4ENF

Crystal structure of the cap-binding domain of polymerase basic protein 2 from influenza virus A/Puerto Rico/8/34(h1n1)

PDB DOI: https://doi.org/10.2210/pdb4ENF/pdb

Classification: TRANSCRIPTION
Organism(s): Influenza A virus (A/Puerto Rico/8/1934(H1N1))
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-04-13 Released: 2013-03-06
Deposition Author(s): Meng, G., Liu, Y., Zheng, X.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.32 ?
R-Value Free: 0.172
R-Value Work: 0.127
R-Value Observed: 0.130

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structural and functional characterization of K339T substitution identified in the PB2 subunit cap-binding pocket of influenza A virus

Liu, Y., Qin, K., Meng, G., Zhang, J., Zhou, J., Zhao, G., Luo, M., Zheng, X.

(2013) J Biol Chem 288: 11013-11023

PubMed: 23436652 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1074/jbc.M112.392878
Primary Citation of Related Structures:
4ENF, 4EQK, 4ES5

PubMed Abstract:
Influenza virus RNA-dependent RNA polymerase is a heterotrimer composed of PA, PB1, and PB2 subunits. RNA-dependent RNA polymerase is required for both transcription and replication of influenza viral RNA taking place in the nucleus of infected cells. A "cap-snatching" mechanism is used to generate a 5'-capped primer for transcription in which the cap-binding domain of PB2 (PB2cap) captures the 5' cap of the host pre-mRNA. Our statistical analysis of PB2 sequences showed that residue Lys(339) located in the cap-binding pocket of H5N1 PB2cap was gradually replaced by Thr(339) over the past decade. To understand the role of this amino acid polymorphism, we solved the crystal structures of PB2cap with or without a pre-mRNA cap analog, m(7)GTP, in the presence of Lys(339) or Thr(339). The structures showed that Lys(339) contributes to binding the γ-phosphate group of m(7)GTP, and the replacement of Lys(339) by Thr eliminates this interaction. Isothermal titration calorimetry analysis showed that Thr(339) attenuated the PB2cap cap binding activity in vitro compared with Lys(339). Further functional studies confirmed that Thr(339)-PB2-containing ribonucleoprotein complex has a reduced influenza polymerase activity and RNA synthesis activity, and a reconstituted H5N1 virus containing the Thr(339) substitution exhibited a lower virulence to mice but more active replication in Madin-Darby canine kidney cells. The K339T substitution in the cap-binding pocket of PB2 modulates the polymerase activity and virulence by regulating the cap binding activity. It is informative to track variations in the cap-binding pocket of PB2 in surveillance of the evolution and spread of influenza virus.

Organizational Affiliation

State Key Lab of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China.

Macromolecule Content

Total Structure Weight: 19.61 kDa
Atom Count: 1,581
Modelled Residue Count: 164
Deposited Residue Count: 170
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polymerase basic protein 2	A	170	Influenza A virus (A/Puerto Rico/8/1934(H1N1))	Mutation(s): 0 Gene Names: PB2
UniProt
Find proteins for P03428 (Influenza A virus (strain A/Puerto Rico/8/1934 H1N1)) Explore P03428 Go to UniProtKB: P03428
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P03428
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BU1 Query on BU1 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	D [auth A], E [auth A]	1,4-BUTANEDIOL C₄ H₁₀ O₂ WERYXYBDKMZEQL-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]
NO3 Query on NO3 Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.32 ?
R-Value Free: 0.172
R-Value Work: 0.127
R-Value Observed: 0.130
Space Group: P 1

Unit Cell:

Length ( ? )	Angle ( ? )
a = 29.489	α = 71.1
b = 37.044	β = 69.84
c = 38.335	γ = 75.85

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2013-03-06

Deposition Author(s):

Meng, G.

Liu, Y.

Zheng, X.

Revision History (Full details and data files)

Version 1.0: 2013-03-06
Type: Initial release
Version 1.1: 2013-07-17
Changes: Database references
Version 1.2: 2024-03-20
Changes: Data collection, Database references, Derived calculations