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- EMDB-4190: A mechanism for the activation of the influenza virus transcriptase -

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Basic information

Entry
Database: EMDB / ID: EMD-4190
TitleA mechanism for the activation of the influenza virus transcriptase
Map dataEM map of influenza C virus RNA dependent RNA polymerase bound to promoter vRNA
Sample
  • Complex: Influenza C virus polymerase bound to promoter vRNA
    • Protein or peptide: Polymerase acidic protein
    • Protein or peptide: RNA-directed RNA polymerase catalytic subunit
    • Protein or peptide: Polymerase basic protein 2
    • RNA: 3' promoter vRNA
    • RNA: 5' promoter vRNA
Function / homology
Function and homology information


symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / cap snatching / 7-methylguanosine mRNA capping / viral transcription / host cell mitochondrion / virion component / endonuclease activity / host cell cytoplasm / Hydrolases; Acting on ester bonds / RNA-directed RNA polymerase ...symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / cap snatching / 7-methylguanosine mRNA capping / viral transcription / host cell mitochondrion / 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 / DNA-templated transcription / host cell nucleus / RNA binding / metal ion binding
Similarity search - Function
Influenza RNA-dependent RNA polymerase subunit PB1 / Influenza RNA-dependent RNA polymerase subunit PB1 / Influenza RNA-dependent RNA polymerase subunit PB2 / PB2, C-terminal / : / : / : / : / : / Influenza RNA polymerase PB2 N-terminal region ...Influenza RNA-dependent RNA polymerase subunit PB1 / Influenza RNA-dependent RNA polymerase subunit PB1 / Influenza RNA-dependent RNA polymerase subunit PB2 / PB2, C-terminal / : / : / : / : / : / 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 helical domain / Influenza RNA polymerase PB2 CAP binding domain / Polymerase acidic protein / RNA-directed RNA polymerase, negative-strand RNA virus / RdRp of negative ssRNA viruses with segmented genomes catalytic domain profile. / Influenza RNA-dependent RNA polymerase subunit PA / Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain / Influenza RNA-dependent RNA polymerase subunit PA
Similarity search - Domain/homology
Polymerase basic protein 2 / RNA-directed RNA polymerase catalytic subunit / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza B virus / Influenza B virus (B/Memphis/13/2003)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.8 Å
AuthorsSerna Martin I / Grimes JM
CitationJournal: Mol Cell / Year: 2018
Title: A Mechanism for the Activation of the Influenza Virus Transcriptase.
Authors: Itziar Serna Martin / Narin Hengrung / Max Renner / Jane Sharps / Mónica Martínez-Alonso / Simonas Masiulis / Jonathan M Grimes / Ervin Fodor /
Abstract: Influenza virus RNA polymerase (FluPol), a heterotrimer composed of PB1, PB2, and PA subunits (P3 in influenza C), performs both transcription and replication of the viral RNA genome. For ...Influenza virus RNA polymerase (FluPol), a heterotrimer composed of PB1, PB2, and PA subunits (P3 in influenza C), performs both transcription and replication of the viral RNA genome. For transcription, FluPol interacts with the C-terminal domain (CTD) of RNA polymerase II (Pol II), which enables FluPol to snatch capped RNA primers from nascent host RNAs. Here, we describe the co-crystal structure of influenza C virus polymerase (FluPol) bound to a Ser5-phosphorylated CTD (pS-CTD) peptide. The position of the CTD-binding site at the interface of PB1, P3, and the flexible PB2 C-terminal domains suggests that CTD binding stabilizes the transcription-competent conformation of FluPol. In agreement, both cap snatching and capped primer-dependent transcription initiation by FluPol are enhanced in the presence of pS-CTD. Mutations of amino acids in the CTD-binding site reduce viral mRNA synthesis. We propose a model for the activation of the influenza virus transcriptase through its association with pS-CTD of Pol II.
History
DepositionDec 2, 2017-
Header (metadata) releaseJan 17, 2018-
Map releaseJun 27, 2018-
UpdateJul 4, 2018-
Current statusJul 4, 2018Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0267
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.0267
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6f5o
  • Surface level: 0.0267
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4190.png

