3L25: Zaire Ebola VP35 interferon inhibitory domain

Crystal structure of Zaire Ebola VP35 interferon inhibitory domain bound to 8 bp dsRNA. Determined by X-ray diffraction at 2.0 Å resolution. Released 26 Jan 2010.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Zaire ebolavirus
Chains: 6
Atoms: 4,627
Mol. weight: 63.47 kDa
Ligands: MG
Released: 26 Jan 2010

Explore 3L25 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3L25 contains 37 α-helices and 20 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: 10 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	221-231	11
β-strand	237	1	1
α-helix	238-252	15
α-helix	256-268	13
α-helix	273-283	11
α-helix	285-287	3
α-helix	290-293	4
β-strand	294-296	3	2
α-helix	300-302	3
β-strand	306	1	1
α-helix	308-310	3
β-strand	311-312	2	2
α-helix	313-315	3
α-helix	320-322	3
β-strand	324-329	6	2
β-strand	335-339	5	2

Chains B and E: 9 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	221-231	11
α-helix	238-252	15
α-helix	256-268	13
α-helix	273-283	11
α-helix	285-287	3
α-helix	290-293	4
β-strand	294-296	3	3
α-helix	300-302	3
α-helix	305-310	6
β-strand	311-312	2	3
α-helix	320-322	3
β-strand	324-329	6	3
β-strand	335-339	5	3

Chain D: 9 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	221-231	11
β-strand	237	1	4
α-helix	238-252	15
α-helix	256-269	14
α-helix	273-283	11
α-helix	285-287	3
α-helix	290-293	4
β-strand	294-297	4	5
α-helix	300-302	3
β-strand	306	1	4
α-helix	308-310	3
β-strand	311-312	2	5
α-helix	320-322	3
β-strand	324-330	7	5
β-strand	335-339	5	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Polymerase cofactor VP35	A, B, D, E	protein	129	Zaire ebolavirus	Q05127 (AlphaFold model)
RNA (5'-r(cpgpcpapupgpcpg)-3')	C, F	RNA	8

Sequence of entity 1 (A, B, D, E), FASTA

>3L25_1 Polymerase cofactor VP35 (chains A, B, D, E)
GHMGKPDISAKDLRNIMYDHLPGFGTAFHQLVQVICKLGKDSNSLDIIHAEFQASLAEGD
SPQCALIQITKRVPIFQDAAPPVIHIRSRGDIPRACQKSLRPVPPSPKIDRGWVCVFQLQ
DGKTLGLKI

Sequence of entity 2 (C, F), FASTA

>3L25_2 RNA (5'-R(*CP*GP*CP*AP*UP*GP*CP*G)-3') (chains C, F)
CGCAUGCG

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1

Water and common crystallization additives (FMT, GOL, NA, CL) are not listed.

Primary citation

Structural basis for dsRNA recognition and interferon antagonism by Ebola VP35. Leung, D.W., Prins, K.C., Borek, D.M. et al. Nat Struct Mol Biol (2010) 17:165-172. DOI 10.1038/nsmb.1765 · PubMed

Other PDB entries of the same protein (UniProt Q05127 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3FKE 1.4 Å, Structure of the Ebola VP35 Interferon Inhibitory Domain
4IBG 1.41 Å, Ebola virus VP35 bound to small molecule
4IBI 1.47 Å, Ebola virus VP35 bound to small molecule
4IBJ 1.54 Å, Ebola virus VP35 bound to small molecule
3L29 1.7 Å, Crystal Structure of Zaire Ebola VP35 interferon inhibitory domain K319A/R322A mutant
4IBC 1.75 Å, Ebola virus VP35 bound to small molecule
4IBB 1.75 Å, Ebola virus VP35 bound to small molecule
4IBD 1.84 Å, Ebola virus VP35 bound to small molecule
4IBK 1.85 Å, Ebola virus VP35 bound to small molecule
4IJE 1.9 Å, Crystal structure of the Zaire ebolavirus VP35 interferon inhibitory domain…
3L27 1.95 Å, Crystal structure of Zaire Ebola VP35 interferon inhibitory domain R312A mutant
4IBE 1.95 Å, Ebola virus VP35 bound to small molecule

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