7K93: DENV2 NS1

DENV2 NS1 in complex with neutralizing 2B7 single chain Fab variable region (scFv). Determined by X-ray diffraction at 2.89 Å resolution. Released 23 Dec 2020.

Method: X-ray diffraction
Resolution: 2.89 Å
Organisms: Dengue virus 2, Mus musculus
Chains: 8
Atoms: 17,581
Mol. weight: 278.46 kDa
Ligands: NAG
Released: 23 Dec 2020

Explore 7K93 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7K93 contains 76 α-helices and 216 β-strands across 8 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, 30 β-strands

Element	Residues	Length	Sheet
β-strand	1-7	7	1
β-strand	12-22	11	1
β-strand	33-36	4	2
α-helix	39-51	13
β-strand	56-57	2	3
α-helix	62-81	20
β-strand	88-90	3	3
β-strand	97	1	4
β-strand	102	1	3
β-strand	133-135	3	3
α-helix	145-147	3
β-strand	148-149	2	3
β-strand	153-157	5	2
β-strand	166-171	6	2
β-strand	178	1	5
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	221	1	4
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: 14 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	1-7	7	1
β-strand	12-22	11	1
β-strand	32-36	5	11
α-helix	39-51	13
β-strand	56-58	3	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	148-150	3	12
β-strand	153-158	6	11
β-strand	165-171	7	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
β-strand	225	1	14
α-helix	227-229	3
β-strand	231	1	7
α-helix	238-240	3
α-helix	245-247	3
β-strand	250	1	14
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	15
α-helix	292-294	3
β-strand	298	1	16
β-strand	299	1	6
β-strand	301	1	17
β-strand	307	1	17
β-strand	310-313	4	15
α-helix	320	1
β-strand	321-325	5	6
β-strand	328-331	4	6
β-strand	336-337	2	15
α-helix	342-344	3
β-strand	347	1	16

Chain C: 14 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	1-7	7	18
β-strand	12-22	11	18
β-strand	33-36	4	19
α-helix	39-51	13
β-strand	56-58	3	20
α-helix	62-81	20
β-strand	86-90	5	20
β-strand	97	1	21
β-strand	102	1	20
β-strand	131-135	5	20
α-helix	145-147	3
β-strand	148-150	3	20
β-strand	153-158	6	19
β-strand	166-171	6	19
β-strand	178	1	22
α-helix	179-180	2
α-helix	181-183	3
β-strand	185-189	5	23
β-strand	192-196	5	23
β-strand	200-207	8	23
β-strand	209-217	9	23
β-strand	221	1	21
β-strand	224	1	22
α-helix	225-226	2
α-helix	227-229	3
β-strand	231	1	24
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	23
β-strand	284-287	4	25
α-helix	292-294	3
β-strand	298	1	26
β-strand	299	1	23
β-strand	301	1	27
β-strand	307	1	27
β-strand	310-313	4	25
α-helix	320	1
β-strand	321-325	5	23
β-strand	328-331	4	23
β-strand	336-337	2	25
α-helix	342-344	3
β-strand	347	1	26

Chain D: 14 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	1-7	7	18
β-strand	12-22	11	18
β-strand	32-36	5	28
α-helix	39-51	13
β-strand	56-58	3	29
α-helix	62-81	20
β-strand	87-90	4	29
β-strand	96-97	2	30
β-strand	102	1	29
β-strand	132-135	4	29
α-helix	145-147	3
β-strand	148-150	3	29
β-strand	153-159	7	28
β-strand	165-171	7	28
β-strand	178	1	31
α-helix	179-180	2
α-helix	181-183	3
β-strand	185-189	5	23
β-strand	192-196	5	23
β-strand	200-207	8	23
β-strand	209-217	9	23
β-strand	220-221	2	30
β-strand	224	1	31
α-helix	225-226	2
α-helix	227-229	3
β-strand	231	1	24
α-helix	238-240	3
α-helix	245-247	3
α-helix	268-270	3
β-strand	273-277	5	23
α-helix	279-280	2
β-strand	284-287	4	32
α-helix	292-294	3
β-strand	298	1	33
β-strand	299	1	23
β-strand	301	1	34
β-strand	307	1	34
β-strand	310-313	4	32
α-helix	320	1
β-strand	321-325	5	23
β-strand	328-331	4	23
β-strand	336-337	2	32
α-helix	342-344	3
β-strand	347	1	33

Chain E: 5 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	35
β-strand	10-12	3	36
β-strand	19-25	7	35
β-strand	33-39	7	36
β-strand	45-51	7	36
β-strand	58-60	3	36
α-helix	62-64	3
β-strand	69-73	5	35
β-strand	78-82	5	35
α-helix	88-90	3
β-strand	92-99	8	36
β-strand	110	1	36
β-strand	114-118	5	36
α-helix	138-140	3
β-strand	141-144	4	37
β-strand	147-150	4	38
β-strand	156-162	7	37
β-strand	167-168	2	39
β-strand	171-172	2	39
β-strand	174-179	6	38
β-strand	186-190	5	38
β-strand	194-195	2	38
β-strand	203-208	6	37
β-strand	211-216	6	37
α-helix	221-223	3
β-strand	225-231	7	38
α-helix	237	1
β-strand	238-239	2	38
β-strand	243-247	5	38

