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- EMDB-10667: Influenza C virus polymerase in complex with human ANP32A - Subclass 2 -

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Basic information

Entry
Database: EMDB / ID: EMD-10667
TitleInfluenza C virus polymerase in complex with human ANP32A - Subclass 2
Map dataRELION 3.1 locally filtered map
Sample
  • Complex: Influenza C virus polymerase in complex with human ANP32A
    • Complex: Influenza C virus polymerases
      • Protein or peptide: Polymerase acidic protein
      • Protein or peptide: RNA-directed RNA polymerase catalytic subunit
      • Protein or peptide: Polymerase basic protein 2
    • Complex: Influenza viral RNA (vRNA) promoter 47mer
      • RNA: RNA (5'-R(*AP*GP*UP*AP*GP*AP*AP*AP*CP*AP*AP*GP*GP*GP*CP*CP*UP*UP*UP*U)-3')
KeywordsInfluenza Polymerase / ANP32 / replication / RNA-dependent RNA 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 / virion component / endonuclease activity / host cell cytoplasm / Hydrolases; Acting on ester bonds / RNA-directed RNA polymerase / viral translational frameshifting ...cap snatching / viral transcription / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / 7-methylguanosine mRNA capping / virion component / endonuclease activity / host cell cytoplasm / Hydrolases; Acting on ester bonds / RNA-directed RNA polymerase / viral translational frameshifting / 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 PB2 / 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 / 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 C virus (C/Johannesburg/1/66) / Influenza A virus (A/nt/60/1968(H3N2))
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsFan H / Carrique L
Funding support United Kingdom, 3 items
OrganizationGrant numberCountry
Wellcome Trust200835/Z/16/Z United Kingdom
Medical Research Council (MRC, United Kingdom)MR/R009945/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/K000241/1 United Kingdom
CitationJournal: Nature / Year: 2020
Title: Host ANP32A mediates the assembly of the influenza virus replicase.
Authors: Loïc Carrique / Haitian Fan / Alexander P Walker / Jeremy R Keown / Jane Sharps / Ecco Staller / Wendy S Barclay / Ervin Fodor / Jonathan M Grimes /
Abstract: Aquatic birds represent a vast reservoir from which new pandemic influenza A viruses can emerge. Influenza viruses contain a negative-sense segmented RNA genome that is transcribed and replicated by ...Aquatic birds represent a vast reservoir from which new pandemic influenza A viruses can emerge. Influenza viruses contain a negative-sense segmented RNA genome that is transcribed and replicated by the viral heterotrimeric RNA polymerase (FluPol) in the context of viral ribonucleoprotein complexes. RNA polymerases of avian influenza A viruses (FluPolA) replicate viral RNA inefficiently in human cells because of species-specific differences in acidic nuclear phosphoprotein 32 (ANP32), a family of essential host proteins for FluPol activity. Host-adaptive mutations, particularly a glutamic-acid-to-lysine mutation at amino acid residue 627 (E627K) in the 627 domain of the PB2 subunit, enable avian FluPolA to overcome this restriction and efficiently replicate viral RNA in the presence of human ANP32 proteins. However, the molecular mechanisms of genome replication and the interplay with ANP32 proteins remain largely unknown. Here we report cryo-electron microscopy structures of influenza C virus polymerase (FluPolC) in complex with human and chicken ANP32A. In both structures, two FluPolC molecules form an asymmetric dimer bridged by the N-terminal leucine-rich repeat domain of ANP32A. The C-terminal low-complexity acidic region of ANP32A inserts between the two juxtaposed PB2 627 domains of the asymmetric FluPolA dimer, suggesting a mechanism for how the adaptive PB2(E627K) mutation enables the replication of viral RNA in mammalian hosts. We propose that this complex represents a replication platform for the viral RNA genome, in which one of the FluPol molecules acts as a replicase while the other initiates the assembly of the nascent replication product into a viral ribonucleoprotein complex.
History
DepositionFeb 7, 2020-
Header (metadata) releaseNov 25, 2020-
Map releaseNov 25, 2020-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.032
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.032
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6y0c
  • Surface level: 0.032
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10667.png

Downloads & links

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Map

FileDownload / File: emd_10667.map.gz / Format: CCP4 / Size: 371.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRELION 3.1 locally filtered map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 460 pix.
= 499.1 Å		1.09 Å/pix.
x 460 pix.
= 499.1 Å		1.09 Å/pix.
x 460 pix.
= 499.1 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.085 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.032 / Movie #1: 0.032
Minimum - Maximum-0.08055804 - 0.163784
Average (Standard dev.)0.000005036301 (±0.001953573)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions460460460
Spacing460460460
CellA=B=C: 499.1 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0851.0851.085
M x/y/z460460460
origin x/y/z0.0000.0000.000
length x/y/z499.100499.100499.100
α/β/γ90.00090.00090.000
start NX/NY/NZ79740
NX/NY/NZ93103213
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS460460460
D min/max/mean-0.0810.1640.000

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Supplemental data

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Half map: #1

Fileemd_10667_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_10667_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Influenza C virus polymerase in complex with human ANP32A

