6EUX: Polymerase basic protein 2

Structure of the midlink and cap-binding domains of influenza B polymerase PB2 subunit with a bound azaindazole cap-binding inhibitor. Determined by X-ray diffraction at 2.05 Å resolution. Released 13 Dec 2017.

Method: X-ray diffraction
Resolution: 2.05 Å
Organism: Influenza B virus (B/Memphis/13/2003)
Chains: 1
Atoms: 1,987
Mol. weight: 33.41 kDa
Ligands: BYB
Released: 13 Dec 2017

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

Secondary structure: helices and β-sheets

6EUX contains 12 α-helices and 17 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, 17 β-strands

Element	Residues	Length	Sheet
α-helix	259-273	15
α-helix	279-286	8
α-helix	309-317	9
β-strand	325-327	3	1
β-strand	330-336	7	1
β-strand	340-347	8	2
β-strand	353-360	8	2
β-strand	363-369	7	1
β-strand	372-379	8	1
β-strand	382-388	7	1
α-helix	393-406	14
α-helix	410-414	5
β-strand	423	1	3
α-helix	428	1
β-strand	429	1	3
α-helix	430-431	2
α-helix	432-442	11
α-helix	444-451	8
β-strand	453-455	3	4
α-helix	456-457	2
β-strand	462-463	2	1
β-strand	464-465	2	5
β-strand	471-472	2	5
β-strand	474-476	3	4
β-strand	479-482	4	1
α-helix	485-488	4
β-strand	505-506	2	6
β-strand	512-514	3	6
α-helix	516-518	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Polymerase basic protein 2	A	protein	292	Influenza B virus (B/Memphis/13/2003)	Q5V8X3

Sequence of entity 1 (A), FASTA

>6EUX_1 Polymerase basic protein 2 (chains A)
GGNKLTESRSQSMIVACRKIIRRSIVASNPLELAVEIANKTVIDTEPLKSCLAAIDGGDV
ACDIIRAALGLKIRQRQRFGRLELKRISGRGFKNDEEILIGNGTIQKIGIWDGEEEFHVR
CGECRGILKKSKMKLEKLLINSAKKEDMRDLIILCMVFSQDTRMFQGVRGEINFLNRAGQ
LLSPMYQLQRYFLNRSNDLFDQWGYEESPKASELHGINESMNASDYTLKGVVVTRNVIDD
FSSTETEKVSITKNLSLIKRTGEVIMGANDVSELESQAQLMITYDTPKMWEM

Ligands and cofactors

ID	Name	Formula	Copies
BYB	(2~{S},3~{S})-3-[[5-fluoranyl-2-(5-fluoranyl-1~{H}-pyrazolo[3,4-b]pyridin-3-yl)…	C19 H18 F2 N6 O2	1

Primary citation

Capped RNA primer binding to influenza polymerase and implications for the mechanism of cap-binding inhibitors. Pflug, A., Gaudon, S., Resa-Infante, P. et al. Nucleic Acids Res (2018) 46:956-971. DOI 10.1093/nar/gkx1210 · PubMed

Other PDB entries of the same protein (UniProt Q5V8X3), best resolution first:

5FML 1.7 Å, Crystal structure of the endonuclease from the PA subunit of influenza B virus bound to…
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
8RN5 2.88 Å, Pseudo-symmetrical influenza B polymerase apo-dimer, ENDO(R) moiety (from "Influenza B…
8RN2 2.89 Å, Monomeric apo-influenza B polymerase, encapsidase conformation

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