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- EMDB-9580: structure of influenza D virus polymerase bound to vRNA promoter ... -

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Basic information

Entry
Database: EMDB / ID: EMD-9580
Titlestructure of influenza D virus polymerase bound to vRNA promoter in Mode B conformation (Class B2)
Map datastructure of influenza D virus polymerase bound to vRNA promoter in Mode B conformation(Class B2)
Sample
  • Complex: Influenza D virus polymerase bound to vRNA promoter in Mode B conformation (Class B2)
    • Protein or peptide: Polymerase 3
    • Protein or peptide: RNA-directed RNA polymerase catalytic subunit
    • Protein or peptide: Polymerase PB2
    • RNA: RNA (5'-R(P*CP*UP*CP*CP*UP*GP*CP*UP*UP*AP*UP*GP*CP*U)-3')
    • RNA: RNA (5'-R(P*AP*GP*CP*AP*GP*UP*AP*GP*CP*AP*AP*GP*GP*AP*G)-3')
Function / homology
Function and homology information


cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / host cell mitochondrion / 7-methylguanosine mRNA capping / virion component / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / nucleotide binding / DNA-templated transcription ...cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / host cell mitochondrion / 7-methylguanosine mRNA capping / virion component / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / nucleotide binding / DNA-templated transcription / host cell nucleus / RNA binding
Similarity search - Function
RNA-dependent RNA polymerase, bunyaviral / Bunyavirus RNA dependent RNA polymerase / 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 / : / : ...RNA-dependent RNA polymerase, bunyaviral / Bunyavirus RNA dependent RNA polymerase / 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 / 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
RNA-directed RNA polymerase catalytic subunit / Polymerase basic protein 2 / Polymerase 3
Similarity search - Component
Biological speciesThogotovirus / Influenza D virus / Influenza D virus (D/swine/Oklahoma/1334/2011) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsPeng Q / Peng R / Qi J / Gao GF / Shi Y
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB08020100 China
CitationJournal: Nat Microbiol / Year: 2019
Title: Structural insight into RNA synthesis by influenza D polymerase.
Authors: Qi Peng / Yuqian Liu / Ruchao Peng / Min Wang / Wei Yang / Hao Song / Yuhai Chen / Sheng Liu / Min Han / Xinzheng Zhang / Peiyi Wang / Jinghua Yan / Buchang Zhang / Jianxun Qi / Tao Deng / ...Authors: Qi Peng / Yuqian Liu / Ruchao Peng / Min Wang / Wei Yang / Hao Song / Yuhai Chen / Sheng Liu / Min Han / Xinzheng Zhang / Peiyi Wang / Jinghua Yan / Buchang Zhang / Jianxun Qi / Tao Deng / George F Gao / Yi Shi /
Abstract: The influenza virus polymerase uses capped RNA primers to initiate transcription, and a combination of terminal and internal de novo initiations for the two-step replication process by binding the ...The influenza virus polymerase uses capped RNA primers to initiate transcription, and a combination of terminal and internal de novo initiations for the two-step replication process by binding the conserved viral genomic RNA (vRNA) or complementary RNA (cRNA) promoter. Here, we determined the apo and promoter-bound influenza D polymerase structures using cryo-electron microscopy and found the polymerase has an evolutionarily conserved stable core structure with inherently flexible peripheral domains. Strikingly, two conformations (mode A and B) of the vRNA promoter were observed where the 3'-vRNA end can bind at two different sites, whereas the cRNA promoter only binds in the mode B conformation. Functional studies confirmed the critical role of the mode B conformation for vRNA synthesis via the intermediate cRNA but not for cRNA production, which is mainly regulated by the mode A conformation. Both conformations participate in the regulation of the transcription process. This work advances our understanding of the regulatory mechanisms for the synthesis of different RNA species by influenza virus polymerase and opens new opportunities for antiviral drug design.
History
DepositionJul 21, 2018-
Header (metadata) releaseJun 12, 2019-
Map releaseJun 12, 2019-
UpdateFeb 12, 2020-
Current statusFeb 12, 2020Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6kut
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9580.png

Downloads & links

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Map

FileDownload / File: emd_9580.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationstructure of influenza D virus polymerase bound to vRNA promoter in Mode B conformation(Class B2)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 180 pix.
= 244.8 Å		1.36 Å/pix.
x 180 pix.
= 244.8 Å		1.36 Å/pix.
x 180 pix.
= 244.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.36 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0298 / Movie #1: 0.035
Minimum - Maximum-0.21670844 - 0.34720275
Average (Standard dev.)0.0006595731 (±0.010945787)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 244.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.361.361.36
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z244.800244.800244.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-38-19-20
NX/NY/NZ858082
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS180180180
D min/max/mean-0.2170.3470.001

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Supplemental data

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Sample components

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Entire : Influenza D virus polymerase bound to vRNA promoter in Mode B con...

