6FS9: Polymerase acidic protein

Influenza B/Memphis/13/03 endonuclease with I38T mutation with bound inhibitor, baloxavir acid (BXA). Determined by X-ray diffraction at 2.28 Å resolution. Released 11 Jul 2018.

Method: X-ray diffraction
Resolution: 2.28 Å
Organism: Influenza B virus (B/Memphis/13/2003)
Chains: 1
Atoms: 1,540
Mol. weight: 24.17 kDa
Ligands: MN, E4Z
Released: 11 Jul 2018

Explore 6FS9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6FS9 contains 9 α-helices and 8 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: 9 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	1-8	8
α-helix	11-23	13
α-helix	32-49	18
β-strand	53-54	2	1
β-strand	60-61	2	1
β-strand	74-75	2	1
β-strand	77-79	3	2
α-helix	85-98	14
α-helix	102-104	3
α-helix	107-108	2
β-strand	110-112	3	2
β-strand	117-124	8	2
α-helix	128-139	12
β-strand	144-149	6	2
β-strand	154-156	3	2
α-helix	164-183	20
α-helix	187-190	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Polymerase acidic protein	A	protein	205	Influenza B virus (B/Memphis/13/2003)	Q5V8Z9

Sequence of entity 1 (A), FASTA

>6FS9_1 Polymerase acidic protein (chains A)
GAMGSGMAMDTFITRNFQTTIIQKAKNTMAEFSEDPELQPAMLFNTCVHLEVCYVISDMN
FLDEEGKSYTALEGQGKEQNLRPQYEVIEGMPRTIAWMVQRSLAQEHGIETPKYLADLFD
YKTKRFIEVGITKGLADDYFWKKKEKLGNSMELMIFSYNQDYSLSNESSLDEEGKGRVLS
RLTELQAELSLKNLWQVLIGEEDVE

Ligands and cofactors

ID	Name	Formula	Copies
MN	Manganese (II) ion	Mn	2
E4Z	Baloxavir acid	C24 H19 F2 N3 O4 S	1

Water and common crystallization additives (CL) are not listed.

Primary citation

Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. Omoto, S., Speranzini, V., Hashimoto, T. et al. Sci Rep (2018) 8:9633-9633. DOI 10.1038/s41598-018-27890-4 · PubMed

Other PDB entries of the same protein (UniProt Q5V8Z9), best resolution first:

5FML 1.7 Å, Crystal structure of the endonuclease from the PA subunit of influenza B virus bound to…
6FS8 1.8 Å, Influenza B/Memphis/13/03 endonuclease with bound inhibitor, baloxavir acid (BXA)
6FSB 1.8 Å, Influenza B/Memphis/13/03 endonuclease with I38T mutation
8BE0 2.34 Å, Early transcription elongation state of influenza B/Mem polymerase backtracked due to…
7Z42 2.42 Å, Influenza B polymerase with Pol II pSer5 CTD peptide mimic bound in site 2B
7R1F 2.58 Å, Early transcription elongation state of influenza B polymerase backtracked due to double…
4WRT 2.7 Å, Crystal structure of Influenza B polymerase with bound vRNA promoter (form FluB2)
8BDR 2.7 Å, Early transcription elongation state of influenza B/Mem polymerase backtracked due to…
8RN3 2.78 Å, Pseudo-symmetrical influenza B polymerase apo-dimer, encapsidase moiety (from "Influenza…
8RN6 2.82 Å, Pseudo-symmetrical influenza B polymerase apo-dimer, ENDO(E) moiety (from "Influenza B…
8RN4 2.87 Å, Pseudo-symmetrical influenza B polymerase apo-dimer, ENDO(T) moiety (from "Influenza B…
6QCW 2.88 Å, Crystal structure of influenza B polymerase initiation state with capped 14-mer RNA primer

Browse structure collections

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