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- EMDB-65296: Structure of Ebinur lake virus polymerase complexed with suramin -

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Basic information

Entry
Database: EMDB / ID: EMD-65296
TitleStructure of Ebinur lake virus polymerase complexed with suramin
Map data
Sample
  • Complex: Structure of Ebinur lake virus polymerase complexed with suramin
    • Protein or peptide: RNA-directed RNA polymerase L
  • Ligand: 8,8'-[CARBONYLBIS[IMINO-3,1-PHENYLENECARBONYLIMINO(4-METHYL-3,1-PHENYLENE)CARBONYLIMINO]]BIS-1,3,5-NAPHTHALENETRISULFON IC ACID
KeywordsViral protein / polymerase / suramin
Function / homology
Function and homology information


host cell / RNA-directed RNA polymerase / nucleotide binding / viral RNA genome replication / hydrolase activity / RNA-directed RNA polymerase activity / DNA-templated transcription / metal ion binding
Similarity search - Function
: / Virus, RNA-directed RNA polymerase L, thumb ring domain / RNA-directed RNA polymerase L, N-terminal / L protein N-terminus / : / RNA-dependent RNA polymerase, bunyaviral / Bunyavirus RNA dependent RNA polymerase / 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 L
Similarity search - Component
Biological speciesPipistrellus nathusii (Nathusius's pipistrelle) / Ebinur lake virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsTang J / Deng Z
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2026
Title: Structural basis for RNA synthesis and inhibition of the orthobunyavirus polymerase.
Authors: Jingjing Tang / Wenhua Kuang / Wei Chen / Hao Wu / Yong Wang / Jinyue Li / Zhiming Yuan / Han Xia / Haiyan Zhao / Zengqin Deng /
Abstract: Orthobunyaviruses are segmented negative-sense RNA viruses that encompass several life-threatening human and animal pathogens. However, no licensed antivirals are currently available. The viral RNA- ...Orthobunyaviruses are segmented negative-sense RNA viruses that encompass several life-threatening human and animal pathogens. However, no licensed antivirals are currently available. The viral RNA-dependent RNA polymerase (RdRp) is a multi-domain enzyme critical for genome replication and transcription, representing a promising target for antiviral drug development. Here, we establish robust in vitro enzymatic activity assays for the Ebinur Lake virus (EBIV) polymerase and identify suramin, a century-old drug, as an inhibitor of EBIV polymerase. We further determine cryo-EM structures of the EBIV polymerase in apo, elongation, and suramin-bound states. These structures reveal conformational rearrangements of the polymerase during RNA synthesis, including conformational transitions of the prime-and-realign (PR) loop and a unique β-hairpin that bridges the zinc-binding domain (ZBD) to the RdRp core. The structural observations are correlated with in vitro enzymatic activity and cell-based minireplicon assays. The suramin-bound structure reveals two distinct inhibitory binding sites. One site sterically clashes with the vRNA promoter. The other site directly blocks RNA template strand binding, thereby inhibiting polymerase activity. These findings advance our understanding of orthobunyavirus RNA synthesis mechanisms and offer a structural framework for the rational design and optimization of antiviral drugs.
History
DepositionJul 8, 2025-
Header (metadata) releaseMay 13, 2026-
Map releaseMay 13, 2026-
UpdateMay 27, 2026-
Current statusMay 27, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65296.png

Downloads & links

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Map

FileDownload / File: emd_65296.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 256 pix.
= 243.2 Å		0.95 Å/pix.
x 256 pix.
= 243.2 Å		0.95 Å/pix.
x 256 pix.
= 243.2 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-1.0780683 - 1.7913448
Average (Standard dev.)-0.00013458812 (±0.05157294)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 243.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_65296_half_map_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_65296_half_map_2.map
Projections & Slices
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Histogram

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Sample components

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Entire : Structure of Ebinur lake virus polymerase complexed with suramin

EntireName: Structure of Ebinur lake virus polymerase complexed with suramin
Components
  • Complex: Structure of Ebinur lake virus polymerase complexed with suramin
    • Protein or peptide: RNA-directed RNA polymerase L
  • Ligand: 8,8'-[CARBONYLBIS[IMINO-3,1-PHENYLENECARBONYLIMINO(4-METHYL-3,1-PHENYLENE)CARBONYLIMINO]]BIS-1,3,5-NAPHTHALENETRISULFON IC ACID

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Supramolecule #1: Structure of Ebinur lake virus polymerase complexed with suramin

SupramoleculeName: Structure of Ebinur lake virus polymerase complexed with suramin
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Pipistrellus nathusii (Nathusius's pipistrelle)

