[English] 日本語
Yorodumi
- EMDB-44989: Structure of influenza A RNP, 4xNP local reconstruction, class 4 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-44989
TitleStructure of influenza A RNP, 4xNP local reconstruction, class 4
Map datafluA RNP STA class 4 composite map with local averaging of each NP subunit
Sample
  • Complex: Influenza A virus RNP complex
    • Protein or peptide: Nucleoprotein
    • RNA: viral RNA
KeywordsInfluenza / Ribonucleoprotein complex / nucleoprotein / VIRAL PROTEIN-RNA complex
Function / homology
Function and homology information


helical viral capsid / viral penetration into host nucleus / host cell / viral nucleocapsid / symbiont entry into host cell / ribonucleoprotein complex / host cell nucleus / structural molecule activity / RNA binding
Similarity search - Function
Influenza virus nucleoprotein (NP) / Influenza virus nucleoprotein
Similarity search - Domain/homology
Biological speciesInfluenza A virus
Methodsubtomogram averaging / cryo EM / Resolution: 9.2 Å
AuthorsPeng R / Chang Y-W
Funding support United States, 1 items
OrganizationGrant numberCountry
David and Lucile Packard Foundation2019-69645 United States
CitationJournal: Science / Year: 2025
Title: Molecular basis of influenza ribonucleoprotein complex assembly and processive RNA synthesis.
Authors: Ruchao Peng / Xin Xu / Binod Nepal / Yikang Gong / Fenglin Li / Max B Ferretti / Mingyang Zhou / Kristen W Lynch / George M Burslem / Sandhya Kortagere / Ronen Marmorstein / Yi-Wei Chang /
Abstract: Influenza viruses replicate and transcribe their genome in the context of a conserved ribonucleoprotein (RNP) complex. By integrating cryo-electron microscopy single-particle analysis and cryo- ...Influenza viruses replicate and transcribe their genome in the context of a conserved ribonucleoprotein (RNP) complex. By integrating cryo-electron microscopy single-particle analysis and cryo-electron tomography, we define the influenza RNP as a right-handed, antiparallel double helix with the viral RNA encapsidated in the minor groove. Individual nucleoprotein subunits are connected by a flexible tail loop that inserts into a conserved pocket in its neighbor. We visualize the viral polymerase in RNP at different functional states, revealing how it accesses the RNA template while maintaining the double-helical architecture of RNP by strand sliding. Targeting the tail loop binding interface, we identify lead compounds as potential anti-influenza inhibitors. These findings elucidate the molecular determinants underpinning influenza virus replication and highlight a promising target for antiviral development.
History
DepositionMay 22, 2024-
Header (metadata) releaseMay 14, 2025-
Map releaseMay 14, 2025-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_44989.png

Downloads & links

-
Map

FileDownload / File: emd_44989.map.gz / Format: CCP4 / Size: 1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationfluA RNP STA class 4 composite map with local averaging of each NP subunit
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.72 Å/pix.
x 64 pix.
= 174.08 Å		2.72 Å/pix.
x 64 pix.
= 174.08 Å		2.72 Å/pix.
x 64 pix.
= 174.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.72 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.49
Minimum - Maximum-0.4842735 - 1.4919233
Average (Standard dev.)0.07285994 (±0.14765567)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions646464
Spacing646464
CellA=B=C: 174.08 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: sharpened map without local averaging

Fileemd_44989_additional_1.map
Annotationsharpened map without local averaging
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half 2

Fileemd_44989_half_map_1.map
Annotationhalf 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half 1

Fileemd_44989_half_map_2.map
Annotationhalf 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Influenza A virus RNP complex

EntireName: Influenza A virus RNP complex
Components
  • Complex: Influenza A virus RNP complex
    • Protein or peptide: Nucleoprotein
    • RNA: viral RNA

-
Supramolecule #1: Influenza A virus RNP complex

SupramoleculeName: Influenza A virus RNP complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Influenza A virus
Molecular weightTheoretical: 3 MDa

-
Macromolecule #1: Nucleoprotein

MacromoleculeName: Nucleoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus
Molecular weightTheoretical: 56.454793 KDa
SequenceString: MATKGTKRSY EQMETDGERQ NATEIRASVG KMIDGIGRFY IQMCTELKLS DYEGRLIQNS LTIERMVLSA FDERRNKYLE EHPSAGKDP KKTGGPIYRR VDGKWRRELI LYDKEEIRRI WRQANNGDDA TAGLTHMMIW HSNLNDATYQ RTRALVRTGM D PRMCSLMQ ...String:
MATKGTKRSY EQMETDGERQ NATEIRASVG KMIDGIGRFY IQMCTELKLS DYEGRLIQNS LTIERMVLSA FDERRNKYLE EHPSAGKDP KKTGGPIYRR VDGKWRRELI LYDKEEIRRI WRQANNGDDA TAGLTHMMIW HSNLNDATYQ RTRALVRTGM D PRMCSLMQ GSTLPRRSGA AGAAVKGVGT MVMELIRMIK RGINDRNFWR GENGRRTRIA YERMCNILKG KFQTAAQRTM VD QVRESRN PGNAEFEDLI FLARSALILR GSVAHKSCLP ACVYGSAVAS GYDFEREGYS LVGIDPFRLL QNSQVYSLIR PNE NPAHKS QLVWMACHSA AFEDLRVSSF IRGTKVVPRG KLSTRGVQIA SNENMETMES STLELRSRYW AIRTRSGGNT NQQR ASSGQ ISIQPTFSVQ RNLPFDRPTI MAAFTGNTEG RTSDMRTEII RLMESARPED VSFQGRGVFE LSDEKATSPI VPSFD MSNE GSYFFGDNAE EYDN

UniProtKB: Nucleoprotein

-
Macromolecule #2: viral RNA

MacromoleculeName: viral RNA / type: rna / ID: 2 / Number of copies: 2
Source (natural)Organism: Influenza A virus
Molecular weightTheoretical: 18.32499 KDa
SequenceString:
UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4 / Details: 1x PBS
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE-PROPANE / Instrument: LEICA EM GP

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 1 / Average electron dose: 3.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.0 µm / Nominal magnification: 64000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 9.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number subtomograms used: 7749
ExtractionNumber tomograms: 289 / Number images used: 126276 / Software - Name: Warp (ver. 1.09)
CTF correctionSoftware - Name: Warp (ver. 1.09) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final 3D classificationNumber classes: 6 / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

8pzq


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross-correlation coefficient
Output model

PDB-9bx0:
Structure of influenza A RNP, 4xNP local reconstruction, class 4

+
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://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