5EFA: Influenza B Lee PB2 cap-binding domain

Structure of Influenza B Lee PB2 cap-binding domain bound to m7GTP. Determined by X-ray diffraction at 1.9 Å resolution. Released 18 Nov 2015.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Influenza B virus
Chains: 1
Atoms: 1,558
Mol. weight: 20.98 kDa
Ligands: MGT
Released: 18 Nov 2015

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

Secondary structure: helices and β-sheets

5EFA contains 8 α-helices and 15 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: 8 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	323-324	2
β-strand	325-327	3	1
β-strand	330-337	8	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	382-389	8	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	432-441	10
α-helix	444-451	8
β-strand	453-455	3	4
α-helix	456-457	2
β-strand	462-463	2	1
β-strand	465	1	5
β-strand	471	1	5
β-strand	474-476	3	4
β-strand	479-482	4	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Polymerase basic protein 2	A	protein	174	Influenza B virus	Q9QLL6 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5EFA_1 Polymerase basic protein 2 (chains A)
MKIRQRQRFGRLELKRISGRGFKNDEEILIGNGTIQKIGIWDGEEEFHVRCGECRGILKK
SQMRMEKLLINSAKKEDMKDLIILCMVFSQDTRMFQGVRGEINFLNRAGQLLSPMYQLQR
YFLNRSNDLFDQWGYEESPKASELHGINELMNASDYTLKGVVVTKNVDHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
MGT	7N-methyl-8-hydroguanosine-5'-triphosphate	C11 H20 N5 O14 P3	1

Primary citation

Molecular Basis of mRNA Cap Recognition by Influenza B Polymerase PB2 Subunit. Xie, L., Wartchow, C., Shia, S. et al. J Biol Chem (2016) 291:363-370. DOI 10.1074/jbc.M115.693051 · PubMed

Other PDB entries of the same protein (UniProt Q9QLL6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5EF9 1.7 Å, Structure of Influenza B Lee PB2 cap-binding domain
5EFC 1.9 Å, Structure of Influenza B Lee PB2 cap-binding domain bound to GTP
6XQA 2.16 Å, Crystal Structure of HLA A*2402 in complex with TYQWVLKNL, an 9-mer epitope from…

Browse structure collections

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