Downloads & links

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Map

FileDownload / File: emd_4190.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM map of influenza C virus RNA dependent RNA polymerase bound to promoter vRNA
Voxel sizeX=Y=Z: 1.35 Å
Density
Contour LevelBy AUTHOR: 0.0267 / Movie #1: 0.0267
Minimum - Maximum-0.07689935 - 0.114877686
Average (Standard dev.)0.0012038854 (±0.007842474)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 216.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z216.000216.000216.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.0770.1150.001

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Supplemental data

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Sample components

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Entire : Influenza C virus polymerase bound to promoter vRNA

EntireName: Influenza C virus polymerase bound to promoter vRNA
Components
  • Complex: Influenza C virus polymerase bound to promoter vRNA
    • Protein or peptide: Polymerase acidic protein
    • Protein or peptide: RNA-directed RNA polymerase catalytic subunit
    • Protein or peptide: Polymerase basic protein 2
    • RNA: 3' promoter vRNA
    • RNA: 5' promoter vRNA

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Supramolecule #1: Influenza C virus polymerase bound to promoter vRNA

SupramoleculeName: Influenza C virus polymerase bound to promoter vRNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Influenza B virus
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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Macromolecule #1: Polymerase acidic protein

MacromoleculeName: Polymerase acidic protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Influenza B virus
Molecular weightTheoretical: 83.232109 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: SMDTFITRNF QTTIIQKAKN TMAEFSEDPE LQPAMLFNIC VHLEVCYVIS DMNFLDEEGK AYTALEGQGK EQNLRPQYEV IEGMPRTIA WMVQRSLAQE HGIETPKYLA DLFDYKTKRF IEVGITKGLA DDYFWKKKEK LGNSMELMIF SYNQDYSLSN E SSLDEEGK ...String:
SMDTFITRNF QTTIIQKAKN TMAEFSEDPE LQPAMLFNIC VHLEVCYVIS DMNFLDEEGK AYTALEGQGK EQNLRPQYEV IEGMPRTIA WMVQRSLAQE HGIETPKYLA DLFDYKTKRF IEVGITKGLA DDYFWKKKEK LGNSMELMIF SYNQDYSLSN E SSLDEEGK GRVLSRLTEL QAELSLKNLW QVLIGEEDVE KGIDFKLGQT ISRLRDISVP AGFSNFEGMR SYIDNIDPKG AI ERNLARM SPLVSVTPKK LTWEDLRPIG PHIYNHELPE VPYNAFLLMS DELGLANMTE GKSKKPKTLA KECLEKYSTL RDQ TDPILI MKSEKANENF LWKLWRDCVN TISNEEMSNE LQKTNYAKWA TGDGLTYQKI MKEVAIDDET MCQEEPKIPN KCRV AAWVQ TEMNLLSTLT SKRALDLPEI GPDVAPVEHV GSERRKYFVN EINYCKASTV MMKYVLFHTS LLNESNASMG KYKVI PITN RVVNEKGESF DMLYGLAVKG QSHLRGDTDV VTVVTFEFSS TDPRVDSGKW PKYTVFRIGS LFVSGREKSV YLYCRV NGT NKIQMKWGME ARRCLLQSMQ QMEAIVEQES SIQGYDMTKA CFKGDRVNSP KTFSIGTQEG KLVKGSFGKA LRVIFTK CL MHYVFGNAQL EGFSAESRRL LLLIQALKDR KGPWVFDLEG MYSGIEECIS NNPWVIQSAY WFNEWLGFEK EGSKVLES V DEIMDE