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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 / EC number: RNA-directed RNA polymerase
Source (natural)Organism: Ebinur lake virus
Molecular weightTheoretical: 199.038438 KDa
Recombinant expressionOrganism: Pichia (fungus)
SequenceString: MEDPMYEQFL QRIQAVRTAT VAKDISADIL EARHDYFGRE LCRALDIEYR NNVLLDEIIL DVYPGVNLME YNVPHVTPAN YIWTGDMLL ILAYKVSVGH DSTEVTYKKY TTLILPVMQE IGINTEICII RANPVTNQIS IVGEQFKRLF PTIPVELNFA R FFELRKML ...String:
MEDPMYEQFL QRIQAVRTAT VAKDISADIL EARHDYFGRE LCRALDIEYR NNVLLDEIIL DVYPGVNLME YNVPHVTPAN YIWTGDMLL ILAYKVSVGH DSTEVTYKKY TTLILPVMQE IGINTEICII RANPVTNQIS IVGEQFKRLF PTIPVELNFA R FFELRKML LDKFADDEEF LMMIAHGDFT LTAPWCQDDT PELIDHPIYQ EFLGSMPPRF VSMFEEAMDF SAYNAERWNT LL YKIKNLT LEDYQDYLNI KSHNIFNMTG DFMKPTQDEI DIGWESMSKR ISQERELTTD INKQKPSIHF IWAQNKDRKL LNS TAKLVF LSNTLQSITE QSTWTDALKA IGVSMDIGNN IGLYENLCAE RKLIARSTGK KVNNKRLEAV KIGKALVLWE QQFI LANEL FKGQERQKFI KNFFGIGKHK TFKDKTSEDL DREKPKILDF NNTRVLMAAR TMVNKNKKFL SQDNTLEFDH PIIST YFDQ VREASIDTAQ VLKKISKTCF WQAITDISTL MRNILAVSQY NRHNTFRVAM CANDSIYGLV FPSSDIKTKR ATIVFC IVC MHNSRDDIMD AGALFTTLET KTKTFVSISK AIRLDKERCQ RIVSSPGLFI LSTLLLYNNN TEISLYDVMN FTFYTSL SI TKSMLSLTEP SRYMIMNSLA ISSHVRDYIA EKFSPYTKTL FSVYMVNLIK RGCATANEQS EKIQVRNIYL SDYDITQK G INDIRNLDSI WFPGKVNLKE YINQIYLPFY FNAKGLHEKH HVMIDLAKTV LEIEMNQRLD QLGIWSKNEK KQHVNLPIL VHSIAKSLIL DTSRHNHLRN RVESRNNFRR SISTISTFTS SKSCIKIGEF QDLKTKEFKA TKKMNEKINQ KFRLANPLFI DDKDADAEI MHCNYDQLKT KVPNYKDYIS VKVFDRLYEL YKTKELDDKP FIEQAMKMMK EHKEFNFTFF NKGQKTSKDR E IFVGEFEA KMCMYVVERI SKERCKLNED EMISEPGDTK LRILEKKAEE EIRYIVEKTK DSILKGDPAH ALKLEINADM SK WSAQDVF FKYFWLVAMD PILYPSEKKR ILYFMCNYMQ KNLILPDDLL SNIMDQRRPY ENDIILESTN GLAQNFVQIK RNW LQGNFN YMSSYVHSCA MLVYKDVAKE AVKLLDGNCL VNSMVHSDDN QTSLSIIQNK LKDNMIIEYV AKLFEAVCLA FGCQ ANMKK TYITHTCKEF VSLFNLHGEP LSIYGRFLLP SVGDCAYIGP YEDLASRLSA AQQSLKHGCP PSYVWVAISC SHWIT HFTY NMMHDQVNSP MQYLPFEDRF QVPTELNGYL SAPLYLIALI GIEADNLWFL LNILKKLVPL DKQKETIQTQ FTAIQD NIN KLTPSELFRL KLLRYLTLDT EITSDSNMGE TSDMRSRSLL TPRKFTTAGS LNKLVSYNDF KNAMNTNEFQ ENLEYME MN PELLVTKGEN KEQYINSILF RYNSKRFKES LSIQAPSQLF VEQILFSHKP IIDYSSIFDK LASMAETEII ENLPDIIG R VTYPQAYQMI TRDITQLPLD IDDIKIVFKY CVLNDPLIIT AANTSLLCVR GAPQDRTGLS ACQMPEFRNM KLIHHSPAL VLKAFSKGTV DIPGADPVEL EKDLLHLKEF VENTGIQEKI QMNIDNPPKH LQGTEVLIYK IRELTKLYQV CYDYVKSTEH KVKVFILPM KSYTSIEFCT LIQGNTISDS KWYTMH

UniProtKB: RNA-directed RNA polymerase L

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Macromolecule #2: 8,8'-[CARBONYLBIS[IMINO-3,1-PHENYLENECARBONYLIMINO(4-METHYL-3,1-P...

MacromoleculeName: 8,8'-[CARBONYLBIS[IMINO-3,1-PHENYLENECARBONYLIMINO(4-METHYL-3,1-PHENYLENE)CARBONYLIMINO]]BIS-1,3,5-NAPHTHALENETRISULFON IC ACID
type: ligand / ID: 2 / Number of copies: 2 / Formula: SVR
Molecular weightTheoretical: 1.29728 KDa

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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

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (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: 2.5 µm / Nominal defocus min: 0.5 µm

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 85378
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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