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- EMDB-33776: The structure of EBOV L-VP35-RNA complex (state2) -

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Basic information

Entry
Database: EMDB / ID: EMD-33776
TitleThe structure of EBOV L-VP35-RNA complex (state2)
Map data
Sample
  • Complex: The complex of EBOV L-VP35
    • Protein or peptide: RNA-directed RNA polymerase L
    • Protein or peptide: VP35 of EBOV L-VP35 complex
  • Ligand: ZINC ION
Keywordspolymerase / complex / VIRAL PROTEIN
Function / homology
Function and homology information


GDP polyribonucleotidyltransferase / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IKBKE activity / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / Transferases; Transferring one-carbon groups; Methyltransferases / virion component / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / symbiont-mediated suppression of host toll-like receptor signaling pathway / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / host cell cytoplasm ...GDP polyribonucleotidyltransferase / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IKBKE activity / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / Transferases; Transferring one-carbon groups; Methyltransferases / virion component / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / symbiont-mediated suppression of host toll-like receptor signaling pathway / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / host cell cytoplasm / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / GTPase activity / ATP binding / cytoplasm
Similarity search - Function
RNA-directed RNA polymerase L, filovirus / Filoviruses VP35 interferon inhibitory domain, beta-sheet subdomain / Filoviridae VP35 protein / Filoviruses VP35 interferon inhibitory domain / Filoviruses VP35 interferon inhibitory domain, helical subdomain / Filoviridae VP35 / Filoviruses VP35 interferon inhibitory domain profile. / Mononegavirales RNA-directed RNA polymerase catalytic domain / Mononegavirus L protein 2-O-ribose methyltransferase / Mononegavirales mRNA-capping domain V ...RNA-directed RNA polymerase L, filovirus / Filoviruses VP35 interferon inhibitory domain, beta-sheet subdomain / Filoviridae VP35 protein / Filoviruses VP35 interferon inhibitory domain / Filoviruses VP35 interferon inhibitory domain, helical subdomain / Filoviridae VP35 / Filoviruses VP35 interferon inhibitory domain profile. / Mononegavirales RNA-directed RNA polymerase catalytic domain / Mononegavirus L protein 2-O-ribose methyltransferase / Mononegavirales mRNA-capping domain V / RNA-directed RNA polymerase L, C-terminal / Mononegavirales RNA dependent RNA polymerase / Mononegavirales mRNA-capping region V / RdRp of negative ssRNA viruses with non-segmented genomes catalytic domain profile. / Mononegavirus L protein 2'-O-ribose methyltransferase domain profile.
Similarity search - Domain/homology
RNA-directed RNA polymerase L / Polymerase cofactor VP35
Similarity search - Component
Biological speciesEbola virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsShi Y / Yuan B / Peng Q
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nature / Year: 2022
Title: Structure of the Ebola virus polymerase complex.
Authors: Bin Yuan / Qi Peng / Jinlong Cheng / Min Wang / Jin Zhong / Jianxun Qi / George F Gao / Yi Shi /
Abstract: Filoviruses, including Ebola virus, pose an increasing threat to the public health. Although two therapeutic monoclonal antibodies have been approved to treat the Ebola virus disease, there are no ...Filoviruses, including Ebola virus, pose an increasing threat to the public health. Although two therapeutic monoclonal antibodies have been approved to treat the Ebola virus disease, there are no approved broadly reactive drugs to control diverse filovirus infection. Filovirus has a large polymerase (L) protein and the cofactor viral protein 35 (VP35), which constitute the basic functional unit responsible for virus genome RNA synthesis. Owing to its conservation, the L-VP35 polymerase complex is a promising target for broadly reactive antiviral drugs. Here we determined the structure of Ebola virus L protein in complex with tetrameric VP35 using cryo-electron microscopy (state 1). Structural analysis revealed that Ebola virus L possesses a filovirus-specific insertion element that is essential for RNA synthesis, and that VP35 interacts extensively with the N-terminal region of L by three protomers of the VP35 tetramer. Notably, we captured the complex structure in a second conformation with the unambiguous priming loop and supporting helix away from polymerase active site (state 2). Moreover, we demonstrated that the century-old drug suramin could inhibit the activity of the Ebola virus polymerase in an enzymatic assay. The structure of the L-VP35-suramin complex reveals that suramin can bind at the highly conserved NTP entry channel to prevent substrates from entering the active site. These findings reveal the mechanism of Ebola virus replication and may guide the development of more powerful anti-filovirus drugs.
History
DepositionJul 6, 2022-
Header (metadata) releaseOct 5, 2022-
Map releaseOct 5, 2022-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33776.png

