3J2P: Dengue virus envelope protein heterotetramer

CryoEM structure of Dengue virus envelope protein heterotetramer. 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: 4
Atoms: 8,804
Mol. weight: 126.54 kDa
Ligands: NAG
Released: 19 Dec 2012

Explore 3J2P in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3J2P contains 30 α-helices and 64 β-strands across 4 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: 12 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	11-13	3	1
β-strand	20-25	6	2
β-strand	31-34	4	1
β-strand	41-48	8	1
β-strand	54	1	3
β-strand	60	1	4
β-strand	63-72	10	5
α-helix	83-86	4
β-strand	92-97	6	5
α-helix	101-104	4
β-strand	111-121	11	5
β-strand	124	1	4
β-strand	129	1	3
β-strand	137-142	6	1
β-strand	162-164	3	1
β-strand	170-175	6	2
β-strand	179-185	7	2
β-strand	196-199	4	6
β-strand	206-209	4	6
α-helix	210-213	4
β-strand	220	1	7
β-strand	232	1	7
β-strand	239-241	3	8
β-strand	249-251	3	8
α-helix	257-263	7
β-strand	268	1	6
β-strand	283-288	6	2
β-strand	292	1	2
β-strand	305-308	4	9
β-strand	320-323	4	10
β-strand	324-327	4	9
β-strand	337-340	4	11
β-strand	351	1	10
β-strand	366-369	4	10
β-strand	377-380	4	11
β-strand	388-390	3	11
α-helix	397-415	19
α-helix	417-422	6
α-helix	429-442	14
α-helix	444-446	3
α-helix	453-468	16
α-helix	474-481	8
α-helix	482-486	5
α-helix	487-492	6

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

Element	Residues	Length
α-helix	23-38	16
α-helix	40-52	13
α-helix	58-70	13

Chain C: 12 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	11-13	3	12
β-strand	20-25	6	13
β-strand	31-34	4	12
β-strand	41-48	8	12
β-strand	54	1	14
β-strand	60	1	15
β-strand	63-72	10	16
α-helix	83-86	4
β-strand	92-97	6	16
α-helix	101-104	4
β-strand	111-121	11	16
β-strand	124	1	15
β-strand	129	1	14
β-strand	137-142	6	12
β-strand	162-164	3	12
β-strand	170-175	6	13
β-strand	179-185	7	13
β-strand	196-200	5	17
β-strand	205-209	5	17
α-helix	210-213	4
β-strand	220	1	18
β-strand	232	1	18
β-strand	239-241	3	19
β-strand	249-251	3	19
α-helix	257-263	7
β-strand	268	1	17
β-strand	283-288	6	13
β-strand	292	1	13
β-strand	305-308	4	20
β-strand	320-323	4	21
β-strand	324-327	4	20
β-strand	337-340	4	22
β-strand	351	1	21
β-strand	366-369	4	21
β-strand	377-380	4	22
β-strand	388-390	3	22
α-helix	397-415	19
α-helix	417-422	6
α-helix	429-442	14
α-helix	444-446	3
α-helix	453-468	16
α-helix	474-481	8
α-helix	482-486	5
α-helix	487-492	6

Molecules and chains

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

Sequence of entity 1 (A, C), FASTA

>3J2P_1 Envelope protein E (chains A, C)
MRCIGISNRDFVEGVSGGSWVDIVLEHGSCVTTMAKNKPTLDFELIETEAKQPATLRKYC
IEAKLTNTTTDSRCPTQGEPSLNEEQDKRFVCKHSMVDRGWGNGCGLFGKGGIVTCAMFT
CKKNMKGKVVQPENLEYTIVITPHSGEEHAVGNDTGKHGKEIKITPQSSITEAELTGYGT
VTMECSPRTGLDFNEMVLLQMENKAWLVHRQWFLDLPLPWLPGADTQGSNWIQKETLVTF
KNPHAKKQDVVVLGSQEGAMHTALTGATEIQMSSGNLLFTGHLKCRLRMDKLQLKGMSYS
MCTGKFKVVKEIAETQHGTIVIRVQYEGDGSPCKIPFEIMDLEKRHVLGRLITVNPIVTE
KDSPVNIEAEPPFGDSYIIIGVEPGQLKLNWFKKGSSIGQMIETTMRGAKRMAILGDTAW
DFGSLGGVFTSIGKALHQVFGAIYGAAFSGVSWIMKILIGVIITWIGMNSRSTSLSVSLV
LVGVVTLYLGVMVQA

Sequence of entity 2 (B, D), FASTA

>3J2P_2 Small envelope protein M (chains B, D)
SVALVPHVGMGLETATETWMSSEGAWKHAQRIETWILRHPGFTIMAAILAYTIGTTHFQR
ALIFILLTAVAPSMT

Ligands and cofactors

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

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…
3J27 3.6 Å, CryoEM structure of Dengue virus
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

Browse structure collections

About this viewer

MolViewer shows 3J2P 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.