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- PDB-8y7o: FluPol-NS2 complex (hexamer) -

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Basic information

Entry
Database: PDB / ID: 8y7o
TitleFluPol-NS2 complex (hexamer)
Components
  • Nuclear export protein
  • Polymerase acidic protein
  • Polymerase basic protein 2
  • RNA-directed RNA polymerase catalytic subunit
KeywordsPROTEIN BINDING
Function / homology
Function and homology information


exit of virus from host cell nucleus through nuclear pore / RNA export from nucleus / cap snatching / viral transcription / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / host cell mitochondrion / 7-methylguanosine mRNA capping / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / virion component / endonuclease activity ...exit of virus from host cell nucleus through nuclear pore / RNA export from nucleus / cap snatching / viral transcription / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / host cell mitochondrion / 7-methylguanosine mRNA capping / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / virion component / endonuclease activity / host cell cytoplasm / Hydrolases; Acting on ester bonds / RNA-directed RNA polymerase / viral translational frameshifting / viral RNA genome replication / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / nucleotide binding / DNA-templated transcription / host cell nucleus / RNA binding / metal ion binding
Similarity search - Function
Influenza nuclear export protein NS2 / Influenza non-structural protein (NS2) / Influenza RNA-dependent RNA polymerase subunit PB2 / PB2, C-terminal / Influenza RNA-dependent RNA polymerase subunit PB1 / Influenza RNA-dependent RNA polymerase subunit PB1 / : / : / Influenza RNA polymerase PB2 N-terminal region / Influenza RNA polymerase PB2 second domain ...Influenza nuclear export protein NS2 / Influenza non-structural protein (NS2) / Influenza RNA-dependent RNA polymerase subunit PB2 / PB2, C-terminal / Influenza RNA-dependent RNA polymerase subunit PB1 / Influenza RNA-dependent RNA polymerase subunit PB1 / : / : / Influenza RNA polymerase PB2 N-terminal region / Influenza RNA polymerase PB2 second domain / : / : / Influenza RNA polymerase PB2 middle domain / Influenza RNA polymerase PB2 C-terminal domain / : / Influenza RNA polymerase PB2 6th domain / : / Influenza RNA polymerase PB2 CAP binding domain / : / Influenza RNA polymerase PB2 helical domain / Polymerase acidic protein / Influenza RNA-dependent RNA polymerase subunit PA / Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain / Influenza RNA-dependent RNA polymerase subunit PA / RNA-directed RNA polymerase, negative-strand RNA virus / RdRp of negative ssRNA viruses with segmented genomes catalytic domain profile.
Similarity search - Domain/homology
Polymerase basic protein 2 / Polymerase acidic protein / RNA-directed RNA polymerase catalytic subunit / Nuclear export protein
Similarity search - Component
Biological speciesInfluenza A virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsPeng, Q. / Sun, J.Q.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81871658 China
National Natural Science Foundation of China (NSFC)32192452 China
CitationJournal: To Be Published
Title: NS2 stabilizes polymerase hexamer to regulate transcription-replication switch of influenza A virus
Authors: Peng, Q. / Sun, J.Q.
History
DepositionFeb 4, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 24, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: Polymerase acidic protein
F: RNA-directed RNA polymerase catalytic subunit
A: Polymerase acidic protein
B: RNA-directed RNA polymerase catalytic subunit
C: Polymerase basic protein 2
S: Nuclear export protein
T: Nuclear export protein
I: Polymerase acidic protein
H: RNA-directed RNA polymerase catalytic subunit
L: Polymerase acidic protein
J: RNA-directed RNA polymerase catalytic subunit
K: Polymerase basic protein 2
U: Nuclear export protein
V: Nuclear export protein
Q: Polymerase acidic protein
R: RNA-directed RNA polymerase catalytic subunit
M: Polymerase acidic protein
N: RNA-directed RNA polymerase catalytic subunit
O: Polymerase basic protein 2
W: Nuclear export protein
X: Nuclear export protein
D: Polymerase basic protein 2
G: Polymerase basic protein 2
P: Polymerase basic protein 2


Theoretical massNumber of molelcules
Total (without water)1,650,00524
Polymers1,650,00524
Non-polymers00
Water00
1
E: Polymerase acidic protein
F: RNA-directed RNA polymerase catalytic subunit
A: Polymerase acidic protein
B: RNA-directed RNA polymerase catalytic subunit
C: Polymerase basic protein 2
S: Nuclear export protein
T: Nuclear export protein
D: Polymerase basic protein 2


Theoretical massNumber of molelcules
Total (without water)550,0028
Polymers550,0028
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_5551
2
I: Polymerase acidic protein
H: RNA-directed RNA polymerase catalytic subunit
L: Polymerase acidic protein
J: RNA-directed RNA polymerase catalytic subunit
K: Polymerase basic protein 2
U: Nuclear export protein
V: Nuclear export protein
G: Polymerase basic protein 2


Theoretical massNumber of molelcules
Total (without water)550,0028
Polymers550,0028
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_5551
3
Q: Polymerase acidic protein
R: RNA-directed RNA polymerase catalytic subunit
M: Polymerase acidic protein
N: RNA-directed RNA polymerase catalytic subunit
O: Polymerase basic protein 2
W: Nuclear export protein
X: Nuclear export protein
P: Polymerase basic protein 2


Theoretical massNumber of molelcules
Total (without water)550,0028
Polymers550,0028
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Polymerase acidic protein


Mass: 84625.414 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/nt/60/1968(H3N2)) / Strain: A/nt/60/1968(H3N2) / Gene: PA / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
References: UniProt: P03434, Hydrolases; Acting on ester bonds
#2: Protein
RNA-directed RNA polymerase catalytic subunit / Polymerase basic protein 1 / PB1


Mass: 86524.086 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Hong Kong/1/1968(H3N2))
Strain: A/Hong Kong/1/1968(H3N2) / Gene: PB1 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q910D6, RNA-directed RNA polymerase
#3: Protein
Polymerase basic protein 2 / RNA-directed RNA polymerase subunit P3


Mass: 89495.930 Da / Num. of mol.: 6 / Mutation: L691R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/nt/60/1968(H3N2)) / Strain: A/nt/60/1968(H3N2) / Gene: PB2 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P03429
#4: Protein
Nuclear export protein / NEP / Non-structural protein 2 / NS2


Mass: 14355.328 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Hong Kong/1/1968(H3N2))
Strain: A/Hong Kong/1/1968 H3N2 / Gene: NS / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q910E4

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1FluPol-NS2 complex (hexamer)COMPLEXall0RECOMBINANT
2FluPolCOMPLEX#1-#31RECOMBINANT
3NS2COMPLEX#41RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
23Influenza A virus (A/Aichi/2/1968(H3N2))387139
32Influenza A virus (A/Aichi/2/1968(H3N2))387139
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 0.001 mm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 351243 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00687770
ELECTRON MICROSCOPYf_angle_d0.546118294
ELECTRON MICROSCOPYf_dihedral_angle_d4.16711642
ELECTRON MICROSCOPYf_chiral_restr0.0412966
ELECTRON MICROSCOPYf_plane_restr0.00415217

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