6ZQU: Mature Dengue virus 2

Name: PDB 6ZQU: Cryo-EM structure of mature Dengue virus 2 at 3.1 angstrom resolution
Published: 2021-01-20
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: virus

Cryo-EM structure of mature Dengue virus 2 at 3.1 angstrom resolution. Determined by electron microscopy at 3.1 Å resolution. Released 20 Jan 2021.

Method: Electron microscopy
Resolution: 3.1 Å
Organism: Dengue virus 2
Chains: 6
Atoms: 13,203
Mol. weight: 190.1 kDa
Ligands: NAG
Released: 20 Jan 2021

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

Secondary structure: helices and β-sheets

6ZQU contains 53 α-helices and 115 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: 15 helices, 39 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4
β-strand	9-12	4	1
β-strand	16	1	2
β-strand	20-26	7	2
β-strand	30-33	4	1
β-strand	41-50	10	1
α-helix	53	1
β-strand	54-72	19	3
β-strand	87	1	4
β-strand	90-99	10	3
α-helix	101-103	3
β-strand	109-129	21	3
α-helix	132-134	3
β-strand	135-143	9	1
β-strand	160-164	5	1
β-strand	165	1	5
β-strand	168	1	5
β-strand	172-174	3	2
β-strand	179	1	6
β-strand	180-186	7	2
α-helix	193-195	3
β-strand	196-201	6	3
β-strand	204-209	6	3
α-helix	210-214	5
β-strand	220-222	3	3
β-strand	232	1	3
α-helix	234-236	3
β-strand	238-241	4	7
α-helix	243-245	3
β-strand	249-252	4	7
α-helix	257-263	7
β-strand	268-270	3	3
β-strand	271-272	2	1
β-strand	276-278	3	1
β-strand	282-288	7	2
β-strand	292	1	6
β-strand	301	1	8
β-strand	306-314	9	9
β-strand	320-326	7	9
β-strand	333-334	2	8
β-strand	338-340	3	10
β-strand	347	1	10
β-strand	350-351	2	9
β-strand	357-358	2	8
β-strand	365-370	6	9
α-helix	371-372	2
β-strand	374-379	6	10
β-strand	388-393	6	10
α-helix	397-415	19
α-helix	416-421	6
β-strand	424	1	2
α-helix	428-447	20
α-helix	453-469	17
α-helix	476-491	16

Chains B and F: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	118-129	12
α-helix	131-145	15
α-helix	150-161	12

Chain C: 15 helices, 39 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3
β-strand	9-12	4	11
β-strand	16	1	12
β-strand	20-26	7	12
β-strand	30-33	4	11
β-strand	41-50	10	11
β-strand	54-72	19	13
β-strand	90-99	10	13
α-helix	101-103	3
β-strand	109-129	21	13
α-helix	132-134	3
β-strand	135-141	7	11
β-strand	147	1	14
β-strand	160-164	5	11
β-strand	165	1	15
β-strand	168	1	15
β-strand	170-174	5	12
β-strand	179	1	16
β-strand	180-184	5	12
α-helix	193-195	3
β-strand	196-201	6	13
β-strand	204-209	6	13
α-helix	210-214	5
β-strand	220-222	3	13
β-strand	232	1	13
α-helix	234-236	3
β-strand	238-241	4	17
α-helix	243-245	3
β-strand	249-252	4	17
α-helix	257-262	6
α-helix	267	1
β-strand	268-270	3	13
β-strand	271-272	2	11
β-strand	276-278	3	11
β-strand	282-288	7	12
β-strand	292	1	16
β-strand	301	1	18
β-strand	306-314	9	14
β-strand	320-326	7	14
β-strand	333-334	2	18
β-strand	338-340	3	19
β-strand	347	1	19
β-strand	350-351	2	14
β-strand	357-358	2	18
β-strand	365-370	6	14
α-helix	371-372	2
β-strand	374-379	6	19
β-strand	388-393	6	19
α-helix	397-415	19
α-helix	416-421	6
β-strand	424	1	12
α-helix	428-447	20
α-helix	453-469	17
α-helix	476-491	16

