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- EMDB-19389: Pseudo-symmetrical influenza B polymerase apo-dimer, core-only mo... -

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Basic information

Entry
Database: EMDB / ID: EMD-19389
TitlePseudo-symmetrical influenza B polymerase apo-dimer, core-only moeity (from "Influenza B polymerase pseudo-symmetrical dimer" | Local refinement)
Map data
Sample
  • Complex: Heterotrimeric complex from a pseudo-symmetrical dimer
    • Protein or peptide: Polymerase acidic protein
    • Protein or peptide: RNA-directed RNA polymerase catalytic subunit
    • Protein or peptide: Polymerase basic protein 2
  • Ligand: MAGNESIUM ION
KeywordsViral polymerase / VIRAL PROTEIN
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 / virion component / endonuclease activity / host cell cytoplasm / Hydrolases; Acting on ester bonds / RNA-directed RNA polymerase ...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 / virion component / endonuclease activity / host cell cytoplasm / Hydrolases; Acting on ester bonds / RNA-directed RNA polymerase / viral RNA genome replication / RNA-directed 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 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 basic protein 2 / RNA-directed RNA polymerase catalytic subunit / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza B virus (B/Memphis/13/2003)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.09 Å
AuthorsArragain B / Cusack S
Funding support France, 1 items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-18-CE18-0028 France
CitationJournal: Nat Commun / Year: 2024
Title: Structures of influenza A and B replication complexes give insight into avian to human host adaptation and reveal a role of ANP32 as an electrostatic chaperone for the apo-polymerase.
Authors: Benoît Arragain / Tim Krischuns / Martin Pelosse / Petra Drncova / Martin Blackledge / Nadia Naffakh / Stephen Cusack /
Abstract: Replication of influenza viral RNA depends on at least two viral polymerases, a parental replicase and an encapsidase, and cellular factor ANP32. ANP32 comprises an LRR domain and a long C-terminal ...Replication of influenza viral RNA depends on at least two viral polymerases, a parental replicase and an encapsidase, and cellular factor ANP32. ANP32 comprises an LRR domain and a long C-terminal low complexity acidic region (LCAR). Here we present evidence suggesting that ANP32 is recruited to the replication complex as an electrostatic chaperone that stabilises the encapsidase moiety within apo-polymerase symmetric dimers that are distinct for influenza A and B polymerases. The ANP32 bound encapsidase, then forms the asymmetric replication complex with the replicase, which is embedded in a parental ribonucleoprotein particle (RNP). Cryo-EM structures reveal the architecture of the influenza A and B replication complexes and the likely trajectory of the nascent RNA product into the encapsidase. The cryo-EM map of the FluB replication complex shows extra density attributable to the ANP32 LCAR wrapping around and stabilising the apo-encapsidase conformation. These structures give new insight into the various mutations that adapt avian strain polymerases to use the distinct ANP32 in mammalian cells.
History
DepositionJan 9, 2024-
Header (metadata) releaseSep 11, 2024-
Map releaseSep 11, 2024-
UpdateSep 11, 2024-
Current statusSep 11, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19389.png

Downloads & links

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Map

FileDownload / File: emd_19389.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 480 pix.
= 403.2 Å		0.84 Å/pix.
x 480 pix.
= 403.2 Å		0.84 Å/pix.
x 480 pix.
= 403.2 Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-2.295567 - 3.6502435
Average (Standard dev.)-0.0007200957 (±0.08357005)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 403.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_19389_msk_1.map
Projections & Slices
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Additional map: #1

Fileemd_19389_additional_1.map
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Half map: #2

Fileemd_19389_half_map_1.map
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Half map: #1

Fileemd_19389_half_map_2.map
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Sample components

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Entire : Heterotrimeric complex from a pseudo-symmetrical dimer

EntireName: Heterotrimeric complex from a pseudo-symmetrical dimer
Components
  • Complex: Heterotrimeric complex from a pseudo-symmetrical dimer
    • Protein or peptide: Polymerase acidic protein
    • Protein or peptide: RNA-directed RNA polymerase catalytic subunit
    • Protein or peptide: Polymerase basic protein 2
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Heterotrimeric complex from a pseudo-symmetrical dimer

SupramoleculeName: Heterotrimeric complex from a pseudo-symmetrical dimer
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Influenza B virus (B/Memphis/13/2003)

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Macromolecule #1: Polymerase acidic protein

MacromoleculeName: Polymerase acidic protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: Hydrolases; Acting on ester bonds
Source (natural)Organism: Influenza B virus (B/Memphis/13/2003)
Molecular weightTheoretical: 83.145023 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MDTFITRNFQ TTIIQKAKNT MAEFSEDPEL QPAMLFNICV HLEVCYVISD MNFLDEEGKA YTALEGQGKE QNLRPQYEVI EGMPRTIAW MVQRSLAQEH GIETPKYLAD LFDYKTKRFI EVGITKGLAD DYFWKKKEKL GNSMELMIFS YNQDYSLSNE S SLDEEGKG ...String:
MDTFITRNFQ TTIIQKAKNT MAEFSEDPEL QPAMLFNICV HLEVCYVISD MNFLDEEGKA YTALEGQGKE QNLRPQYEVI EGMPRTIAW MVQRSLAQEH GIETPKYLAD LFDYKTKRFI EVGITKGLAD DYFWKKKEKL GNSMELMIFS YNQDYSLSNE S SLDEEGKG RVLSRLTELQ AELSLKNLWQ VLIGEEDVEK GIDFKLGQTI SRLRDISVPA GFSNFEGMRS YIDNIDPKGA IE RNLARMS PLVSVTPKKL TWEDLRPIGP HIYNHELPEV PYNAFLLMSD ELGLANMTEG KSKKPKTLAK ECLEKYSTLR DQT DPILIM KSEKANENFL WKLWRDCVNT ISNEEMSNEL QKTNYAKWAT GDGLTYQKIM KEVAIDDETM CQEEPKIPNK CRVA AWVQT EMNLLSTLTS KRALDLPEIG PDVAPVEHVG SERRKYFVNE INYCKASTVM MKYVLFHTSL LNESNASMGK YKVIP ITNR VVNEKGESFD MLYGLAVKGQ SHLRGDTDVV TVVTFEFSST DPRVDSGKWP KYTVFRIGSL FVSGREKSVY LYCRVN GTN KIQMKWGMEA RRCLLQSMQQ MEAIVEQESS IQGYDMTKAC FKGDRVNSPK TFSIGTQEGK LVKGSFGKAL RVIFTKC LM HYVFGNAQLE GFSAESRRLL LLIQALKDRK GPWVFDLEGM YSGIEECISN NPWVIQSAYW FNEWLGFEKE GSKVLESV D EIMDE

UniProtKB: Polymerase acidic protein

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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: 2 / Enantiomer: LEVO / EC number: RNA-directed RNA polymerase
Source (natural)Organism: Influenza B virus (B/Memphis/13/2003)
Molecular weightTheoretical: 84.433266 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
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

UniProtKB: RNA-directed RNA polymerase catalytic subunit

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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 (B/Memphis/13/2003)
Molecular weightTheoretical: 90.95832 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
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 VESMGWALSG WSHPQFEKGG GSGGGSGGSA WSHPQFEK

UniProtKB: Polymerase basic protein 2

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 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: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.09 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 34404
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-8rn7:
Pseudo-symmetrical influenza B polymerase apo-dimer, core-only moeity (from "Influenza B polymerase pseudo-symmetrical dimer" | Local refinement)

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