6IW1: YFV-17D sE in postfusion state

Crystal structure of YFV-17D sE in postfusion state. Determined by X-ray diffraction at 3.1 Å resolution. Released 13 Feb 2019.

Method: X-ray diffraction
Resolution: 3.1 Å
Organism: Yellow fever virus (strain 17D vaccine)
Chains: 3
Atoms: 8,698
Mol. weight: 129.7 kDa
Released: 13 Feb 2019

Explore 6IW1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6IW1 contains 40 α-helices and 115 β-strands across 3 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, 39 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	1
α-helix	6	1
β-strand	7	1	2
β-strand	11-13	3	3
β-strand	17	1	4
β-strand	18-26	9	3
β-strand	30-33	4	1
β-strand	34	1	5
β-strand	35	1	1
β-strand	38-51	14	1
β-strand	54-72	19	6
α-helix	83-85	3
β-strand	90-99	10	6
α-helix	101-103	3
β-strand	109-129	21	6
α-helix	132-134	3
β-strand	136-143	8	1
β-strand	156-162	7	1
β-strand	167-172	6	3
β-strand	176-184	9	3
β-strand	193-198	6	6
β-strand	201-206	6	6
α-helix	207-211	5
β-strand	217-219	3	6
β-strand	226	1	6
α-helix	228-230	3
β-strand	232-234	3	7
α-helix	235-237	3
β-strand	244-246	3	7
α-helix	247-249	3
α-helix	251-257	7
β-strand	263	1	6
β-strand	265	1	1
β-strand	273-275	3	1
β-strand	280-288	9	3
β-strand	293	1	5
β-strand	295	1	2
β-strand	298-299	2	8
α-helix	300	1
β-strand	304-312	9	9
β-strand	318-324	7	9
β-strand	330-331	2	8
α-helix	332-333	2
β-strand	334-337	4	10
β-strand	345	1	10
β-strand	348-349	2	9
β-strand	355-356	2	8
β-strand	363-368	6	9
α-helix	369-370	2
β-strand	372-378	7	10
α-helix	381-383	3
β-strand	385-391	7	10

Chain B: 13 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	11
β-strand	11-13	3	12
β-strand	16-17	2	3
β-strand	19-26	8	12
β-strand	27	1	11
β-strand	30-33	4	11
β-strand	34	1	13
β-strand	35	1	11
β-strand	38-51	14	11
β-strand	54-72	19	14
α-helix	83-85	3
β-strand	90-99	10	14
α-helix	101-103	3
β-strand	109-129	21	14
α-helix	132-134	3
β-strand	136-143	8	11
β-strand	156-162	7	11
β-strand	167-172	6	12
β-strand	176-184	9	12
β-strand	193-198	6	14
β-strand	201-206	6	14
α-helix	207-211	5
β-strand	217-219	3	14
β-strand	226	1	14
α-helix	228-230	3
β-strand	232-234	3	15
α-helix	235-237	3
β-strand	244-246	3	15
α-helix	247-249	3
α-helix	251-257	7
α-helix	258-260	3
β-strand	262-263	2	14
β-strand	265-266	2	11
β-strand	273-275	3	11
β-strand	280-287	8	12
β-strand	293	1	13
β-strand	298-299	2	16
α-helix	300	1
β-strand	304-312	9	17
β-strand	318-324	7	17
β-strand	330-331	2	16
α-helix	332-333	2
β-strand	334-337	4	18
β-strand	348-349	2	17
β-strand	355-356	2	16
β-strand	361-368	8	17
α-helix	369-370	2
β-strand	372-378	7	18
α-helix	381-383	3
β-strand	385-391	7	18

