Structure of PDB 8pnq Chain B

Receptor sequence

>8pnqB (length=744) Species: 1318616 (Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9)))

MDVNPTLLFLKVPVQNAISTTFPYTGDPPYSHGTGTGYTMDTVNRTHKYS
EKGKWTTNTETGAPQLNPIDGPLPEDNEPSGYAQTDCVLEAMAFLEESHP
GIFENSCLETMEIVQQTRVDKLTQGRQTYDWTLNRNQPAATALANTIEVF
RSNGLTANESGRLIDFLKDVMDSMDKEEMEITTHFQRKRRVRDNMTKKMV
TQRTIGKKKQRLNKRSYLIRALTLNTMTKDAERGKLKRRAIATPGMQIRG
FVYFVEALARSICEKLEQSGLPVGGNEKKAKLANVVRKMMTNSQDTELSF
TITGDNTKWNENQNPRMFLAMITYITRNQPEWFRNVLSIAPIMFSNKMAR
LGKGYMFESKSMKLRTQVPAEMLANIDLKYFNKSTREKIEKIRPLLIDGT
ASLSPGMMMGMFNMLSTVLGVSILNLGQKKYTKTTYWWDGLQSSDDFALI
VNAPNHEGIQAGVDRFYRTCKLVGINMSKKKSYINRTGTFEFTSFFYRYG
FVANFSMELPSFGVSGINESADMSVGVTVIKNNMINNDLGPATAQMALQL
FIKDYRYTYRCHRGDTQIQTRRAFELGKLWEQTRSKAGLLVSDGGPNLYN
IRNLHIPEVCLKWELMDEDYQGRLCNPMNPFVSHKEIDSVSMEYDAVATT
HSWIPKRNRSILNTSQRGILEDEQMYQKCCNLFEKFFPSSSYRRPVGISS
MVEAMVSRARIDARIDFESGRIKKEEFAEIMKICSTIEELRRQK

3D structure

• PDB: 8pnq The host RNA polymerase II C-terminal domain is the anchor for replication of the influenza virus genome.
• Chain: B
• Resolution: 2.88 Å

Enzymatic activity

• Enzyme Commision number: 2.7.7.48: RNA-directed RNA polymerase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	rna	B	Y30 H32 G33 T34 G125 R126 Q127 R135 N136 K198 V200 R203 M227 K229 I241 A242 T243 R249 P272 V273 G274 M356 R365 G410 M414 N532 Y557 R560 I568 Q569 S633 R670 I674 L675 N676 T677	Y30 H32 G33 T34 G125 R126 Q127 R135 N136 K198 V200 R203 M227 K229 I241 A242 T243 R249 P272 V273 G274 M356 R365 G410 M414 N532 Y557 R560 I568 Q569 S633 R657 I661 L662 N663 T664
BS02	rna	B	Y24 S444 D445 D446 M507 P510 R706	Y24 S444 D445 D446 M507 P510 R693
BS03	2KH	B	R239 D305 N306 K308 W309 N310 M409 G410 D445 K481	R239 D305 N306 K308 W309 N310 M409 G410 D445 K481
BS04	MG	B	D305 D445 D446	D305 D445 D446
BS05	MG	B	D305 N306 D445	D305 N306 D445

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0003723 RNA binding
• GO:0003968 RNA-dependent RNA polymerase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0001172 RNA-templated transcription
• GO:0006351 DNA-templated transcription
• GO:0019083 viral transcription
• GO:0039523 symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity
• GO:0039694 viral RNA genome replication

Cellular Component

• GO:0005737 cytoplasm
• GO:0030430 host cell cytoplasm
• GO:0042025 host cell nucleus

External links

• PDB: RCSB:8pnq, PDBe:8pnq, PDBj:8pnq
• PDBsum: 8pnq
• PubMed: 38316757
• UniProt: M9TLW3