[English] 日本語
Yorodumi
- EMDB-64768: Coupling of polymerase-nucleoprotein-RNA in an influenza virus mi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-64768
TitleCoupling of polymerase-nucleoprotein-RNA in an influenza virus mini ribonucleoprotein complex
Map data
Sample
  • Complex: FluPol_State Out
    • Protein or peptide: Polymerase acidic protein
    • Protein or peptide: RNA-directed RNA polymerase catalytic subunit
    • Protein or peptide: Polymerase basic protein 2
    • RNA: RNA (5'-R(P*CP*AP*CP*CP*CP*UP*GP*CP*U)-3')
    • RNA: RNA (5'-R(P*AP*GP*UP*AP*GP*AP*AP*AP*CP*AP*AP*GP*GP*GP*UP*G)-3')
KeywordsInfluenza virus / ribonucleoprotein complex / polymerase / cryo-EM / VIRAL PROTEIN/RNA / VIRAL PROTEIN-RNA complex
Function / homology
Function and homology information


cap snatching / viral transcription / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / 7-methylguanosine mRNA capping / host cell mitochondrion / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / virion component / endonuclease activity / Hydrolases; Acting on ester bonds / host cell cytoplasm ...cap snatching / viral transcription / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / 7-methylguanosine mRNA capping / host cell mitochondrion / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / virion component / endonuclease activity / Hydrolases; Acting on ester bonds / host cell cytoplasm / symbiont-mediated suppression of host gene expression / viral translational frameshifting / RNA-directed RNA polymerase / viral RNA genome replication / nucleotide binding / RNA-directed RNA polymerase activity / DNA-templated transcription / host cell nucleus / RNA binding / metal ion binding
Similarity search - Function
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-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 acidic protein / RNA-directed RNA polymerase catalytic subunit / Polymerase basic protein 2
Similarity search - Component
Biological speciesInfluenza A virus (A/Victoria/3/1975(H3N2))
Methodsingle particle reconstruction / cryo EM / Resolution: 3.62 Å
AuthorsKang H / Yang Y / Liu Y / Li M / Zhang L / Lin Y / Rao Z / Lou Z
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Coupling of polymerase-nucleoprotein-RNA in an influenza virus mini ribonucleoprotein complex
Authors: Kang H / Yang Y / Liu Y / Li M / Zhang L / Lin Y / Rao Z / Lou Z
History
DepositionMay 22, 2025-
Header (metadata) releaseOct 8, 2025-
Map releaseOct 8, 2025-
UpdateOct 8, 2025-
Current statusOct 8, 2025Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_64768.png

Downloads & links

-
Map

FileDownload / File: emd_64768.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 440 pix.
= 466.4 Å		1.06 Å/pix.
x 440 pix.
= 466.4 Å		1.06 Å/pix.
x 440 pix.
= 466.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.11
Minimum - Maximum-0.05595102 - 1.9222031
Average (Standard dev.)0.00034245738 (±0.01320213)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 466.39996 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_64768_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_64768_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : FluPol_State Out

EntireName: FluPol_State Out
Components
  • Complex: FluPol_State Out
    • Protein or peptide: Polymerase acidic protein
    • Protein or peptide: RNA-directed RNA polymerase catalytic subunit
    • Protein or peptide: Polymerase basic protein 2
    • RNA: RNA (5'-R(P*CP*AP*CP*CP*CP*UP*GP*CP*U)-3')
    • RNA: RNA (5'-R(P*AP*GP*UP*AP*GP*AP*AP*AP*CP*AP*AP*GP*GP*GP*UP*G)-3')

-
Supramolecule #1: FluPol_State Out

SupramoleculeName: FluPol_State Out / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Influenza A virus (A/Victoria/3/1975(H3N2))

