9I2O

PB2 cap-binding domain of human pathogenic influenza A virus H5N1 in complex with m7GTP

PDB DOI: https://doi.org/10.2210/pdb9I2O/pdb

Classification: RNA BINDING PROTEIN
Organism(s): Influenza A virus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-01-21 Released: 2025-01-29
Deposition Author(s): Falke, S., Lewe, P., Witt, S., Wrenger, C., Meents, A.
Funding Organization(s): Helmholtz Association, German Federal Ministry for Education and Research

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.72 Å
R-Value Free:
0.206 (Depositor), 0.206 (DCC)
R-Value Work:
0.182 (Depositor), 0.183 (DCC)
R-Value Observed:
0.185 (Depositor)

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

PB2 cap-binding domain of human pathogenic influenza A virus H5N1 in complex with m7GTP

Falke, S., Lewe, P., Witt, S., Wrenger, C., Meents, A.

To be published.

Macromolecule Content

Total Structure Weight: 21.91 kDa
Atom Count: 1,432
Modelled Residue Count: 163
Deposited Residue Count: 188
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polymerase basic protein 2	A	188	Influenza A virus	Mutation(s): 0 Gene Names: PB2
UniProt
Find proteins for Q6DNL8 (Influenza A virus (strain A/Chicken/Hong Kong/YU22/2002 H5N1 genotype Z)) Explore Q6DNL8 Go to UniProtKB: Q6DNL8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6DNL8
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 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 B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE C₁₁ H₂₀ N₅ O₁₄ P₃ BUJQMJUTTBGELS-KQYNXXCUSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.72 Å
R-Value Free: 0.206 (Depositor), 0.206 (DCC)
R-Value Work: 0.182 (Depositor), 0.183 (DCC)
R-Value Observed: 0.185 (Depositor)

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.75	α = 90
b = 81.75	β = 90
c = 55.009	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
PHENIX	phasing
XSCALE	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-01-29

Deposition Author(s):

Funding Organization	Location	Grant Number
Helmholtz Association	Germany	--
German Federal Ministry for Education and Research	Germany	--

Revision History (Full details and data files)

Version 1.0: 2025-01-29
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.