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- EMDB-65297: Structure of Ebinur lake virus polymerase at the elongation state -

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Basic information

Entry
Database: EMDB / ID: EMD-65297
TitleStructure of Ebinur lake virus polymerase at the elongation state
Map data
Sample
  • Complex: Structure of Ebinur lake virus polymerase elongation complex
    • Protein or peptide: RNA-directed RNA polymerase L
    • RNA: RNA (5'-R(*GP*UP*AP*UP*AP*UP*CP*UP*CP*CP*AP*UP*UP*AP*UP*UP*UP*UP*UP*AP*UP*CP*C)-3')
    • RNA: RNA (5'-R(*GP*GP*AP*UP*AP*AP*AP*AP*AP*UP*AP*AP*U)-3')
KeywordsViral protein / polymerase / elongation complex / L protein / RNA / VIRAL PROTEIN/RNA / VIRAL PROTEIN-RNA complex
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 speciesEbinur lake virus / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.31 Å
AuthorsTang J / Deng Z
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structural basis for RNA synthesis and inhibition of the orthobunyavirus polymerase
Authors: Tang J / Deng Z
History
DepositionJul 8, 2025-
Header (metadata) releaseMay 13, 2026-
Map releaseMay 13, 2026-
UpdateMay 13, 2026-
Current statusMay 13, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65297.png

Downloads & links

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Map

FileDownload / File: emd_65297.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 220 pix.
= 209. Å		0.95 Å/pix.
x 220 pix.
= 209. Å		0.95 Å/pix.
x 220 pix.
= 209. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.131
Minimum - Maximum-1.2392933 - 1.7738066
Average (Standard dev.)0.0018741002 (±0.05755626)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 209.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_65297_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_65297_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 : Structure of Ebinur lake virus polymerase elongation complex

EntireName: Structure of Ebinur lake virus polymerase elongation complex
Components
  • Complex: Structure of Ebinur lake virus polymerase elongation complex
    • Protein or peptide: RNA-directed RNA polymerase L
    • RNA: RNA (5'-R(*GP*UP*AP*UP*AP*UP*CP*UP*CP*CP*AP*UP*UP*AP*UP*UP*UP*UP*UP*AP*UP*CP*C)-3')
    • RNA: RNA (5'-R(*GP*GP*AP*UP*AP*AP*AP*AP*AP*UP*AP*AP*U)-3')

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Supramolecule #1: Structure of Ebinur lake virus polymerase elongation complex

SupramoleculeName: Structure of Ebinur lake virus polymerase elongation complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1, #3, #2
Source (natural)Organism: Ebinur lake 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 / EC number: RNA-directed RNA polymerase
Source (natural)Organism: Ebinur lake virus
Molecular weightTheoretical: 259.756969 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 KWYTMHYLKQ VLGGTMKGHM MTTSTSEQVI AAECFRVLTH FADAFVEEGS R VSFLNEIL DKFTYKNVSV NYLLNVLLAS SNRLDFIPLL FRTKMLTQQD LNKFDALKTN ERVSWNNWQT NRGLNSGIID LT ISGYLRS IRIVGEDNKL KIAELTIPNF LPNTIFHAGN KLLNSRHNLK FEYMEEYVLD DKYNYYITYQ KKRANLYTYQ VST VDHIWR RNEEGNQKRG KRYNKMVPVC PVVVSSRDEM FKISMQNVFS LNLTNFNLTK LFVSPDEVAT IKKAHMSKMM FFSG PQIKA GIIDLTTLMR TQELLTLNYD NLCKSSIIPF CRILACNGEE PGELIFLSDE VMEFTISEEI ESMPIFTIRY QKRGN SSMT YKNAIRTLVA NGVDEIKEVF DFSGEGFYSK KNLGIINTIC STIEVLETNE WSTILLNSFH IAMLLENMDR EFHLFS MPG AFFSNVANGT INWTKLLKFV KSLPAVKKEP WSMMMERFIE KTVYLIEREI NKEVDFNDFL EELEYQSGKS MFTFF

UniProtKB: RNA-directed RNA polymerase L

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Macromolecule #2: RNA (5'-R(*GP*GP*AP*UP*AP*AP*AP*AP*AP*UP*AP*AP*U)-3')

MacromoleculeName: RNA (5'-R(*GP*GP*AP*UP*AP*AP*AP*AP*AP*UP*AP*AP*U)-3') / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 4.197598 KDa
SequenceString:
GGAUAAAAAU AAU

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Macromolecule #3: RNA (5'-R(*GP*UP*AP*UP*AP*UP*CP*UP*CP*CP*AP*UP*UP*AP*UP*UP*UP*UP*...

MacromoleculeName: RNA (5'-R(*GP*UP*AP*UP*AP*UP*CP*UP*CP*CP*AP*UP*UP*AP*UP*UP*UP*UP*UP*AP*UP*CP*C)-3')
type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 7.146177 KDa
SequenceString:
GUAUAUCUCC AUUAUUUUUA UCC

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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
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: 3.31 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 217551
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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