EntireName: Influenza C virus polymerase in complex with human ANP32A
Components
  • Complex: Influenza C virus polymerase in complex with human ANP32A
    • Complex: Influenza C virus polymerases
      • Protein or peptide: Polymerase acidic protein
      • Protein or peptide: RNA-directed RNA polymerase catalytic subunit
      • Protein or peptide: Polymerase basic protein 2
    • Complex: Influenza viral RNA (vRNA) promoter 47mer
      • RNA: RNA (5'-R(*AP*GP*UP*AP*GP*AP*AP*AP*CP*AP*AP*GP*GP*GP*CP*CP*UP*UP*UP*U)-3')

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Supramolecule #1: Influenza C virus polymerase in complex with human ANP32A

SupramoleculeName: Influenza C virus polymerase in complex with human ANP32A
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: Influenza C virus polymerases

SupramoleculeName: Influenza C virus polymerases / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3
Source (natural)Organism: Influenza C virus (C/Johannesburg/1/66)

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Supramolecule #3: Influenza viral RNA (vRNA) promoter 47mer

SupramoleculeName: Influenza viral RNA (vRNA) promoter 47mer / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4 / Details: Synthetic RNA
Source (natural)Organism: Influenza A virus (A/nt/60/1968(H3N2))

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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 / EC number: Hydrolases; Acting on ester bonds
Source (natural)Organism: Influenza C virus (C/Johannesburg/1/66)
Molecular weightTheoretical: 82.025531 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSKTFAEIAE AFLEPEAVRI AKEAVEEYGD HERKIIQIGI HFQVCCMFCD EYLSTNGSDR FVLIEGRKRG TAVSLQNELC KSYDLEPLP FLCDIFDREE KQFVEIGITR KADDSYFQSK FGKLGNSCKI FVFSYDGRLD KNCEGPMEEQ KLRIFSFLAT A ADFLRKEN ...String:
MSKTFAEIAE AFLEPEAVRI AKEAVEEYGD HERKIIQIGI HFQVCCMFCD EYLSTNGSDR FVLIEGRKRG TAVSLQNELC KSYDLEPLP FLCDIFDREE KQFVEIGITR KADDSYFQSK FGKLGNSCKI FVFSYDGRLD KNCEGPMEEQ KLRIFSFLAT A ADFLRKEN MFNEIFLPDN EETIIEMKKG KTFLELRDES VPLPFQTYEQ MKDYCEKFKG NPRELASKVS QMQSNIKLPI KH YEQNKFR QIRLPKGPMA PYTHKFLMEE AWMFTKISDP ERSRAGEILI DFFKKGNLSA IRPKDKPLQG KYPIHYKNLW NQI KAAIAD RTMVINENDH SEFLGGIGRA SKKIPEISLT QDVITTEGLK QSENKLPEPR SFPRWFNAEW MWAIKDSDLT GWVP MAEYP PADNELEDYA EHLNKTMEGV LQGTNCAREM GKCILTVGAL MTECRLFPGK IKVVPIYARS KERKSMQEGL PVPSE MDCL FGICVKSKSH LNKDDGMYTI ITFEFSIREP NLEKHQKYTV FEAGHTTVRM KKGESVIGRE VPLYLYCRTT ALSKIK NDW LSKARRCFIT TMDTVETICL RESAKAEENL VEKTLNEKQM WIGKKNGELI AQPLREALRV QLVQQFYFCI YNDSQLE GF CNEQKKILMA LEGDKKNKSS FGFNPEGLLE KIEECLINNP MCLFMAQRLN ELVIEASKRG AKFFKTD

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: 1 / Enantiomer: LEVO / EC number: RNA-directed RNA polymerase
Source (natural)Organism: Influenza C virus (C/Johannesburg/1/66)
Molecular weightTheoretical: 86.145945 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MEINPYLMFL NNDVTSLIST TYPYTGPPPM SHGSSTKYTL ETIKRTYDYS RTSVEKTSKV FNIPRRKFCN CLEDKDELVK PTGNVDISS LLGLAEMMEK RMGEGFFKHC VMEAETEILK MHFSRLTEGR QTYDWTSERN MPAATALQLT VDAIKETEGP F KGTTMLEY ...String:
MEINPYLMFL NNDVTSLIST TYPYTGPPPM SHGSSTKYTL ETIKRTYDYS RTSVEKTSKV FNIPRRKFCN CLEDKDELVK PTGNVDISS LLGLAEMMEK RMGEGFFKHC VMEAETEILK MHFSRLTEGR QTYDWTSERN MPAATALQLT VDAIKETEGP F KGTTMLEY CNKMIEMLDW KEIKFKKVKT VVRREKDKRS GKEIKTKVPV MGIDSIKHDE FLIRALTINT MAKDGERGKL QR RAIATPG MIVRPFSKIV ETVAQKICEK LKESGLPVGG NEKKAKLKTT VTSLNARMNS DQFAVNITGD NSKWNECQQP EAY LALLAY ITKDSSDLMK DLCSVAPVLF CNKFVKLGQG IRLSNKRKTK EVIIKAEKMG KYKNLMREEY KNLFEPLEKY IQKD VCFLP GGMLMGMFNM LSTVLGVSTL CYMDEELKAK GCFWTGLQSS DDFVLFAVAS NWSNIHWTIR RFNAVCKLIG INMSL EKSY GSLPELFEFT SMFFDGEFVS NLAMELPAFT TAGVNEGVDF TAAMSIIKTN MINNSLSPST ALMALRICLQ EFRATY RVH PWDSRVKGGR MKIINEFIKT IENKDGLLIA DGGKLMNNIS TLHIPEEVLK FEKMDEQYRN RVFNPKNPFT NFDKTID IF RAHGPIRVEE NEAVVSTHSF RTRANRTLLN TDMRAMMAEE KRYQMVCDMF KSVFESADIN PPIGAMSIGE AIEEKLLE R AKMKRDIGAI EDSEYEEIKD IIRDAKKARL ESR