Chain C: 14 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	19
α-helix	6	1
β-strand	7	1	20
β-strand	11-13	3	4
β-strand	16-17	2	12
β-strand	19-26	8	4
β-strand	27	1	19
β-strand	30-33	4	19
β-strand	34	1	21
β-strand	41-51	11	19
β-strand	54-72	19	22
α-helix	83-85	3
β-strand	90-99	10	22
α-helix	101-103	3
β-strand	109-129	21	22
α-helix	132-134	3
β-strand	136-143	8	19
β-strand	156-162	7	19
β-strand	167-172	6	4
β-strand	176-185	10	4
β-strand	193-198	6	22
β-strand	201-206	6	22
α-helix	207-211	5
β-strand	217-219	3	22
β-strand	226	1	22
α-helix	228-230	3
β-strand	232-234	3	23
α-helix	235-237	3
β-strand	244-246	3	23
α-helix	247-249	3
α-helix	251-257	7
α-helix	258-260	3
β-strand	262-264	3	22
β-strand	265	1	19
β-strand	273-275	3	19
β-strand	280-287	8	4
β-strand	293	1	21
β-strand	295	1	20
β-strand	298-299	2	24
α-helix	300	1
β-strand	302-312	11	25
β-strand	318-326	9	25
β-strand	330-331	2	24
α-helix	332-333	2
β-strand	334-337	4	26
β-strand	345	1	26
β-strand	348-349	2	25
β-strand	355-356	2	24
β-strand	363-368	6	25
α-helix	369-370	2
β-strand	372-378	7	26
α-helix	381-383	3
β-strand	385-391	7	26

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Envelope protein E	A, B, C	protein	395	Yellow fever virus (strain 17D vaccine)	P03314 (AlphaFold model)

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

>6IW1_1 Envelope protein E (chains A, B, C)
AHCIGITDRDFIEGVHGGTWVSATLEQDKCVTVMAPDKPSLDISLETVAIDRPAEVRKVC
YNAVLTHVKINDKCPSTGEAHLAEENEGDNACKRTYSDRGWGNGCGLFGKGSIVACAKFT
CAKSMSLFEVDQTKIQYVIRAQLHVGAKQENWNTDIKTLKFDALSGSQEVEFIGYGKATL
ECQVQTAVDFGNSYIAEMETESWIVDRQWAQDLTLPWQSGSGGVWREMHHLVEFEPPHAA
TIRVLALGNQEGSLKTALTGAMRVTKDTNDNNLYKLHGGHVSCRVKLSALTLKGTSYKIC
TDKMFFVKNPTDTGHGTVVMQVKVSKGAPCRIPVIVADDLTAAINKGILVTVNPIASTND
DEVLIEVNPPFGDSYIIVGRGDSRLTYQWHKEGSS

Primary citation

Double Lock of a Human Neutralizing and Protective Monoclonal Antibody Targeting the Yellow Fever Virus Envelope. Lu, X., Xiao, H., Li, S. et al. Cell Rep (2019) 26:438-446.e5. DOI 10.1016/j.celrep.2018.12.065 · PubMed

Other PDB entries of the same protein (UniProt P03314 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3EVF 1.45 Å, Crystal structure of Me7-GpppA complex of yellow fever virus methyltransferase and…
9SKO 1.49 Å, Crystal structure of HLA-A0201 in complex with peptide LLWNGPMAVS
3EVA 1.5 Å, Crystal structure of yellow fever virus methyltransferase complexed with…
3EVD 1.5 Å, Crystal structure of GTP complex of yellow fever virus methyltransferase and…
3EVC 1.6 Å, Crystal structure of GTP complex of yellow fever virus methyltransferase and…
3EVE 1.7 Å, Crystal structure of GpppA complex of yellow fever virus methyltransferase and…
5N6B 1.71 Å, Human Leukocyte Antigen Class I A02 Carrying LLWNPGMAV
1YKS 1.8 Å, Crystal structure of yellow fever virus NS3 helicase
3EVB 1.85 Å, Crystal structure of yellow fever virus methyltransferase complexed with…
9SKP 1.89 Å, Crystal structure of HLA-A0201 in complex with peptide SLLWNGPMAV
6SSA 2.11 Å, Human Leukocyte Antigen Class I A02 Carrying LLWNGPMQV
6SS8 2.24 Å, Human Leukocyte Antigen Class I A02 Carrying LLWNGPIAV

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