6FS8: Polymerase acidic protein

Influenza B/Memphis/13/03 endonuclease with bound inhibitor, baloxavir acid (BXA). Determined by X-ray diffraction at 1.8 Å resolution. Released 11 Jul 2018.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Influenza B virus (B/Memphis/13/2003)
Chains: 2
Atoms: 3,267
Mol. weight: 48.22 kDa
Ligands: MN, E4Z
Released: 11 Jul 2018

Explore 6FS8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6FS8 contains 16 α-helices and 15 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: 8 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	1-8	8
α-helix	11-23	13
α-helix	32-48	17
β-strand	52-53	2	3
β-strand	74-75	2	3
β-strand	77-79	3	4
α-helix	85-99	15
β-strand	110-112	3	4
β-strand	117-124	8	4
α-helix	128-139	12
β-strand	144-149	6	4
β-strand	154-156	3	4
α-helix	159-161	3
α-helix	164-183	20
α-helix	187-191	5

Chain B: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	1-8	8
α-helix	11-23	13
α-helix	32-51	20
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
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	187-191	5

Molecules and chains

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

Sequence of entity 1 (A, B), FASTA

>6FS8_1 Polymerase acidic protein (chains A, B)
GAMGSGMAMDTFITRNFQTTIIQKAKNTMAEFSEDPELQPAMLFNICVHLEVCYVISDMN
FLDEEGKSYTALEGQGKEQNLRPQYEVIEGMPRTIAWMVQRSLAQEHGIETPKYLADLFD
YKTKRFIEVGITKGLADDYFWKKKEKLGNSMELMIFSYNQDYSLSNESSLDEEGKGRVLS
RLTELQAELSLKNLWQVLIGEEDVE

Ligands and cofactors

ID	Name	Formula	Copies
MN	Manganese (II) ion	Mn	4
E4Z	Baloxavir acid	C24 H19 F2 N3 O4 S	2

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…
6FSB 1.8 Å, Influenza B/Memphis/13/03 endonuclease with I38T mutation
6FS9 2.28 Å, Influenza B/Memphis/13/03 endonuclease with I38T mutation with bound inhibitor,…
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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