-
Macromolecule #1: Polymerase acidic protein

MacromoleculeName: Polymerase acidic protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: Hydrolases; Acting on ester bonds
Source (natural)Organism: Influenza A virus (A/Victoria/3/1975(H3N2))
Molecular weightTheoretical: 82.998781 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEDFVRQCFN PMIVELAEKA MKEYGEDLKI ETNKFAAICT HLEVCFMYSD FHFINEQGES IVVELDDPNA LLKHRFEIIE GRDRTMAWT VVNSICNTTG AEKPKFLPDL YDYKENRFIE IGVTRREVHI YYLEKANKIK SENTHIHIFS FTGEEMATKA D YTLDEESR ...String:
MEDFVRQCFN PMIVELAEKA MKEYGEDLKI ETNKFAAICT HLEVCFMYSD FHFINEQGES IVVELDDPNA LLKHRFEIIE GRDRTMAWT VVNSICNTTG AEKPKFLPDL YDYKENRFIE IGVTRREVHI YYLEKANKIK SENTHIHIFS FTGEEMATKA D YTLDEESR ARIKTRLFTI RQEMANRGLW DSFRQSERGE ETIEERFEIT GTMRRLADQS LPPNFSCLEN FRAYVDGFEP NG CIEGKLS QMSKEVNAKI EPFLKTTPRP IKLPDGPPCF QRSKFLLMDA LKLSIEDPSH EGEGIPLYDA IKCMRTFFGW KEP YIVKPH ERGINSNYLL SWKQVLAELQ DIENEEKIPR TKNMKKTSQL KWALGENMAP EKVDFDNCRD ISDLKQYDSD EPEL RSLSS WIQNEFNKAC ELTDSIWIEL DEIGEDVAPI EYIASMRRNY FTAEVSHCRA TEYIMKGVYI NTALLNASCA AMDDF QLIP MISKCRTKEG RRKTNLYGFI IKGRSHLRND TDVVNFVSME FSLTDPRLEP HKWEKYCVLE IGDMLLRSAI GQMSRP MFL YVRTNGTSKI KMKWGMEMRR CLLQSLQQIE SMIEAESSVK EKDMTKEFFE NKSETWPIGE SPKGVEEGSI GKVCRTL LA KSVFNSLYAS PQLEGFSAES RKLLLVVQAL RDNLEPGTFD LGGLYEAIEE CLINDPWVLL NASWFNSFLT HALR

UniProtKB: Polymerase acidic protein

-
Macromolecule #2: RNA-directed RNA polymerase catalytic subunit

MacromoleculeName: RNA-directed RNA polymerase catalytic subunit / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA-directed RNA polymerase
Source (natural)Organism: Influenza A virus (A/Victoria/3/1975(H3N2))
Molecular weightTheoretical: 86.578172 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDVNPTLLFL KVPAQNAIST TFPYTGDPPY SHGTGTGYTM DTVNRTHQYS EKGKWTTNTE TGAPQLNPID GPLPEDNEPS GYAQTDCVL EAMAFLEESH PGIFENSCLE TMEVVQQTRV DRLTQGRQTY DWTLNRNQPA ATALANTIEV FRSNGLTANE S GRLIDFLK ...String:
MDVNPTLLFL KVPAQNAIST TFPYTGDPPY SHGTGTGYTM DTVNRTHQYS EKGKWTTNTE TGAPQLNPID GPLPEDNEPS GYAQTDCVL EAMAFLEESH PGIFENSCLE TMEVVQQTRV DRLTQGRQTY DWTLNRNQPA ATALANTIEV FRSNGLTANE S GRLIDFLK DVIESMDKEE MEITTHFQRK RRVRDNMTKK MVTQRTIGKK KQRVNKRSYL IRALTLNTMT KDAERGKLKR RA IATPGMQ IRGFVYFVET LARSICEKLE QSGLPVGGNE KKAKLANVVR KMMTNSQDTE LSFTITGDNT KWNENQNPRM FLA MITYIT KNQPEWFRNI LSIAPIMFSN KMARLGKGYM FESKRMKLRT QIPAEMLASI DLKYFNESTR KKIEKIRPLL IDGT ASLSP GMMMGMFNML STVLGVSILN LGQKKYTKTT YWWDGLQSSD DFALIVNAPN HEGIQAGVDR FYRTCKLVGI NMSKK KSYI NRTGTFEFTS FFYRYGFVAN FSMELPSFGV SGINESADMS IGVTVIKNNM INNDLGPATA QMALQLFIKD YRYTYR CHR GDTQIQTRRS FELKKLWEQT RSKAGLLVSD GGPNLYNIRN LHIPEVCLKW ELMDEDYQGR LCNPLNPFVS HKEIESV NN AVVMPAHGPA KSMEYDAVAT THSWIPKRNR SILNTSQRGI LEDEQMYQKC CNLFEKFFPS SSYRRPVGIS SMVEAMVS R ARIDARIDFE SGRIKKEEFS EIMKICSTIE ELRRQK