Chain D: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	108-109	2
α-helix	118-129	12
α-helix	131-145	15
α-helix	150-161	12

Chain E: 13 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	9-12	4	20
β-strand	16	1	21
β-strand	20-26	7	21
β-strand	30-33	4	20
β-strand	41-50	10	20
β-strand	54-72	19	22
β-strand	87	1	4
β-strand	90-99	10	22
α-helix	101-103	3
β-strand	109-129	21	22
α-helix	132-134	3
β-strand	137-141	5	20
β-strand	160-164	5	20
β-strand	165	1	23
β-strand	168	1	23
β-strand	172-174	3	21
β-strand	179	1	24
β-strand	180-184	5	21
α-helix	193-195	3
β-strand	196-201	6	22
β-strand	204-209	6	22
α-helix	210-214	5
β-strand	220-222	3	22
β-strand	232	1	22
α-helix	234-236	3
β-strand	238-241	4	25
α-helix	243-245	3
β-strand	249-252	4	25
α-helix	257-263	7
β-strand	268-270	3	22
β-strand	271-272	2	20
β-strand	276-278	3	20
β-strand	282-288	7	21
β-strand	292	1	24
β-strand	306-314	9	26
β-strand	320-326	7	26
β-strand	334	1	27
β-strand	338-340	3	28
β-strand	350-351	2	26
β-strand	357	1	27
β-strand	365-370	6	26
α-helix	371-372	2
β-strand	374-379	6	28
β-strand	388-393	6	28
α-helix	397-415	19
α-helix	416-421	6
β-strand	424	1	21
α-helix	428-447	20
α-helix	453-469	17
α-helix	476-491	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Genome polyprotein	A, C, E	protein	495	Dengue virus 2	P29990
Genome polyprotein	B, D, F	protein	75	Dengue virus 2	O11875

Sequence of entity 1 (A, C, E), FASTA

>6ZQU_1 Genome polyprotein (chains A, C, E)
MRCIGMSNRDFVEGVSGGSWVDIVLEHGSCVTTMAKNKPTLDFELIKTEAKQPATLRKYC
IEAKLTNTTTESRCPTQGEPSLNEEQDKRFVCKHSMVDRGWGNGCGLFGKGGIVTCAMFR
CKKNMEGKVVQPENLEYTIVITPHSGEEHAVGNDTGKHGKEIKITPQSSITEAELTGYGT
VTMECSPRTGLDFNEMVLLQMENKAWLVHRQWFLDLPLPWLPGADTQGSNWIQKETLVTF
KNPHAKKQDVVVLGSQEGAMHTALTGATEIQMSSGNLLFTGHLKCRLRMDKLQLKGMSYS
MCTGKFKVVKEIAETQHGTIVIRVQYEGDGSPCKIPFEIMDLEKRHVLGRLITVNPIVTE
KDSPVNIEAEPPFGDSYIIIGVEPGQLKLNWFKKGSSIGQMFETTMRGAKRMAILGDTAW
DFGSLGGVFTSIGKALHQVFGAIYGAAFSGVSWTMKILIGVIITWIGMNSRSTSLSVTLV
LVGIVTLYLGVMVQA

Sequence of entity 2 (B, D, F), FASTA

>6ZQU_2 Genome polyprotein (chains B, D, F)
SVALVPHVGMGLETRTETWMSSEGAWKHVQRIETWILRHPGFTMMAAILAYTIGTTHFQR
ALIFILLTAVTPSMT

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	6

Primary citation

Flavivirus maturation leads to the formation of an occupied lipid pocket in the surface glycoproteins. Renner, M., Dejnirattisai, W., Carrique, L. et al. Nat Commun (2021) 12:1238-1238. DOI 10.1038/s41467-021-21505-9 · 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
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

Browse structure collections

About this viewer

MolViewer shows 6ZQU directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.