Downloads & links

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Map

FileDownload / File: emd_33776.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 360 pix.
= 298.8 Å		0.83 Å/pix.
x 360 pix.
= 298.8 Å		0.83 Å/pix.
x 360 pix.
= 298.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.006
Minimum - Maximum-0.052404724 - 0.086558156
Average (Standard dev.)0.00008193632 (±0.0017761175)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 298.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : The complex of EBOV L-VP35

EntireName: The complex of EBOV L-VP35
Components
  • Complex: The complex of EBOV L-VP35
    • Protein or peptide: RNA-directed RNA polymerase L
    • Protein or peptide: VP35 of EBOV L-VP35 complex
  • Ligand: ZINC ION

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Supramolecule #1: The complex of EBOV L-VP35

SupramoleculeName: The complex of EBOV L-VP35 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Ebola virus

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Macromolecule #1: RNA-directed RNA polymerase L

MacromoleculeName: RNA-directed RNA polymerase L / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Ebola virus
Molecular weightTheoretical: 252.863734 KDa
Recombinant expressionOrganism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
SequenceString: MATQHTQYPD ARLSSPIVLD QCDLVTRACG LYSSYSLNPQ LRNCKLPKHI YRLKYDVTVT KFLSDVPVAT LPIDFIVPIL LKALSGNGF CPVEPRCQQF LDEIIKYTMQ DALFLKYYLK NVGAQEDCVD DHFQEKILSS IQGNEFLHQM FFWYDLAILT R RGRLNRGN ...String:
MATQHTQYPD ARLSSPIVLD QCDLVTRACG LYSSYSLNPQ LRNCKLPKHI YRLKYDVTVT KFLSDVPVAT LPIDFIVPIL LKALSGNGF CPVEPRCQQF LDEIIKYTMQ DALFLKYYLK NVGAQEDCVD DHFQEKILSS IQGNEFLHQM FFWYDLAILT R RGRLNRGN SRSTWFVHDD LIDILGYGDY VFWKIPISLL PLNTQGIPHA AMDWYQTSVF KEAVQGHTHI VSVSTADVLI MC KDLITCR FNTTLISKIA EVEDPVCSDY PNFKIVSMLY QSGDYLLSIL GSDGYKIIKF LEPLCLAKIQ LCSKYTERKG RFL TQMHLA VNHTLEEITE IRALKPSQAH KIREFHRTLI RLEMTPQQLC ELFSIQKHWG HPVLHSETAI QKVKKHATVL KALR PIVIF ETYCVFKYSI AKHYFDSQGS WYSVTSDRNL TPGLNSYIKR NQFPPLPMIK ELLWEFYHLD HPPLFSTKII SDLSI FIKD RATAVERTCW DAVFEPNVLG YNPPHKFSTK RVPEQFLEQE NFSIENVLSY AQKLEYLLPQ YRNFSFSLKE KELNVG RTF GKLPYPTRNV QTLCEALLAD GLAKAFPSNM MVVTEREQKE SLLHQASWHH TSDDFGEHAT VRGSSFVTDL EKYNLAF RY EFTAPFIEYC NRCYGVKNVF NWMHYTIPQC YMHVSDYYNP PHNLTLENRN NPPEGPSSYR GHMGGIEGLQ QKLWTSIS C AQISLVEIKT GFKLRSAVMG DNQCITVLSV FPLETDADEQ EQSAEDNAAR VAASLAKVTS ACGIFLKPDE TFVHSGFIY FGKKQYLNGV QLPQSLKTAT RMAPLSDAIF DDLQGTLASI GTAFERSISE TRHIFPCRIT AAFHTFFSVR ILQYHHLGFN KGFDLGQLT LGKPLDFGTI SLALAVPQVL GGLSFLNPEK CFYRNLGDPV TSGLFQLKTY LRMIEMDDLF LPLIAKNPGN C TAIDFVLN PSGLNVPGSQ DLTSFLRQIV RRTITLSAKN KLINTLFHAS ADFEDEMVCK WLLSSTPVMS RFAADIFSRT PS GKRLQIL GYLEGTRTLL ASKIINNNTE TPVLDRLRKI TLQRWSLWFS YLDHCDNILA EALTQITCTV DLAQILREYS WAH ILEGRP LIGATLPCMI EQFKVVWLKP YEQCPQCSNA KQPGGKPFVS VAVKKHIVSA WPNASRISWT IGDGIPYIGS RTED KIGQP AIKPKCPSAA LREAIELASR LTWVTQGSSN SDLLIKPFLE ARVNLSVQEI LQMTPSHYSG NIVHRYNDQY SPHSF MANR MSNSATRLIV STNTLGEFSG GGQSARDSNI IFQNVINYAV ALFDIKFRNT EATDIQYNRA HLHLTKCCTR EVPAQY LTY TSTLDLDLTR YRENELIYDN NPLKGGLNCN ISFDNPFFQG KQLNIIEDDL IRLPHLSGWE LAKTIMQSII SDSNNSS TD PISSGETRSF TTHFLTYPKI GLLYSFGAFV SYYLGNTILR TKKLTLDNFL YYLTTQIHNL PHRSLRILKP TFKHASVM S RLMSIDPHFS IYIGGAAGDR GLSDAARLFL RTSISSFLTF VKEWIINRGT IVPLWIVYPL EGQNPTPVNN FLHQIVELL VHDSSRHQAF KTTINDHVHP HDNLVYTCKS TASNFFHASL AYWRSRHRNS NRKDLTRNSS TGSSTNNSDG HIKRSQEQTT RDPHDGTER SLVLQMSHEI KRTTIPQENT HQGPSFQSFL SDSACGTANP KLNFDRSRHN VKSQDHNSAS KREGHQIISH R LVLPFFTL SQGTRQLTSS NESQTQDEIS KYLRQLRSVI DTTVYCRFTG IVSSMHYKLD EVLWEIENFK SAVTLAEGEG AG ALLLIQK YQVKTLFFNT LATESSIESE IVSGMTTPRM LLPVMSKFHN DQIEIILNNS ASQITDITNP TWFKDQRARL PRQ VEVITM DAETTENINR SKLYEAVHKL ILHHVDPSVL KAVVLKVFLS DTEGMLWLND NLAPFFATGY LIKPITSSAR SSEW YLCLT NFLSTTRKMP HQNHLSCKQV ILTALQLQIQ RSPYWLSHLT QYADCDLHLS YIRLGFPSLE KVLYHRYNLV DSKRG PLVS VTQHLAHLRA EIRELTNDYN QQRQSRTQTY HFIRTAKGRI TKLVNDYLKF FLIVQALKHN GTWQAEFKKL PELISV CNR FYHIRDCNCE ERFLVQTLYL HRMQDSEVKL IERLTGLLSL FPDGLYRFD

