RCSB PDB - 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)

 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)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 
    0.232 (Depositor), 0.237 (DCC) 
  • R-Value Work: 
    0.189 (Depositor), 0.197 (DCC) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted MGTClick on this verticalbar to view detailsBest fitted GTPClick on this verticalbar to view detailsBest fitted CTPClick on this verticalbar to view details

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 


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Polymerase acidic protein738Influenza A virusMutation(s): 0 
Gene Names: PA
UniProt
Find proteins for H6QM92 (Influenza A virus)
Explore H6QM92 
Go to UniProtKB:  H6QM92
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupH6QM92
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-directed RNA polymerase catalytic subunit776Influenza A virusMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupH6QM91
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Polymerase basic protein 2809Influenza A virusMutation(s): 0 
Gene Names: PB2
UniProt
Find proteins for H6QM90 (Influenza A virus)
Explore H6QM90 
Go to UniProtKB:  H6QM90
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupH6QM90
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MGT (Subject of Investigation/LOI)
Query on MGT

Download Ideal Coordinates CCD File 
O [auth C]7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE
C11 H20 N5 O14 P3
BUJQMJUTTBGELS-KQYNXXCUSA-N
GTP (Subject of Investigation/LOI)
Query on GTP

Download Ideal Coordinates CCD File 
K [auth B]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
CTP (Subject of Investigation/LOI)
Query on CTP

Download Ideal Coordinates CCD File 
J [auth B]CYTIDINE-5'-TRIPHOSPHATE
C9 H16 N3 O14 P3
PCDQPRRSZKQHHS-XVFCMESISA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A],
G [auth B],
H [auth B],
I [auth B],
N [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
L [auth B],
M [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free:  0.232 (Depositor), 0.237 (DCC) 
  • R-Value Work:  0.189 (Depositor), 0.197 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.937α = 90
b = 119.005β = 90
c = 251.381γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
autoPROCdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted MGTClick on this verticalbar to view detailsBest fitted GTPClick on this verticalbar to view detailsBest fitted CTPClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)FranceANR-18-CE11-0028

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-18
    Type: Initial release