6IW4: YFV-17D sE in prefusion state

Crystal structure of YFV-17D sE in prefusion state. Determined by X-ray diffraction at 2.8 Å resolution. Released 13 Feb 2019.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Yellow fever virus (strain 17D vaccine)
Chains: 2
Atoms: 5,958
Mol. weight: 86.47 kDa
Released: 13 Feb 2019

Explore 6IW4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6IW4 contains 24 α-helices and 65 β-strands across 2 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, 33 β-strands

Element	Residues	Length	Sheet
β-strand	9-13	5	1
β-strand	20-26	7	2
β-strand	30-34	5	1
β-strand	41-50	10	1
α-helix	53-54	2
β-strand	55-72	18	1
β-strand	90-99	10	1
α-helix	101-103	3
β-strand	109-129	21	1
α-helix	132-134	3
β-strand	136-143	8	1
α-helix	149-154	6
β-strand	157-161	5	1
β-strand	168-172	5	2
β-strand	176-180	5	2
α-helix	182	1
β-strand	183-185	3	2
β-strand	194-198	5	1
β-strand	201-205	5	1
α-helix	207-211	5
β-strand	217-218	2	1
β-strand	226	1	1
α-helix	228-231	4
β-strand	232-234	3	3
α-helix	235-237	3
β-strand	244-246	3	3
α-helix	251-257	7
α-helix	262	1
β-strand	263-266	4	1
β-strand	274-276	3	1
β-strand	280-286	7	2
β-strand	290	1	2
β-strand	298-299	2	4
β-strand	304-312	9	5
β-strand	318-324	7	5
β-strand	330-331	2	4
β-strand	334-337	4	6
β-strand	345	1	6
α-helix	347	1
β-strand	348-349	2	5
β-strand	356	1	4
β-strand	361-368	8	5
α-helix	369-370	2
β-strand	372-378	7	6
β-strand	385-391	7	6

Chain B: 12 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	9-13	5	7
β-strand	20-26	7	8
β-strand	30-35	6	7
β-strand	38-50	13	7
α-helix	53-54	2
β-strand	55-72	18	7
β-strand	90-99	10	7
α-helix	101-103	3
β-strand	109-129	21	7
β-strand	136-143	8	7
α-helix	149-154	6
β-strand	157-161	5	7
β-strand	168-172	5	8
β-strand	176-180	5	8
α-helix	182	1
β-strand	183-185	3	8
β-strand	194-198	5	7
β-strand	201-205	5	7
α-helix	207-211	5
β-strand	217-218	2	7
β-strand	226	1	7
α-helix	228-231	4
β-strand	232-234	3	9
α-helix	235-237	3
β-strand	244-246	3	9
α-helix	247-249	3
α-helix	251-257	7
α-helix	262	1
β-strand	263-266	4	7
β-strand	274-276	3	7
β-strand	280-286	7	8
β-strand	290	1	8
β-strand	298-299	2	10
β-strand	304-312	9	11
β-strand	318-324	7	11
β-strand	330-331	2	10
α-helix	332-333	2
β-strand	334-337	4	12
β-strand	348-349	2	11
β-strand	356	1	10
β-strand	361-368	8	11
α-helix	369-370	2
β-strand	372-378	7	12
β-strand	385-391	7	12

Molecules and chains

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

Sequence of entity 1 (A, B), FASTA

>6IW4_1 Envelope protein E (chains A, B)
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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