3J27: Dengue virus

Name: PDB 3J27: CryoEM structure of Dengue virus
Published: 2012-12-19
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: virus

CryoEM structure of Dengue virus. Determined by electron microscopy at 3.6 Å resolution. Released 19 Dec 2012.

Method: Electron microscopy
Resolution: 3.6 Å
Organism: Dengue virus 2
Chains: 6
Atoms: 13,206
Mol. weight: 189.81 kDa
Ligands: NAG
Released: 19 Dec 2012

Explore 3J27 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3J27 contains 49 α-helices and 109 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, 36 β-strands

Element	Residues	Length	Sheet
β-strand	11-13	3	1
β-strand	20-24	5	2
β-strand	30-34	5	1
β-strand	41-48	8	1
β-strand	53-54	2	3
β-strand	59	1	4
β-strand	60-72	13	5
α-helix	83-86	4
β-strand	87	1	6
β-strand	92-97	6	5
α-helix	101-103	3
β-strand	111-124	14	5
β-strand	129-130	2	3
β-strand	137-143	7	1
β-strand	162-164	3	1
β-strand	170-175	6	2
β-strand	179-185	7	2
β-strand	196	1	7
β-strand	199-200	2	8
β-strand	205-206	2	8
β-strand	209	1	7
α-helix	210-213	4
β-strand	220	1	4
β-strand	232	1	4
β-strand	239-241	3	9
β-strand	249-251	3	9
α-helix	257-264	8
α-helix	268	1
β-strand	269	1	8
β-strand	284-288	5	2
β-strand	305-308	4	10
β-strand	320	1	11
β-strand	324-327	4	10
β-strand	333	1	12
β-strand	338-340	3	13
β-strand	351	1	11
β-strand	358	1	12
β-strand	369	1	11
β-strand	377-379	3	13
β-strand	388-390	3	13
α-helix	397-412	16
α-helix	417-422	6
α-helix	429-442	14
α-helix	444-446	3
β-strand	450	1	14
α-helix	453-468	16
α-helix	475-481	7
α-helix	482-486	5
α-helix	487-492	6

Chain B: 3 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	9	1	14
α-helix	23-38	16
α-helix	42-52	11
α-helix	58-70	13

Chain C: 15 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	10-13	4	15
α-helix	16-19	4
β-strand	20-25	6	16
β-strand	31-34	4	15
β-strand	41-50	10	15
β-strand	54	1	17
β-strand	59	1	18
β-strand	60-75	16	19
α-helix	83-86	4
β-strand	87	1	6
β-strand	90-97	8	19
α-helix	101-103	3
β-strand	111-124	14	19
β-strand	127-128	2	20
β-strand	129	1	17
α-helix	132-134	3
β-strand	135-142	8	15
β-strand	161-164	4	15
β-strand	171-175	5	16
β-strand	179-185	7	16
β-strand	196-202	7	20
β-strand	204-209	6	20
α-helix	210-213	4
β-strand	220	1	18
β-strand	232	1	18
α-helix	234-236	3
β-strand	239-241	3	21
β-strand	249-251	3	21
α-helix	257-264	8
β-strand	268-269	2	20
β-strand	283-288	6	16
β-strand	306-307	2	22
β-strand	320-324	5	23
β-strand	325-326	2	22
β-strand	334	1	24
β-strand	337-340	4	25
β-strand	350-351	2	23
β-strand	357	1	24
β-strand	365-370	6	23
β-strand	374	1	26
β-strand	377-380	4	25
β-strand	388-390	3	25
β-strand	393	1	26
α-helix	398-413	16
α-helix	417-422	6
α-helix	429-442	14
α-helix	453-457	5
α-helix	458-466	9
α-helix	475-481	7
α-helix	482-486	5
α-helix	487-492	6

Chain D: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	22-38	17
α-helix	40-52	13
α-helix	58-70	13

Chain E: 12 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	10-13	4	27
β-strand	20-25	6	28
β-strand	31-34	4	27
β-strand	41-50	10	27
β-strand	54-55	2	29
β-strand	60	1	30
β-strand	64-72	9	31
α-helix	83-86	4
β-strand	90-97	8	31
β-strand	111-120	10	31
β-strand	124	1	30
β-strand	128-129	2	29
β-strand	135-143	9	27
β-strand	162	1	27
β-strand	171-175	5	28
β-strand	179-185	7	28
α-helix	187-189	3
β-strand	196-200	5	29
β-strand	205-209	5	29
α-helix	210-213	4
β-strand	220	1	32
β-strand	232	1	32
β-strand	239-241	3	33
β-strand	249-251	3	33
α-helix	257-261	5
β-strand	283-288	6	28
β-strand	292	1	28
β-strand	306-310	5	34
β-strand	314	1	35
β-strand	320	1	35
β-strand	323-326	4	34
β-strand	334	1	36
β-strand	338-340	3	37
β-strand	351	1	35
β-strand	357	1	36
β-strand	366	1	34
β-strand	369	1	35
β-strand	375-379	5	37
β-strand	388-392	5	37
α-helix	398-412	15
α-helix	420-422	3
α-helix	428-437	10
α-helix	439-443	5
α-helix	453-468	16
α-helix	475-481	7
α-helix	482-487	6
α-helix	488-492	5

Chain F: 3 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	23-38	16
α-helix	40-52	13
β-strand	56	1	38
α-helix	58-70	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Envelope protein E	A, C, E	protein	495	Dengue virus 2	P14340
Small envelope protein M	B, D, F	protein	75	Dengue virus 2	P14340

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

>3J27_1 Envelope protein E (chains A, C, E)
MRCIGISNRDFVEGVSGGSWVDIVLEHGSCVTTMAKNKPTLDFELIETEAKQPATLRKYC
IEAKLTNTTTDSRCPTQGEPSLNEEQDKRFVCKHSMVDRGWGNGCGLFGKGGIVTCAMFT
CKKNMKGKVVQPENLEYTIVITPHSGEEHAVGNDTGKHGKEIKITPQSSITEAELTGYGT
VTMECSPRTGLDFNEMVLLQMENKAWLVHRQWFLDLPLPWLPGADTQGSNWIQKETLVTF
KNPHAKKQDVVVLGSQEGAMHTALTGATEIQMSSGNLLFTGHLKCRLRMDKLQLKGMSYS
MCTGKFKVVKEIAETQHGTIVIRVQYEGDGSPCKIPFEIMDLEKRHVLGRLITVNPIVTE
KDSPVNIEAEPPFGDSYIIIGVEPGQLKLNWFKKGSSIGQMIETTMRGAKRMAILGDTAW
DFGSLGGVFTSIGKALHQVFGAIYGAAFSGVSWIMKILIGVIITWIGMNSRSTSLSVSLV
LVGVVTLYLGVMVQA

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

>3J27_2 Small envelope protein M (chains B, D, F)
SVALVPHVGMGLETATETWMSSEGAWKHAQRIETWILRHPGFTIMAAILAYTIGTTHFQR
ALIFILLTAVAPSMT

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3

Primary citation

Cryo-EM structure of the mature dengue virus at 3.5-A resolution. Zhang, X., Ge, P., Yu, X. et al. Nat Struct Mol Biol (2012) 20:105-110. DOI 10.1038/nsmb.2463 · PubMed

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

6FLC 2.0 Å, 2C8 Fab bound to EDIII of DenV 2
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…
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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