UniProtKB: RNA-directed RNA polymerase catalytic subunit

-
Macromolecule #3: Polymerase basic protein 2

MacromoleculeName: Polymerase basic protein 2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus (A/Victoria/3/1975(H3N2))
Molecular weightTheoretical: 86.243445 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MERIKELRNL MSQSRTREIL TKTTVDHMAI IKKYTSGRQE KNPSLRMKWM MAMKYPITAD KRITEMVPER NEQGQTLWSK MSDAGSDRV MVSPLAVTWW NRNGPVTSTV HYPKVYKTYF DKVERLKHGT FGPVHFRNQV KIRRRVDINP GHADLSAKEA Q DVIMEVVF ...String:
MERIKELRNL MSQSRTREIL TKTTVDHMAI IKKYTSGRQE KNPSLRMKWM MAMKYPITAD KRITEMVPER NEQGQTLWSK MSDAGSDRV MVSPLAVTWW NRNGPVTSTV HYPKVYKTYF DKVERLKHGT FGPVHFRNQV KIRRRVDINP GHADLSAKEA Q DVIMEVVF PNEVGARILT SESQLTITKE KKEELQDCKI SPLMVAYMLE RELVRKTRFL PVAGGTSSVY IEVLHLTQGT CW EQMYTPG GEVRNDDIDQ SLIIAARNIV RRASVSADPL ASLLEMCHST QIGGTRMVDI LRQNPTEEQA VDICKAAMGL RIS SSFSFG GFTFKRTSGS SIKREEEVLT GNLQTLKIRV HEGYEEFTMV GKRATAILRK ATRRLVQLIV SGRDEQSIAE AIIV AMVFS QEDCMIKAVR GDLNFVNRAN QRLNPMHQLL RHFQKDAKVL FQNWGIEHID NVMGMVGVLP DMTPSTEMSM RGIRV SKMG VDEYSSTERV VVSIDRFLRV RDQRGNVLLS PEEVSETHGT ERLTITYSSS MMWEINGPES VLVNTYQWII RNWETV KIQ WSQNPTMLYN KMEFEPFQSL VPKAIRGQYS GFVRTLFQQM RDVLGTFDTT QIIKLLPFAA APPKQSRMQF SSLTVNV RG SGMRILVRGN SPVFNYNKTT KRLTILGKDA GTLIEDPDES TSGVESAVLR GFLILGKEDR RYGPALSINE LSNLAKGE K ANVLIGQGDV VLVMKRKRDS SILTDSQTAT KRIRMAIN

UniProtKB: Polymerase basic protein 2

-
Macromolecule #4: RNA (5'-R(P*CP*AP*CP*CP*CP*UP*GP*CP*U)-3')

MacromoleculeName: RNA (5'-R(P*CP*AP*CP*CP*CP*UP*GP*CP*U)-3') / type: rna / ID: 4 / Number of copies: 1
Source (natural)Organism: Influenza A virus (A/Victoria/3/1975(H3N2))
Molecular weightTheoretical: 2.767695 KDa
SequenceString:
CACCCUGCU

-
Macromolecule #5: RNA (5'-R(P*AP*GP*UP*AP*GP*AP*AP*AP*CP*AP*AP*GP*GP*GP*UP*G)-3')

MacromoleculeName: RNA (5'-R(P*AP*GP*UP*AP*GP*AP*AP*AP*CP*AP*AP*GP*GP*GP*UP*G)-3')
type: rna / ID: 5 / Number of copies: 1
Source (natural)Organism: Influenza A virus (A/Victoria/3/1975(H3N2))
Molecular weightTheoretical: 5.248232 KDa
SequenceString:
AGUAGAAACA AGGGUG

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.62 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 112185
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: PROJECTION MATCHING

+
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