3EVA: Yellow fever virus methyltransferase

Name: PDB 3EVA: Crystal structure of yellow fever virus methyltransferase complexed with S-adenosyl-L-homocysteine
Published: 2009-01-06
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

Crystal structure of yellow fever virus methyltransferase complexed with S-adenosyl-L-homocysteine. Determined by X-ray diffraction at 1.5 Å resolution. Released 6 Jan 2009.

Method: X-ray diffraction
Resolution: 1.5 Å
Organism: Yellow fever virus
Chains: 1
Atoms: 2,327
Mol. weight: 31.68 kDa
Ligands: SAH
Released: 6 Jan 2009

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

Secondary structure: helices and β-sheets

3EVA contains 12 α-helices and 13 β-strands across 1 chain. 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, 13 β-strands

Element	Residues	Length	Sheet
α-helix	8-17	10
α-helix	21-29	9
β-strand	33-36	4	1
α-helix	38-45	8
β-strand	53	1	2
α-helix	58-67	10
β-strand	75-80	6	3
α-helix	86-92	7
β-strand	97-103	7	3
α-helix	110-114	5
β-strand	118	1	4
α-helix	121-123	3
β-strand	124-127	4	3
α-helix	136-137	2
β-strand	142-145	4	3
α-helix	154-172	19
β-strand	178-183	6	3
α-helix	189-202	14
β-strand	205-207	3	3
β-strand	219-222	4	3
α-helix	229-245	17
β-strand	252-255	4	1
α-helix	256-257	2
β-strand	258	1	2
β-strand	261	1	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
RNA-directed RNA polymerase NS5	A	protein	277	Yellow fever virus	P03314 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3EVA_1 RNA-directed RNA polymerase NS5 (chains A)
MGSANGKTLGEVWKRELNLLDKRQFELYKRTDIVEVDRDTARRHLAEGKVDTGVAVSRGT
AKLRWFHERGYVKLEGRVIDLGCGRGGWCYYAAAQKEVSGVKGFTLGRDGHEKPMNVQSL
GWNIITFKDKTDIHRLEPVKCDTLLCDIGESSSSSVTEGERTVRVLDTVEKWLACGVDNF
CVKVLAPYMPDVLEKLELLQRRFGGTVIRNPLSRNSTHEMYYVSGARSNVTFTVNQTSRL
LMRRMRRPTGKVTLEADVILPIGTRSVGSSSHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
SAH	S-adenosyl-L-homocysteine	C14 H20 N6 O5 S	1

Primary citation

Analysis of flavivirus NS5 methyltransferase cap binding. Geiss, B.J., Thompson, A.A., Andrews, A.J. et al. J Mol Biol (2009) 385:1643-1654. DOI 10.1016/j.jmb.2008.11.058 · 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
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
6SS7 2.5 Å, Human Leukocyte Antigen Class I A02 Carrying LLWAGPMAV

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