASVKMSCKASGCTLTNCFMHWMKQKP
GQDLEWIGYINPYNDMTKYSENFKGKATLTSDKSSSTAFMELSSLTSEDSAVYYCARGYL
LRTGCFDYWGQGTTLTVSSAKTTPPSVYPLAPGCGDTTGSSVTLGCLVKGYFPESVTVTW
NSGSLSSSVHTFPALLQSGLYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLEPSG
PISTINPCPPCKECHKCPAPNLEGGPSV

Sequence of entity 3 (D, F), FASTA

>6WER_3 2B7 Fab light chain (chains D, F)
METDTLLLWVLLLWVPGSTGNIVLTQSPASLAVSLGQRATISCRASESVDSYGYSFMHWY
QQKPGQPPKVLIYLASNLESGVPARFSGSGSRTDFTLTIDPVEADDAATYYCQQNNENPL
TFGAGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQ
NGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2

Primary citation

Structural basis for antibody inhibition of flavivirus NS1-triggered endothelial dysfunction. Biering, S.B., Akey, D.L., Wong, M.P. et al. Science (2021) 371:194-200. DOI 10.1126/science.abc0476 · PubMed

Other PDB entries of the same protein (UniProt P29990), best resolution first:

7K93 2.89 Å, DENV2 NS1 in complex with neutralizing 2B7 single chain Fab variable region (scFv)
4O6B 3.0 Å, Dengue Type2 Virus Non-structural protein 1 (NS1) Form 1 crystal
6ZQU 3.1 Å, Cryo-EM structure of mature Dengue virus 2 at 3.1 angstrom resolution
6WY1 3.42 Å, Crystal structure of an engineered thermostable dengue virus 2 envelope protein dimer
2R69 3.8 Å, Crystal structure of Fab 1A1D-2 complexed with E-DIII of Dengue virus at 3.8 angstrom…
3J42 21.0 Å, Obstruction of Dengue Virus Maturation by Fab Fragments of the 2H2 Antibody
3J8D 26.0 Å, Cryoelectron microscopy of dengue-Fab E104 complex at pH 5.5

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