EntireName: Influenza D virus polymerase bound to vRNA promoter in Mode B conformation (Class B2)
Components
  • Complex: Influenza D virus polymerase bound to vRNA promoter in Mode B conformation (Class B2)
    • Protein or peptide: Polymerase 3
    • Protein or peptide: RNA-directed RNA polymerase catalytic subunit
    • Protein or peptide: Polymerase PB2
    • RNA: RNA (5'-R(P*CP*UP*CP*CP*UP*GP*CP*UP*UP*AP*UP*GP*CP*U)-3')
    • RNA: RNA (5'-R(P*AP*GP*CP*AP*GP*UP*AP*GP*CP*AP*AP*GP*GP*AP*G)-3')

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Supramolecule #1: Influenza D virus polymerase bound to vRNA promoter in Mode B con...

SupramoleculeName: Influenza D virus polymerase bound to vRNA promoter in Mode B conformation (Class B2)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Thogotovirus
Recombinant expressionOrganism: Spodoptera (butterflies/moths) / Recombinant cell: SF9
Molecular weightExperimental: 270 KDa

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Macromolecule #1: Polymerase 3

MacromoleculeName: Polymerase 3 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Influenza D virus
Molecular weightTheoretical: 83.036086 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSSVIREIAK RFLEQATINI AEEVVREYGD HERTMISVGV HFQACCLISD EYTLEDETTP RYVLLEGLKR QEAISKQNNI CSTLGLEPL RNLADIFDRK TRRFLEVGIT KRESDEYYQE KFNKIGNDMD IHVFTYEGKY FSNNPNGLED IQKTRIFTFL S FVSDELRK ...String:
MSSVIREIAK RFLEQATINI AEEVVREYGD HERTMISVGV HFQACCLISD EYTLEDETTP RYVLLEGLKR QEAISKQNNI CSTLGLEPL RNLADIFDRK TRRFLEVGIT KRESDEYYQE KFNKIGNDMD IHVFTYEGKY FSNNPNGLED IQKTRIFTFL S FVSDELRK ENMFTEMYVT EEGAPELEMY KSKLFIAMRD ESVPLPYINY EHLRTRCETF KRNQAECEAK VADVASRLKI KL EHLEENK LRPLEIPKEK EAPYTHKFLM KDAWFFAKPH DSERAQPQQI LYDFFEAANM GFMTTSPKPI FGKQGLMYHS LWG QTKRAI KDKRNELEPS EQRDFLCGIG RASKKIQEDK WQESREEEFK QEETKGAAKR GFPTWFNEEW LWAMRDSGDG DNKI GDWIP MAEMPPCKNE MEDYAKKMCE ELESKIQGTN CAREMSKLIH TIGSLHTECR NFPGKVKIVP IYCRGTLRGE STDCL FGIA IKGKSHLNKD DGMYTVVTFE FSTEEPNPSK HEKYTVFEAG TVPVEAVVLT PKRERVLKEK KLFLYCRTTG MSKLKN DWF SKCRRCLIPT METVEQIVLK ECALKEENRV SEMLENKRAW IAHENGENLT RLVSTKLKDL CRMLIVTQFY YCIYNDN QL EGFCNEQKKF LMFLQADKDS KSAFTFNQKG LYEKIEECIV SNPLCIFLAD RLNKLFLVAK SNGAKYFE

