[English] 日本語
Yorodumi
- EMDB-4512: Influenza B polymerase elongation complex -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: EMD-4512
TitleInfluenza B polymerase elongation complex
Map data
SampleInfluenza polzmerase elongation complex
  • Polymerase acidic protein
  • RNA-directed RNA polymerase catalytic subunit
  • Polymerase basic protein 2
  • (nucleic-acidNucleic acid) x 3
  • ligand
Function / homology
Function and homology information


cap snatching / suppression by virus of host RNA polymerase II activity / 7-methylguanosine mRNA capping / viral transcription / virion / ec:2.7.7.48: / viral RNA genome replication / endonuclease activity / RNA-directed 5'-3' RNA polymerase activity / host cell cytoplasm ...cap snatching / suppression by virus of host RNA polymerase II activity / 7-methylguanosine mRNA capping / viral transcription / virion / ec:2.7.7.48: / viral RNA genome replication / endonuclease activity / RNA-directed 5'-3' RNA polymerase activity / host cell cytoplasm / ec:3.1.-.-: / transcription, DNA-templated / host cell nucleus / nucleotide binding / RNA binding / metal ion binding
Influenza RNA-dependent RNA polymerase subunit PA / RdRp of negative ssRNA viruses with segmented genomes catalytic domain profile. / Influenza RNA-dependent RNA polymerase subunit PB2 / Influenza RNA-dependent RNA polymerase subunit PA / Influenza RNA-dependent RNA polymerase subunit PB1 / PA/PA-X superfamily / Polymerase acidic protein / PB2, C-terminal / RNA-directed RNA polymerase, negative-strand RNA virus / Influenza RNA-dependent RNA polymerase subunit PB2 / Influenza RNA-dependent RNA polymerase subunit PB1
RNA-directed RNA polymerase catalytic subunit / Polymerase acidic protein / Polymerase basic protein 2
Biological speciesInfluenza B virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsCusack S / Kouba T
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2019
Title: Structural snapshots of actively transcribing influenza polymerase.
Authors: Tomas Kouba / Petra Drncová / Stephen Cusack /
Abstract: Influenza virus RNA-dependent RNA polymerase uses unique mechanisms to transcribe its single-stranded genomic viral RNA (vRNA) into messenger RNA. The polymerase is initially bound to a promoter ...Influenza virus RNA-dependent RNA polymerase uses unique mechanisms to transcribe its single-stranded genomic viral RNA (vRNA) into messenger RNA. The polymerase is initially bound to a promoter comprising the partially base-paired 3' and 5' extremities of the RNA. A short, capped primer, 'cap-snatched' from a nascent host polymerase II transcript, is directed towards the polymerase active site to initiate RNA synthesis. Here we present structural snapshots, as determined by X-ray crystallography and cryo-electron microscopy, of actively initiating influenza polymerase as it transitions towards processive elongation. Unexpected conformational changes unblock the active site cavity to allow establishment of a nine-base-pair template-product RNA duplex before the strands separate into distinct exit channels. Concomitantly, as the template translocates, the promoter base pairs are broken and the template entry region is remodeled. These structures reveal details of the influenza polymerase active site that will help optimize nucleoside analogs or other compounds that directly inhibit viral RNA synthesis.
Validation ReportPDB-ID: 6qct

SummaryFull reportAbout validation report
DateDeposition: Dec 30, 2018 / Header (metadata) release: Apr 24, 2019 / Map release: Jun 5, 2019 / Update: Jun 19, 2019

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.2
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6qct
  • Surface level: 0.2
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_4512.map.gz / Format: CCP4 / Size: 115.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 312 pix.
= 259.303 Å
0.83 Å/pix.
x 312 pix.
= 259.303 Å
0.83 Å/pix.
x 312 pix.
= 259.303 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8311 Å
Density
Contour LevelBy AUTHOR: 0.2 / Movie #1: 0.2
Minimum - Maximum-0.14768311 - 0.25948656
Average (Standard dev.)0.00016624953 (±0.011908364)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions312312312
Spacing312312312
CellA=B=C: 259.3032 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.831099358974360.831099358974360.83109935897436
M x/y/z312312312
origin x/y/z0.0000.0000.000
length x/y/z259.303259.303259.303
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS312312312
D min/max/mean-0.2220.6950.003

-
Supplemental data

-
Sample components

+
Entire Influenza polzmerase elongation complex

EntireName: Influenza polzmerase elongation complex / Number of components: 10

+
Component #1: protein, Influenza polzmerase elongation complex

ProteinName: Influenza polzmerase elongation complex / Recombinant expression: No

+
Component #2: protein, Influenza polzmerase elongation complex

ProteinName: Influenza polzmerase elongation complex / Recombinant expression: No
SourceSpecies: Influenza B virus
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

+
Component #3: protein, Influenza polzmerase elongation complex

ProteinName: Influenza polzmerase elongation complex / Recombinant expression: No
SourceSpecies: Influenza B virus
Source (engineered)Expression System: synthetic construct (others)

+
Component #4: protein, Polymerase acidic protein

ProteinName: Polymerase acidic protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 85.822781 kDa
SourceSpecies: Influenza B virus
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

+
Component #5: protein, RNA-directed RNA polymerase catalytic subunit

ProteinName: RNA-directed RNA polymerase catalytic subunit / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 86.207016 kDa
SourceSpecies: Influenza B virus
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

+
Component #6: protein, Polymerase basic protein 2

ProteinName: Polymerase basic protein 2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 90.844109 kDa
SourceSpecies: Influenza B virus
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

+
Component #7: nucleic-acid, 5 end

nucleic acidName: 5 end / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
AGUAGUAACA AGAG
MassTheoretical: 4.55782 kDa
SourceSpecies: Influenza B virus

+
Component #8: nucleic-acid, 3 end

nucleic acidName: 3 end / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
UAUACCUCUG CUUCUGCUAU U
MassTheoretical: 6.52582 kDa
SourceSpecies: Influenza B virus

+
Component #9: nucleic-acid, capped RNA

nucleic acidName: capped RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
(GTG)AAUGCUAUA AUAGCAGAAG
MassTheoretical: 6.919171 kDa
SourceSpecies: Influenza B virus

+
Component #10: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 22 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 34000
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

-
Atomic model buiding

Output model

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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