5FML: PB2 subunit of influenza B polymerase

Crystal structure of the endonuclease from the PA subunit of influenza B virus bound to the PB2 subunit NLS peptide. Determined by X-ray diffraction at 1.7 Å resolution. Released 13 Jan 2016.

Method: X-ray diffraction
Resolution: 1.7 Å
Organism: INFLUENZA B VIRUS
Chains: 2
Atoms: 1,918
Mol. weight: 26.79 kDa
Ligands: MG
Released: 13 Jan 2016

Explore 5FML in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5FML contains 11 α-helices and 8 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: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	748-764	17

Chain B: 10 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	52-55	4	1
β-strand	60-62	3	1
α-helix	63-66	4
α-helix	70-72	3
β-strand	73-75	3	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	154-155	2	2
α-helix	164-183	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
PB2 subunit of influenza B polymerase	A	protein	29	INFLUENZA B VIRUS	Q5V8X3
Pa subunit of influenza B polymerase	B	protein	202	INFLUENZA B VIRUS	Q5V8Z9

Sequence of entity 1 (A), FASTA

>5FML_1 PB2 SUBUNIT OF INFLUENZA B POLYMERASE (chains A)
KRYSALSNDISQGIKRQRMTVESMGWALS

Sequence of entity 2 (B), FASTA

>5FML_2 PA SUBUNIT OF INFLUENZA B POLYMERASE (chains B)
MGSMAMDTFITRNFQTTIIQKAKNTMAEFSEDPELQPAMLFNICVHLEVCYVISDMNFLD
EEGKSYTALEGQGKEQNLRPQYEVIEGMPRTIAWMVQRSLAQEHGIETPKYLADLFDYKT
KRFIEVGITKGLADDYFWKKKEKLGNSMELMIFSYNQDYSLSNESSLDEEGKGRVLSRLT
ELQAELSLKNLWQVLIGEEDVE

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2

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

Primary citation

Influenza Polymerase Can Adopt an Alternative Configuration Involving a Radical Repacking of Pb2 Domains. Thierry, E., Guilligay, D., Kosinski, J. et al. Mol Cell (2016) 61:125. DOI 10.1016/J.MOLCEL.2015.11.016 · PubMed

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

6EUX 2.05 Å, Structure of the midlink and cap-binding domains of influenza B polymerase PB2 subunit…
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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