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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 D virus
Molecular weightTheoretical: 86.138844 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MEINPYLLML NNDITSMISL TYPYTGAPPM SHGTSTKYSM ETVSRTYSYS RTKKEVPSGI FPIERRKFCN TIEDKENLEK PNGNVDINF MLSLAEMLEE KMGKGFFKFC ANEAEAEILK MHFSKLTEGR QTYDWTSERN MPAATALQLT VDAIQETQGT F KGTTMVEY ...String:
MEINPYLLML NNDITSMISL TYPYTGAPPM SHGTSTKYSM ETVSRTYSYS RTKKEVPSGI FPIERRKFCN TIEDKENLEK PNGNVDINF MLSLAEMLEE KMGKGFFKFC ANEAEAEILK MHFSKLTEGR QTYDWTSERN MPAATALQLT VDAIQETQGT F KGTTMVEY CNKILEMMDW PEVKFKKVRM IVQRHWDPKT KKEIKMKSPT LMITKIGREE FIKRICTINT MAKDGERGKY KR RAIATPG MGIRPFSKIV ETLAQKICER LAESGLPVGG NEKKAKLKTT VSSTNSKLQE GQFMVNITGD NSKWNECQQP EAY LAMLAY ITKDSSNLMK DLCSVAPTLF CNKYVKMGQG FRAKNKRKTK EIVIPAKKMK ERKELMNAEW RDLFETIEPY MDGE CCFLG GGMLMGMFNM LSTVFGVMTL NYREEALARR NCYWTGLQSS DDFVLFCISR TWPEMEMTIL KFIAVCKLMG INMSL EKSY GCLPELFEFT SMFFSGDFVS NIALELPAFT TAGMNEGTDF TAAMSVIRTN MINNGLSPGT ALMALRICLQ EFRATY RVH PYDSGVKNHR MKIIRKFIET IENKDGLLIS DGGKLMNNIS SLHIPEEILK EDLMDPSYRN RVFNPRNPFT QFEKTVD IF KASGPIRVEE NEAVVSTHSF RTRSNRTLLN TDMRAMALEE KRYQVVCNMY RSVFESADVN TPIGSMSMGE AIEAKILD R ARTQFENGII GGEEYSEIKR LIEDAKRQRL SV

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Macromolecule #3: Polymerase PB2

MacromoleculeName: Polymerase PB2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Influenza D virus (D/swine/Oklahoma/1334/2011) / Strain: D/swine/Oklahoma/1334/2011
Molecular weightTheoretical: 88.480484 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSLLLTLAKE YANLTKDKKS CKLLSQGTVS SYTTFKKWTT SRKEKNPSLR MRWAMGSKFP IMANREILEE AGIPEQWEGI DLWSKKDDV SKLGMVLASP AAITYWNFCG PGVDNSSVIK DVYKAKFMKK ERWRETLWGP MNFELVGKQR RVVETQPVEI K LNQKEIKE ...String:
MSLLLTLAKE YANLTKDKKS CKLLSQGTVS SYTTFKKWTT SRKEKNPSLR MRWAMGSKFP IMANREILEE AGIPEQWEGI DLWSKKDDV SKLGMVLASP AAITYWNFCG PGVDNSSVIK DVYKAKFMKK ERWRETLWGP MNFELVGKQR RVVETQPVEI K LNQKEIKE LTMWVLFEDE ANLASKFIQE NFSLVLSLRE LYKGKAVNKD VAAFMIAHQF SPEKRFLPTF GPIRPERMEL LH CLGGDFW KIEAVTAGSL NEEQKKRDVR AVARKICLRA SVDLFTPAEK IRDYIASVTM RFGTVERTFE DVIRNSDDIS AEV TLCKAA LGCELGKSMS FGNLNLRKVS GEAETMEKTV YWGLKPIKYK CWRGEETFYC ELRKVTCMFR RSEGLDWANI GPGS PEERR ELLAMVMIFC RDGRFFESAP VNIDESFFRT RLNKEIPYQY VLLKWVRQSR DNLDALLSTR GLIPAHIGQF GKGMG IDGS SSSSMVYKGV MLSKTPIDIV ESKEKHRLFL NDNIEAVTER GAMVASIMDL SEDNRETFND VTFNHVDLAV LKDEKT AII KIYRSLVERI NTDDDGLPAL IMGKRYLELY QLDEVKDAVG LIPKRMLGAY SYQARQLIQS QIKNDSYSLP EIIKLLP FC YSPPKKMLFD GTFHFKNQMY VRPGINTNLF SFSKTDKSKI YVNGSAVKIK LVLGDDEMDT SLAFVEGFQV CEYDPRAP L IPRRDLRLIG FGKKVRVFVG QGQEKTLVRT SSKRAASHDV SKNIRRMRLE V

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

MacromoleculeName: RNA (5'-R(P*CP*UP*CP*CP*UP*GP*CP*UP*UP*AP*UP*GP*CP*U)-3')
type: rna / ID: 4 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 4.337563 KDa
SequenceString:
CUCCUGCUUA UGCU

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

MacromoleculeName: RNA (5'-R(P*AP*GP*CP*AP*GP*UP*AP*GP*CP*AP*AP*GP*GP*AP*G)-3')
type: rna / ID: 5 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 4.918042 KDa
SequenceString:
AGCAGUAGCA AGGAG

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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

Concentration0.8 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / 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
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4.1)
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6ab7
PDB Unreleased entry


Details: Influenza D virus plolymerase
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 53068
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.0)
Final 3D classificationSoftware - Name: RELION (ver. 2.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-6kut:
Structure of influenza D virus polymerase bound to vRNA promoter in Mode B conformation (Class B2)

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