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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 B virus
Molecular weightTheoretical: 84.433266 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MNINPYFLFI DVPIQAAIST TFPYTGVPPY SHGTGTGYTI DTVIRTHEYS NKGKQYISDV TGCTMVDPTN GPLPEDNEPS AYAQLDCVL EALDRMDEEH PGLFQAASQN AMETLMVTTV DKLTQGRQTF DWTVCRNQPA ATALNTTITS FRLNDLNGAD K GGLIPFCQ ...String:
MNINPYFLFI DVPIQAAIST TFPYTGVPPY SHGTGTGYTI DTVIRTHEYS NKGKQYISDV TGCTMVDPTN GPLPEDNEPS AYAQLDCVL EALDRMDEEH PGLFQAASQN AMETLMVTTV DKLTQGRQTF DWTVCRNQPA ATALNTTITS FRLNDLNGAD K GGLIPFCQ DIIDSLDRPE MTFFSVKNIK KKLPAKNRKG FLIKRIPMKV KDKITKVEYI KRALSLNTMT KDAERGKLKR RA IATAGIQ IRGFVLVVEN LAKNICENLE QSGLPVGGNE KKAKLSNAVA KMLSNCPPGG ISMTVTGDNT KWNECLNPRI FLA MTERIT RDSPIWFRDF CSIAPVLFSN KIARLGKGFM ITSKTKRLKA QIPCPDLFSI PLERYNEETR AKLKKLKPFF NEEG TASLS PGMMMGMFNM LSTVLGVAAL GIKNIGNKEY LWDGLQSSDD FALFVNAKDE ETCMEGINDF YRTCKLLGIN MSKKK SYCN ETGMFEFTSM FYRDGFVSNF AMELPSFGVA GVNESADMAI GMTIIKNNMI NNGMGPATAQ TAIQLFIADY RYTYKC HRG DSKVEGKRMK IIKELWENTK GRDGLLVADG GPNIYNLRNL HIPEIVLKYN LMDPEYKGRL LHPQNPFVGH LSIEGIK EA DITPAHGPVK KMDYDAVSGT HSWRTKRNRS ILNTDQRNMI LEEQCYAKCC NLFEACFNSA SYRKPVGQHS MLEAMAHR L RMDARLDYES GRMSKDDFEK AMAHLGEIGY I

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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 B virus
Molecular weightTheoretical: 88.028211 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MTLAKIELLK QLLRDNEAKT VLKQTTVDQY NIIRKFNTSR IEKNPSLRMK WAMCSNFPLA LTKGDMANRI PLEYKGIQLK TNAEDIGTK GQMCSIAAVT WWNTYGPIGD TEGFERVYES FFLRKMRLDN ATWGRITFGP VERVRKRVLL NPLTKEMPPD E ASNVIMEI ...String:
MTLAKIELLK QLLRDNEAKT VLKQTTVDQY NIIRKFNTSR IEKNPSLRMK WAMCSNFPLA LTKGDMANRI PLEYKGIQLK TNAEDIGTK GQMCSIAAVT WWNTYGPIGD TEGFERVYES FFLRKMRLDN ATWGRITFGP VERVRKRVLL NPLTKEMPPD E ASNVIMEI LFPKEAGIPR ESTWIHRELI KEKREKLKGT MITPIVLAYM LERELVARRR FLPVAGATSA EFIEMLHCLQ GE NWRQIYH PGGNKLTESR SQSMIVACRK IIRRSIVASN PLELAVEIAN KTVIDTEPLK SCLAAIDGGD VACDIIRAAL GLK IRQRQR FGRLELKRIS GRGFKNDEEI LIGNGTIQKI GIWDGEEEFH VRCGECRGIL KKSKMKLEKL LINSAKKEDM RDLI ILCMV FSQDTRMFQG VRGEINFLNR AGQLLSPMYQ LQRYFLNRSN DLFDQWGYEE SPKASELHGI NESMNASDYT LKGVV VTRN VIDDFSSTET EKVSITKNLS LIKRTGEVIM GANDVSELES QAQLMITYDT PKMWEMGTTK ELVQNTYQWV LKNLVT LKA QFLLGKEDMF QWDAFEAFES IIPQKMAGQY SGFARAVLKQ MRDQEVMKTD QFIKLLPFCF SPPKLRSNGE PYQFLKL VL KGGGENFIEV RKGSPLFSYN PQTEVLTICG RMMSLKGKIE DEERNRSMGN AVLAGFLVSG KYDPDLGDFK TIEELEKL K PGEKANILLY QGKPVKVVKR KRYSALSNDI SQGIKRQRMT VESMGWALS

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Macromolecule #4: 3' promoter vRNA

MacromoleculeName: 3' promoter vRNA / type: rna / ID: 4 / Number of copies: 1
Source (natural)Organism: Influenza B virus (B/Memphis/13/2003)
Molecular weightTheoretical: 4.321563 KDa
SequenceString:
UAUACCUCUG CUUC

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Macromolecule #5: 5' promoter vRNA

MacromoleculeName: 5' promoter vRNA / type: rna / ID: 5 / Number of copies: 1
Source (natural)Organism: Influenza B virus (B/Memphis/13/2003)
Molecular weightTheoretical: 4.55782 KDa
SequenceString:
AGUAGUAACA AGAG

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 2.09 e/Å2
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5d98

Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. vlion)
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 9.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 9159
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-6f5o:
A mechanism for the activation of the influenza virus transcriptase

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