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 C virus (C/Johannesburg/1/66)
Molecular weightTheoretical: 104.272359 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSLLLTIAKE YKRLCQDAKA AQMMTVGTVS NYTTFKKWTT SRKEKNPSLR MRWAMSSKFP IIANKRMLEE AQIPKEHNNV ALWEDTEDV SKRDHVLASA SCINYWNFCG PCVNNSEVIK EVYKSRFGRL ERRKEIMWKE LRFTLVDRQR RRVDTQPVEQ R LRTGEIKD ...String:
MSLLLTIAKE YKRLCQDAKA AQMMTVGTVS NYTTFKKWTT SRKEKNPSLR MRWAMSSKFP IIANKRMLEE AQIPKEHNNV ALWEDTEDV SKRDHVLASA SCINYWNFCG PCVNNSEVIK EVYKSRFGRL ERRKEIMWKE LRFTLVDRQR RRVDTQPVEQ R LRTGEIKD LQMWTLFEDE APLASKFILD NYGLVKEMRS KFANKPLNKE VVAHMLEKQF NPESRFLPVF GAIRPERMEL IH ALGGETW IQEANTAGIS NVDQRKNDIR AVCRKVCLAA NASIMNAKSK LVEYIKSTSM RIGETERKLE ELILETDDVS PEV TLCKSA LGGQLGKTLS FGPMLLKKIS GSGVKVKDTV YIQGVRAVQF EYWSEQEEFY GEYKSATALF SRKERSLEWI TIGG GINED RKRLLAMCMI FCRDGDYFKD APATITMADL STKLGREIPY QYVMMNWIQK SEDNLEALLY SRGIVETNPG KMGSS MGID GSKRAIKSLR AVTIQSGKID MPESKEKIHL ELSDNLEAFD SSGRIVATIL DLPSDKKVTF QDVSFQHPDL AVLRDE KTA ITKGYEALIK RLGTGDNDIP SLIAKKDYLS LYNLPEVKLM APLIRPNRKG VYSRVARKLV STQVTTGHYS LHELIKV LP FTYFAPKQGM FEGRLFFSND SFVEPGVNNN VFSWSKADSS KIYCHGIAIR VPLVVGDEHM DTSLALLEGF SVCENDPR A PMVTRQDLID VGFGQKVRLF VGQGSVRTFK RTASQRAASS DVNKNVKKIK MSNENLYFQG ELKTAALAQH DEAVDNKFN KEQQNAFYEI LHLPNLNEEQ RNAFIQSLKD DPSQSANLLA EAKKLNDAQA PKVDNKFNKE QQNAFYEILH LPNLNEEQRN AFIQSLKAD PSQSANLLAE AKKLNGAQAP KVDANSAGKS T

UniProtKB: Polymerase basic protein 2

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Macromolecule #4: RNA (5'-R(*AP*GP*UP*AP*GP*AP*AP*AP*CP*AP*AP*GP*GP*GP*CP*CP*UP*UP*...

MacromoleculeName: RNA (5'-R(*AP*GP*UP*AP*GP*AP*AP*AP*CP*AP*AP*GP*GP*GP*CP*CP*UP*UP*UP*U)-3')
type: rna / ID: 4 / Number of copies: 1
Source (natural)Organism: Influenza A virus (A/nt/60/1968(H3N2))
Molecular weightTheoretical: 14.901737 KDa
SequenceString:
AGUAGAAACA AGGGUAUUUU UCUUUACUAG UCUACCCUGC UUUUGCU

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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

Concentration0.28 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
25.0 mMC8H18N2O4SHEPES
150.0 mMNaCLsodium chloride
0.005 %C58H114O26Tween 20
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 294 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-30 / Number grids imaged: 1 / Number real images: 9287 / Average exposure time: 2.0 sec. / Average electron dose: 32.1 e/Å2
Details: Single specimen tilt of 20 degrees for around three quarter of the images
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 130000
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

Particle selectionNumber selected: 2312045
Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 57000
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 2.12)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 10 / Avg.num./class: 83000 / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

DetailsThe structure has been determined by single particle cryo-EM. PDB ids 5D98 and 6RR7 were used as initial models after rigid body fitting in chimera.
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-6y0c:
Influenza C virus polymerase in complex with human ANP32A - Subclass 2

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