6EPK: Envelope protein E

Crystal structure of the precursor membrane protein-envelope protein heterodimer from the yellow fever virus. Determined by X-ray diffraction at 2.7 Å resolution. Released 31 Oct 2018.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: Yellow fever virus
Chains: 4
Atoms: 8,103
Mol. weight: 119.57 kDa
Released: 31 Oct 2018

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

Secondary structure: helices and β-sheets

6EPK contains 33 α-helices and 93 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: 15 helices, 39 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4
β-strand	9-13	5	1
β-strand	14	1	2
α-helix	15	1
β-strand	16	1	3
β-strand	18	1	3
β-strand	20-26	7	4
β-strand	27	1	1
β-strand	30-35	6	1
β-strand	38-51	14	1
α-helix	53-54	2
β-strand	55-73	19	5
α-helix	83-86	4
β-strand	90-99	10	5
β-strand	109-129	21	5
β-strand	135-143	9	1
α-helix	149-151	3
α-helix	152-155	4
β-strand	157-162	6	1
β-strand	168-172	5	4
β-strand	176-185	10	4
β-strand	193-198	6	5
β-strand	201-206	6	5
α-helix	207-211	5
β-strand	217-218	2	5
β-strand	225-226	2	5
α-helix	228-231	4
β-strand	232-234	3	6
α-helix	235-237	3
β-strand	244-246	3	6
α-helix	247-249	3
α-helix	251-258	8
β-strand	262-264	3	5
β-strand	265-266	2	1
β-strand	273-275	3	1
α-helix	276	1
β-strand	280-286	7	4
β-strand	290	1	4
α-helix	297-298	2
β-strand	299	1	7
α-helix	300	1
β-strand	305-312	8	8
β-strand	318-324	7	8
β-strand	330-331	2	7
β-strand	334-337	4	9
β-strand	348-349	2	8
β-strand	355-356	2	7
β-strand	361-368	8	8
α-helix	369-370	2
β-strand	372-378	7	9
β-strand	385-391	7	9
β-strand	398-400	3	1
β-strand	404	1	2
β-strand	406	1	4

Chain B: 1 helix, 8 β-strands

Element	Residues	Length	Sheet
β-strand	502-506	5	5
β-strand	509-513	5	5
α-helix	516-518	3
β-strand	522-525	4	10
β-strand	528-532	5	10
β-strand	539-548	10	5
β-strand	551-552	2	10
β-strand	563-566	4	10
β-strand	571-578	8	5

Chain D: 16 helices, 38 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4
β-strand	9-13	5	11
β-strand	14	1	12
α-helix	15	1
β-strand	16	1	13
β-strand	18	1	13
β-strand	20-26	7	14
β-strand	27	1	11
β-strand	30-35	6	11
β-strand	38-51	14	11
α-helix	53-54	2
β-strand	55-73	19	15
α-helix	83-85	3
β-strand	90-99	10	15
β-strand	109-129	21	15
β-strand	135-143	9	11
α-helix	149-151	3
α-helix	152-155	4
β-strand	157-162	6	11
β-strand	168-172	5	14
β-strand	176-185	10	14
β-strand	193-198	6	15
β-strand	201-206	6	15
α-helix	207-211	5
β-strand	217-218	2	15
α-helix	224-225	2
β-strand	226	1	15
α-helix	228-230	3
β-strand	232-234	3	16
α-helix	235-237	3
β-strand	244-246	3	16
α-helix	247-249	3
α-helix	251-259	9
β-strand	262-264	3	15
β-strand	265-266	2	11
β-strand	273-275	3	11
α-helix	276-277	2
β-strand	280-286	7	14
β-strand	290	1	14
α-helix	297-298	2
β-strand	299	1	17
α-helix	300	1
β-strand	305-312	8	18
β-strand	318-324	7	18
β-strand	330-331	2	17
β-strand	334-337	4	19
β-strand	348-349	2	18
β-strand	355-356	2	17
β-strand	361-368	8	18
α-helix	369-370	2
β-strand	372-378	7	19
β-strand	385-391	7	19
β-strand	398-400	3	11
β-strand	404	1	12

Chain E: 1 helix, 8 β-strands

Element	Residues	Length	Sheet
β-strand	502-506	5	15
β-strand	509-513	5	15
α-helix	516-518	3
β-strand	522-525	4	20
β-strand	528-532	5	20
β-strand	539-549	11	15
β-strand	551-552	2	20
β-strand	563-566	4	20
β-strand	571-578	8	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Envelope protein E	A, D	protein	427	Yellow fever virus	Q6DV88
Precursor Membrane Protein	B, E	protein	89	Yellow fever virus	P03314 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>6EPK_1 Envelope protein E (chains A, D)
AHCIGITDRDFIEGVHGGTWVSATLEQDKCVTVMAPDKPSLDISLETVAIDGPAEARKVC
YNAVLTHVKINDKCPSTGEAHLAEENEGDNACKRTYSDRGWGNGCGLFGKGSIVACAKFT
CAKSMSLFEVDQTKIQYVIRAQLHVGAKQENWNTDIKTLKFDALSGSQEAEFTGYGKATL
ECQVQTAVDFGNSYIAEMEKESWIVDRQWAQDLTLPWQSGSGGVWREMHHLVEFEPPHAA
TIRVLALGNQEGSLKTALTGAMRVTKDTNDNNLYKLHGGHVSCRVKLSALTLKGTSYKMC
TDKMSFVKNPTDTGHGTVVMQVKVPKGAPCKIPVIVADDLTAAINKGILVTVNPIASTND
DEVLIEVNPPFGDSYIIVGTGDSRLTYQWHKEDDDDKAGWSHPQFEKGGGSGGGSGGGSW
SHPQFEK

Sequence of entity 2 (B, E), FASTA

>6EPK_2 Precursor Membrane Protein (chains B, E)
VTLVRKNRWLLLNVTSEDLGKTFSVGTGNCTTNILEAKYWCPDSMEYNCPNLSPREEPDD
IDCWCYGVENVRVAYGKCDSAGRSRRSRR

Primary citation

New insight into flavivirus maturation from structure/function studies of the yellow fever virus envelope protein complex. Crampon, E., Covernton, E., Vaney, M.C. et al. mBio (2023). DOI 10.1128/mbio.00706-23

Other PDB entries of the same protein (UniProt Q6DV88), best resolution first:

8OFN 3.48 Å, Structure of the yellow fever virus (Asibi strain) dimeric envelope protein
2JQM Yellow Fever Envelope Protein Domain III NMR Structure (S288-K398)
2JV6 YF ED3 Protein NMR Structure

Browse structure collections

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