UniProtKB: RNA-directed RNA polymerase L

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Macromolecule #2: VP35 of EBOV L-VP35 complex

MacromoleculeName: VP35 of EBOV L-VP35 complex / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Ebola virus
Molecular weightTheoretical: 37.48943 KDa
Recombinant expressionOrganism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
SequenceString: MTTRTKGRGH TVATTQNDRM PGPELSGWIS EQLMTGRIPV NDIFCDIENN PGLCYASQMQ QTKPNPKMRN SQTQTDPICN HSFEEVVQT LASLATVVQQ QTIASESLEQ RITSLENGLK PVYDMAKTIS SLNRVCAEMV AKYDLLVMTT GRATATAAAT E AYWAEHGQ ...String:
MTTRTKGRGH TVATTQNDRM PGPELSGWIS EQLMTGRIPV NDIFCDIENN PGLCYASQMQ QTKPNPKMRN SQTQTDPICN HSFEEVVQT LASLATVVQQ QTIASESLEQ RITSLENGLK PVYDMAKTIS SLNRVCAEMV AKYDLLVMTT GRATATAAAT E AYWAEHGQ PPPGPSLYEE SAIRGKIESR DETVPQSVRE AFNNLDSTTS LTEENFGKPD ISAKDLRNIM YDHLPGFGTA FH QLVQVIC KLGKDSNSLD IIHAEFQASL AEGDSPQCAL IQITKRVPIF QDAAPPVIHI RSRGDIPRAC QKSLRPVPPS PKI DRGWVC VFQLQDGKTL GLKI

UniProtKB: Polymerase cofactor VP35

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Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 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: 7.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 475325
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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