9F37

Replication-like initiation state of influenza polymerase with GTP and CTP at respectively the -1 and +1 positions (strain A/little yellow-shouldered bat/Guatemala/060/2010/H17N10)

PDB DOI: https://doi.org/10.2210/pdb9F37/pdb

Classification: VIRAL PROTEIN
Organism(s): Influenza A virus
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2024-04-25 Released: 2024-09-18
Deposition Author(s): Cusack, S., Drncova, P.
Funding Organization(s): Agence Nationale de la Recherche (ANR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.91 Å
R-Value Free: 0.232
R-Value Work: 0.189

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

High-resolution structure of a replication-initiation like configuration of influenza polymerase active site visualises the essential role of a conserved dibasic motif in the PA subunit

Cusack, S., Drncova, P., Krischuns, T., Naffakh, N.

(2024) bioRxiv

DOI: https://doi.org/10.1101/2023.11.20.567839

Macromolecule Content

Total Structure Weight: 278.28 kDa
Atom Count: 19,019
Modelled Residue Count: 2,204
Deposited Residue Count: 2,360
Unique protein chains: 3
Unique nucleic acid chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polymerase acidic protein	A	738	Influenza A virus	Mutation(s): 0 Gene Names: PA
UniProt
Find proteins for H6QM92 (Influenza A virus) Explore H6QM92 Go to UniProtKB: H6QM92
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	H6QM92
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-directed RNA polymerase catalytic subunit	B	776	Influenza A virus	Mutation(s): 0 Gene Names: PB1 EC: 2.7.7.48
UniProt
Find proteins for H6QM91 (Influenza A virus) Explore H6QM91 Go to UniProtKB: H6QM91
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	H6QM91
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Polymerase basic protein 2	C	809	Influenza A virus	Mutation(s): 0 Gene Names: PB2
UniProt
Find proteins for H6QM90 (Influenza A virus) Explore H6QM90 Go to UniProtKB: H6QM90
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	H6QM90
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 4
Molecule	Chains	Length	Organism	Image
3' end of the vRNA promoter	D [auth R]	21	Influenza A virus
Sequence Annotations Expand
Reference Sequence

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Entity ID: 5
Molecule	Chains	Length	Organism	Image
5' end of the vRNA promoter	E [auth V]	16	Influenza A virus
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MGT (Subject of Investigation/LOI) Query on MGT Download Ideal Coordinates CCD File SDF format, chain O [auth C] MOL2 format, chain O [auth C]	O [auth C]	7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE C₁₁ H₂₀ N₅ O₁₄ P₃ BUJQMJUTTBGELS-KQYNXXCUSA-N		Interactions Focus chain O [auth C]
GTP (Subject of Investigation/LOI) Query on GTP Download Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B]	K [auth B]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain K [auth B]
CTP (Subject of Investigation/LOI) Query on CTP Download Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B]	J [auth B]	CYTIDINE-5'-TRIPHOSPHATE C₉ H₁₆ N₃ O₁₄ P₃ PCDQPRRSZKQHHS-XVFCMESISA-N		Interactions Focus chain J [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain N [auth C] MOL2 format, chain F [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain N [auth C]	F [auth A], G [auth B], H [auth B], I [auth B], N [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain N [auth C]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B]	L [auth B], M [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Focus chain M [auth B]