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- EMDB-35866: PKR and NS1 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-35866
TitlePKR and NS1 complex
Map data
Sample
  • Complex: PKR and NS1 complex
    • Protein or peptide: Interferon-induced, double-stranded RNA-activated protein kinase
    • Protein or peptide: Non-structural protein 1
KeywordsPKR / NS1 / PKR and NS1 complex / VIRUS / TRANSFERASE-VIRAL PROTEIN complex
Function / homology
Function and homology information


regulation of NLRP3 inflammasome complex assembly / Inhibition of PKR / eukaryotic translation initiation factor 2alpha kinase activity / symbiont-mediated suppression of host mRNA processing / response to interferon-alpha / negative regulation of osteoblast proliferation / symbiont-mediated suppression of host PKR/eIFalpha signaling / regulation of hematopoietic progenitor cell differentiation / positive regulation of stress-activated MAPK cascade / protein phosphatase regulator activity ...regulation of NLRP3 inflammasome complex assembly / Inhibition of PKR / eukaryotic translation initiation factor 2alpha kinase activity / symbiont-mediated suppression of host mRNA processing / response to interferon-alpha / negative regulation of osteoblast proliferation / symbiont-mediated suppression of host PKR/eIFalpha signaling / regulation of hematopoietic progenitor cell differentiation / positive regulation of stress-activated MAPK cascade / protein phosphatase regulator activity / SUMOylation of immune response proteins / regulation of hematopoietic stem cell differentiation / regulation of hematopoietic stem cell proliferation / protein serine/threonine kinase inhibitor activity / negative regulation of viral genome replication / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / positive regulation of chemokine production / endoplasmic reticulum unfolded protein response / antiviral innate immune response / cellular response to amino acid starvation / positive regulation of cytokine production / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / response to virus / PKR-mediated signaling / Evasion by RSV of host interferon responses / ISG15 antiviral mechanism / positive regulation of non-canonical NF-kappaB signal transduction / double-stranded RNA binding / Interferon alpha/beta signaling / kinase activity / positive regulation of NF-kappaB transcription factor activity / defense response to virus / host cell cytoplasm / protein autophosphorylation / positive regulation of MAPK cascade / negative regulation of translation / non-specific serine/threonine protein kinase / protein kinase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / ribosome / protein phosphorylation / translation / negative regulation of cell population proliferation / protein serine kinase activity / protein serine/threonine kinase activity / virus-mediated perturbation of host defense response / negative regulation of apoptotic process / host cell nucleus / perinuclear region of cytoplasm / RNA binding / nucleoplasm / ATP binding / identical protein binding / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
EIF2AK2, first double-stranded RNA binding domain / EIF2AK2, second double-stranded RNA binding domain / Influenza A virus NS1 protein / Influenza A virus NS1, effector domain-like superfamily / Influenza non-structural protein (NS1) / Influenza non-structural protein (NS1) / : / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. ...EIF2AK2, first double-stranded RNA binding domain / EIF2AK2, second double-stranded RNA binding domain / Influenza A virus NS1 protein / Influenza A virus NS1, effector domain-like superfamily / Influenza non-structural protein (NS1) / Influenza non-structural protein (NS1) / : / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / S15/NS1, RNA-binding / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Interferon-induced, double-stranded RNA-activated protein kinase / Non-structural protein 1
Similarity search - Component
Biological speciesHomo sapiens (human) / Influenza A virus (strain A/Memphis/102/1972 H3N2)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.67 Å
AuthorsHan CW / Kim HJ
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of PKR and NS1 complex
Authors: Han CW
History
DepositionApr 7, 2023-
Header (metadata) releaseApr 10, 2024-
Map releaseApr 10, 2024-
UpdateApr 10, 2024-
Current statusApr 10, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35866.png

Downloads & links

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Map

FileDownload / File: emd_35866.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.14 Å/pix.
x 256 pix.
= 292.864 Å		1.14 Å/pix.
x 256 pix.
= 292.864 Å		1.14 Å/pix.
x 256 pix.
= 292.864 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.144 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0596
Minimum - Maximum-0.6754777 - 0.8869757
Average (Standard dev.)0.00024075221 (±0.030573979)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 292.864 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_35866_additional_1.map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_35866_half_map_1.map
Projections & Slices
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Histogram

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Half map: #2

Fileemd_35866_half_map_2.map
Projections & Slices
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Sample components

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Entire : PKR and NS1 complex

EntireName: PKR and NS1 complex
Components
  • Complex: PKR and NS1 complex
    • Protein or peptide: Interferon-induced, double-stranded RNA-activated protein kinase
    • Protein or peptide: Non-structural protein 1

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Supramolecule #1: PKR and NS1 complex

SupramoleculeName: PKR and NS1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Interferon-induced, double-stranded RNA-activated protein kinase

MacromoleculeName: Interferon-induced, double-stranded RNA-activated protein kinase
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 19.705418 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSHMEMAGDL SAGFFMEELN TYRQKQGVVL KYQELPNSGP PHDRRFTFQV IIDGREFPEG EGRSKKEAKN AAAKLAVEIL NKEKKAVSP LLLTTTNSSE GLSMGNYIGL INRIAQKKRL TVNYEQCASG VHGPEGFHYK CKMGQKEYSI GTGSTKQEAK Q LAAKLAYL QILSEETGSG C

UniProtKB: Interferon-induced, double-stranded RNA-activated protein kinase

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Macromolecule #2: Non-structural protein 1

MacromoleculeName: Non-structural protein 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus (strain A/Memphis/102/1972 H3N2)
Molecular weightTheoretical: 13.795988 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
TPASRYITDM TIEELSRDWF MLMPKQKVEG PLCIRIDQAI MDKNIMLKAN FSVIFDRLET LILLRAFTEE GAIVGEISPL PSFPGHTIE DVKNAIGVLI GGLEWNDNTV RVSKTLQRFA WGS

UniProtKB: Non-structural protein 1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.8
GridModel: Quantifoil R2/2 / Material: GOLD / Mesh: 200
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 39.99 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.8 µm

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3ee8

Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.67 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 49802
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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