6FHH | pdb_00006fhh

Crystal structure of bat influenza A/H17N10 polymerase with viral RNA promoter bound to a 22-mer modified Pol II CTD peptide with serine 5 thiophosphorylated.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.258 (Depositor), 0.255 (DCC) 
  • R-Value Work: 
    0.213 (Depositor), 0.218 (DCC) 
  • R-Value Observed: 
    0.215 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6FHH

This is version 2.1 of the entry. See complete history. 

Literature

Towards New Anti-Influenza Therapeutics: Structure-Activity Relationships in the Interaction between Heterotrimeric Influenza Polymerase and Pol II C-terminal domain

Claron, M., Lukarska, M., Uhrig, U., Sehr, P., Drncova, P., Lewis, J.D., Will, D.W., Cusack, S.

To be published.

Macromolecule Content 

  • Total Structure Weight: 282.03 kDa 
  • Atom Count: 18,457 
  • Modeled Residue Count: 2,230 
  • Deposited Residue Count: 2,401 
  • Unique protein chains: 4
  • Unique nucleic acid chains: 2

Macromolecules


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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Polymerase acidic protein738Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10))Mutation(s): 0 
Gene Names: PA
UniProt
Find proteins for H6QM92 (Influenza A virus)
Explore H6QM92 
Go to UniProtKB:  H6QM92
Entity Groups
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UniProt GroupH6QM92
Sequence Annotations
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Reference Sequence
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|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
RNA-directed RNA polymerase catalytic subunit776Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10))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
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UniProt GroupH6QM91
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Reference Sequence
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|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Polymerase basic protein 2809Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10))Mutation(s): 0 
Gene Names: PB2
UniProt
Find proteins for H6QM90 (Influenza A virus)
Explore H6QM90 
Go to UniProtKB:  H6QM90
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UniProt GroupH6QM90
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
TYR-SER-PRO-THR-TPS-PRO-SERF [auth X],
G [auth Y]		22Homo sapiensMutation(s): 0 
Find similar nucleic acids by:  Sequence
Entity ID: 4
MoleculeChains LengthOrganismImage
RNA (5'-R(*UP*AP*UP*AP*CP*CP*UP*CP*UP*GP*CP*UP*U)-3')D [auth R]18Influenza A virus
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 5
MoleculeChains LengthOrganismImage
RNA (5'-R(P*AP*GP*UP*AP*GP*UP*AP*AP*CP*AP*AP*GP*AP*GP*GP*G)-3')E [auth V]16Influenza A virus
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PO4

Query on PO4


Download:Ideal Coordinates CCD File
H [auth A]
I [auth A]
J [auth A]
L [auth B]
M [auth B]
H [auth A],
I [auth A],
J [auth A],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
S [auth C],
T [auth C],
U [auth C],
V [auth C],
W [auth C]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN

Query on ZN


Download:Ideal Coordinates CCD File
K [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
2RX
Query on 2RX		F [auth X],
G [auth Y]		L-PEPTIDE LINKINGC3 H8 N O5 P SSER

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.258 (Depositor), 0.255 (DCC) 
  • R-Value Work:  0.213 (Depositor), 0.218 (DCC) 
  • R-Value Observed: 0.215 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 267.77α = 90
b = 147.81β = 97.08
c = 88.41γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
European Research CouncilFrance322586

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-30
    Type: Initial release
  • Version 2.0: 2023-02-01
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Other, Polymer sequence, Source and taxonomy, Structure summary
  • Version 2.1: 2024-02-07
    Changes: Data collection, Derived calculations, Refinement description