[English] 日本語
Yorodumi
- PDB-8y7o: FluPol-NS2 complex (hexamer) -

+
Open data


ID or keywords:

Loading...

-
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 / 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 ...exit of virus from host cell nucleus through nuclear pore / 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 RNA genome replication / RNA-dependent RNA polymerase activity / nucleotide binding / virus-mediated perturbation of host defense response / 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 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 6th domain / Influenza RNA polymerase PB2 C-terminal 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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)

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more