Chain G: 6 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	40
β-strand	10-12	3	41
β-strand	19-25	7	40
β-strand	33-39	7	41
β-strand	45-51	7	41
β-strand	58-60	3	41
α-helix	62-64	3
β-strand	69-73	5	40
β-strand	78-82	5	40
α-helix	88-90	3
β-strand	92-99	8	41
β-strand	110	1	41
β-strand	114-118	5	41
α-helix	139-140	2
β-strand	141-144	4	42
β-strand	147-149	3	43
β-strand	156-162	7	42
β-strand	167-168	2	44
β-strand	171-172	2	44
β-strand	174-179	6	43
β-strand	186-190	5	43
β-strand	194-195	2	43
α-helix	196	1
β-strand	203-208	6	42
β-strand	211-216	6	42
α-helix	221-223	3
β-strand	225-231	7	43
α-helix	237	1
β-strand	238-239	2	43
β-strand	243-246	4	43

Chain I: 5 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	45
α-helix	7-9	3
β-strand	10-12	3	46
β-strand	19-25	7	45
β-strand	33-39	7	46
β-strand	45-51	7	46
β-strand	58-60	3	46
α-helix	62-64	3
β-strand	69-73	5	45
β-strand	78-82	5	45
α-helix	88-90	3
β-strand	92-99	8	46
β-strand	110	1	46
β-strand	114-118	5	46
β-strand	141-144	4	47
β-strand	147-150	4	48
β-strand	156-162	7	47
β-strand	167-168	2	49
β-strand	171-172	2	49
β-strand	174-179	6	48
β-strand	186-191	5	48
β-strand	195-196	2	48
β-strand	204-209	6	47
β-strand	212-217	6	47
α-helix	222-224	3
β-strand	227-232	6	48
α-helix	238	1
β-strand	239-240	2	48
β-strand	244-248	5	48

Chain K: 5 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	50
α-helix	7-9	3
β-strand	10-12	3	51
β-strand	19-25	7	50
β-strand	33-39	7	51
β-strand	46-52	7	51
β-strand	57-60	4	51
α-helix	62-64	3
β-strand	69-73	5	50
β-strand	78-82	5	50
α-helix	88-90	3
β-strand	92-99	8	51
β-strand	110	1	51
β-strand	114-118	5	51
β-strand	141-144	4	52
β-strand	147-150	4	53
β-strand	156-162	7	52
β-strand	167-168	2	54
β-strand	171-172	2	54
β-strand	174-179	6	53
β-strand	186-190	5	53
β-strand	194-195	2	53
β-strand	203-208	6	52
β-strand	211-216	6	52
α-helix	221-223	3
β-strand	225-231	7	53
α-helix	237	1
β-strand	238-239	2	53
β-strand	243-247	5	53

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Non-structural protein 1	A, B, C, D	protein	376	Dengue virus 2	P29990
2B7 single chain fab variable region	E, G, I, K	protein	251	Mus musculus

Sequence of entity 1 (A, B, C, D), FASTA

>7K93_1 Non-structural protein 1 (chains A, B, C, D)
AHHHHHHSSGVDLGTENLYFQSNADSGCVVSWKNKELKCGSGIFITDNVHTWTEQYKFQP
ESPSKLASAIQKAHEEGICGIRSVTRLENLMWKQITPELNHILSENEVKLTIMTGDIKGI
MQAGKRSLRPQPTELKYSWKTWGKAKMLSTESHNQTFLIDGPETAECPNTNRAWNSLEVE
DYGFGVFTTNIWLKLKEKQDVFCDSKLMSAAIKDNRAVHADMGYWIESALNDTWKIEKAS
FIEVKNCHWPKSHTLWSNGVLESEMIIPKNLAGPVSQHNYRPGYHTQITGPWHLGKLEMD
FDFCDGTTVVVTEDCGNRGPSLRTTTASGKLITEWCCRSCTLPPLRYRGEDGCWYGMEIR
PLKEKEENLVNSLVTA

Sequence of entity 2 (E, G, I, K), FASTA

>7K93_2 2B7 single chain fab variable region (chains E, G, I, K)
SNAEVQLQQSGPELVKPGASVKMSCKASGCTLTNCFMHWMKQKPGQDLEWIGYINPYNDM
TKYSENFKGKATLTSDKSSSTAFMELSSLTSEDSAVYYCARGYLLRTGCFDYWGQGTTLT
VSSGGSGGGSGGGSGGGSGGNIVLTQSPASLAVSLGQRATISCRASESVDSYGYSFMHWY
QQKPGQPPKVLIYLASNLESGVPARFSGSGSRTDFTLTIDPVEADDAATYYCQQNNENPL
TFGAGTKLELK

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4

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:

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…
6WER 3.96 Å, DENV2 NS1 in complex with neutralizing 2B7 Fab fragment
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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