4GSX: Dengue virus serotype 1 sE containing stem

High resolution structure of dengue virus serotype 1 sE containing stem. Determined by X-ray diffraction at 1.9 Å resolution. Released 19 Dec 2012.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Dengue virus 1
Chains: 2
Atoms: 6,673
Mol. weight: 94.52 kDa
Ligands: NAG, CD
Released: 19 Dec 2012

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

Secondary structure: helices and β-sheets

4GSX contains 35 α-helices and 74 β-strands across 2 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: 19 helices, 36 β-strands

Element	Residues	Length	Sheet
α-helix	3	1
β-strand	4-5	2	1
α-helix	6-7	2
α-helix	8-10	3
β-strand	11-13	3	2
β-strand	18-26	9	2
β-strand	31-33	3	1
β-strand	35	1	3
β-strand	41-51	11	1
α-helix	53	1
β-strand	54-72	19	4
α-helix	83-86	4
β-strand	90-99	10	4
α-helix	101-103	3
β-strand	109-129	21	4
α-helix	132-134	3
β-strand	135-143	9	1
β-strand	160-164	5	1
β-strand	170-175	6	2
β-strand	179-187	9	2
α-helix	188	1
β-strand	196-201	6	4
β-strand	204-209	6	4
α-helix	210-214	5
β-strand	220-222	3	4
β-strand	232	1	4
α-helix	234-236	3
β-strand	238-240	3	5
β-strand	250-252	3	5
α-helix	257-263	7
β-strand	268-270	3	4
β-strand	271-273	3	1
β-strand	276-279	4	1
β-strand	282-290	9	2
β-strand	294	1	3
α-helix	300	1
β-strand	301	1	6
α-helix	302	1
β-strand	306-308	3	7
α-helix	311-312	2
β-strand	313-314	2	7
β-strand	320-326	7	7
β-strand	333-334	2	6
α-helix	335-336	2
β-strand	337-341	5	8
β-strand	346	1	8
β-strand	351	1	7
β-strand	357-358	2	6
β-strand	365-369	5	7
α-helix	371-372	2
β-strand	374-380	7	8
α-helix	383-385	3
β-strand	387-393	7	8
α-helix	394-396	3
α-helix	400-402	3

Chain B: 16 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	9
α-helix	6-7	2
α-helix	8-10	3
β-strand	11-13	3	10
β-strand	18-26	9	10
β-strand	30-34	5	9
β-strand	35	1	11
β-strand	40-51	12	9
α-helix	53	1
β-strand	54-72	19	12
α-helix	83-85	3
β-strand	90-98	9	12
β-strand	110-129	20	12
α-helix	132-134	3
β-strand	135-143	9	9
β-strand	160-164	5	9
β-strand	170-175	6	10
β-strand	179-187	9	10
α-helix	188	1
β-strand	196-201	6	12
β-strand	204-209	6	12
α-helix	210-214	5
β-strand	220-222	3	12
β-strand	232	1	12
α-helix	234-236	3
β-strand	238-240	3	13
β-strand	244	1	14
β-strand	247	1	14
β-strand	250-252	3	13
α-helix	257-264	8
α-helix	268	1
β-strand	269-270	2	12
β-strand	272-273	2	9
β-strand	276-279	4	9
β-strand	282-290	9	10
β-strand	294	1	11
α-helix	300	1
β-strand	301	1	15
α-helix	302	1
β-strand	306-308	3	16
β-strand	313-314	2	16
β-strand	320-326	7	16
β-strand	333-334	2	15
α-helix	335-336	2
β-strand	337-341	5	17
β-strand	346	1	17
β-strand	351	1	16
β-strand	357-358	2	15
β-strand	365-369	5	16
α-helix	371-372	2
β-strand	374-380	7	17
β-strand	387-393	7	17
α-helix	394-396	3
α-helix	400-402	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Envelope protein E	A, B	protein	427	Dengue virus 1	P17763 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4GSX_1 Envelope protein E (chains A, B)
GHHHHHHHHGSSTSNGMRCVGIGNRDFVEGLSGATWVDVVLEHGSCVTTMAKDKPTLDIE
LLKTEVTNPAVLRKLCIEAKISNTTTDSRCPTQGEATLVEEQDTNFVCRRTFVDRGHGNG
CGLFGKGSLITCAKFKCVTKLEGKIVQYENLKYSVIVTVHTGDQHQVGNETTEHGTIATI
TPQAPTSEIQLTDYGALTLDCSPRTGLDFNEMVLLTMEKKSWLVHKQWFLDLPLPWTSGA
STSQETWNRQDLLVTFKTAHAKKQEVVVLGSQEGAMHTALTGATEIQTSGTTTIFAGHLK
CRLKMDKLTLKGMSYVMCTGSFKLEKEVAETQHGTVLVQVKYEGTDAPCKIPFSSQDEKG
VTQNGRLITANPIVTDKEKPVNIEAEPPFGESYIVVGAGEKALKLSWFKKGSSIGKMFEA
TARGARR

Ligands and cofactors

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

Water and common crystallization additives (CL) are not listed.

Primary citation

Structure of a dengue virus envelope protein late-stage fusion intermediate. Klein, D.E., Choi, J.L., Harrison, S.C. J Virol (2013) 87:2287-2293. DOI 10.1128/JVI.02957-12 · 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
4AL8 1.66 Å, Structure of Dengue virus DIII in complex with Fab 2H12
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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