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- EMDB-48790: 3.09A Bornavirus L-P complex (without incubation with RNA/NTP) (s... -

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Basic information

Entry
Database: EMDB / ID: EMD-48790
Title3.09A Bornavirus L-P complex (without incubation with RNA/NTP) (state 1)
Map data3.09A Bornavirus L-P complex (without incubation with RNA/NTP) - sharpened map (state 1)
Sample
  • Complex: Bornavirus L-P complex (without incubation with RNA/NTP) (state 1)
    • Protein or peptide: RNA-directed RNA polymerase
    • Protein or peptide: P protein
  • Ligand: ZINC ION
KeywordsBornavirus / L protein / phosphoprotein / RNA-dependent RNA polymerase / PRNTase / GDP polyribonucleotidyl transferase / RNA capping / viral replication / TRANSFERASE / VIRAL PROTEIN
Function / homology
Function and homology information


virion component / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA-directed RNA polymerase / RNA-directed RNA polymerase activity / ATP binding
Similarity search - Function
Borna disease virus P24 / Borna disease virus P24 protein / Mononegavirales RNA-directed RNA polymerase catalytic domain / Mononegavirales mRNA-capping domain V / Mononegavirales RNA dependent RNA polymerase / Mononegavirales mRNA-capping region V / RdRp of negative ssRNA viruses with non-segmented genomes catalytic domain profile.
Similarity search - Domain/homology
RNA-directed RNA polymerase / P protein
Similarity search - Component
Biological speciesOrthobornavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.09 Å
AuthorsLiu B / Yang G / Wang D
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: Structural insights into the dynamic mechanism of bornavirus polymerase.
Authors: Ge Yang / Dong Wang / Bin Liu /
Abstract: Borna disease virus 1 (BoDV-1), an emerging zoonotic pathogen from the family, is neurotropic and can infect a variety of mammalian hosts, including humans. Linked to severe encephalitis and high ...Borna disease virus 1 (BoDV-1), an emerging zoonotic pathogen from the family, is neurotropic and can infect a variety of mammalian hosts, including humans. Linked to severe encephalitis and high mortality, BoDV-1 currently lacks licensed treatments or vaccines. The BoDV-1 polymerase complex, comprising the large (L) and phosphoprotein (P) subunits, is crucial for viral replication and transcription, making it a promising target for antiviral intervention. Here, we present the cryoelectron microscopy structure of the apo BoDV-1 L-P complex, revealing a unique "mitten-shaped" architecture. The structure characterizes key domains involved in RNA synthesis, including RNA-dependent RNA polymerase, polyribonucleotidyltransferase, and an inactive methyltransferase domain. While no RNA or NTPs were visible, we observed distinct conformational states, showing large-scale rearrangements of the P tetramer and L domains, as well as remodeling of the RNA template, nucleoside triphosphates, and nascent RNA entrances and/or exits, upon introducing RNA and NTPs. These findings highlight the dynamic structural changes probably associated with polymerase activity and advance the understanding of the BoDV-1 polymerase mechanisms, offering a basis for developing targeted antiviral strategies against this deadly pathogen.
History
DepositionJan 24, 2025-
Header (metadata) releaseSep 10, 2025-
Map releaseSep 10, 2025-
UpdateOct 15, 2025-
Current statusOct 15, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48790.png

Downloads & links

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Map

FileDownload / File: emd_48790.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3.09A Bornavirus L-P complex (without incubation with RNA/NTP) - sharpened map (state 1)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.66 Å/pix.
x 384 pix.
= 254.976 Å		0.66 Å/pix.
x 384 pix.
= 254.976 Å		0.66 Å/pix.
x 384 pix.
= 254.976 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.664 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.031170184 - 1.9261047
Average (Standard dev.)0.0015500922 (±0.026383763)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 254.97598 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: 3.09A Bornavirus L-P complex (without incubation with RNA/NTP)...

Fileemd_48790_additional_1.map
Annotation3.09A Bornavirus L-P complex (without incubation with RNA/NTP) - unsharpened map (state 1)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_48790_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_48790_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Bornavirus L-P complex (without incubation with RNA/NTP) (state 1)

EntireName: Bornavirus L-P complex (without incubation with RNA/NTP) (state 1)
Components
  • Complex: Bornavirus L-P complex (without incubation with RNA/NTP) (state 1)
    • Protein or peptide: RNA-directed RNA polymerase
    • Protein or peptide: P protein
  • Ligand: ZINC ION

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Supramolecule #1: Bornavirus L-P complex (without incubation with RNA/NTP) (state 1)

SupramoleculeName: Bornavirus L-P complex (without incubation with RNA/NTP) (state 1)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Orthobornavirus
Molecular weightTheoretical: 280 KDa

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Macromolecule #1: RNA-directed RNA polymerase

MacromoleculeName: RNA-directed RNA polymerase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA-directed RNA polymerase
Source (natural)Organism: Orthobornavirus
Molecular weightTheoretical: 191.888734 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSFHASLLRE EETPRPVAGI NRTDQSLKNP LLGTEVSFCL KSSSLPHHVR ALGQIKARNL ASCDYYLLFR QVVLPPEVYP IGVLIRAAE AILTVIVSAW KLEHMTKTLY SSVRYALTNP RVRAQLELHI AYQRIVGQVS YSREADIGPK RLGNMSLQFV Q SLVIATID ...String:
MSFHASLLRE EETPRPVAGI NRTDQSLKNP LLGTEVSFCL KSSSLPHHVR ALGQIKARNL ASCDYYLLFR QVVLPPEVYP IGVLIRAAE AILTVIVSAW KLEHMTKTLY SSVRYALTNP RVRAQLELHI AYQRIVGQVS YSREADIGPK RLGNMSLQFV Q SLVIATID TTSCLMTYNH FLAAADTAKS RCHLLIASVV QGALWEQGSF LDHIINLIDT IDSINLPHDD YFTIIKSISP YS QGLVMGR HNVSVSSDFA SVFTIPESCP QLDSLLKKLL QLDPVLLLMV SSVQKSWYFP EIRMVDGSRE QLHKMRVELE TPQ ALLSYG HTLLSIFRAE FIKGYVSKNA KWPPVHLLPG CDKSIKNARE LGRWSPAFDR RWQLFAKVVI LRIADLDMDP DFND IVSDK AIISSRRDWV FEYNAAAFWK KYGERLERPP ARSGPSRLVN ALIDGRLDNI PALLEPFYRG AVEFEDRLTV LVPKE KELK VKGRFFSKQT LAIRIYQVVA EAALKNEVMP YLKTHSMTMS STALTHLLNR LSHTITKGDS FVINLDYSSW CNGFRP ELQ APICRQLDQM FNCGYFFRTG CTLPCFTTFI IQDRFNPPYS FRGEPVEDGV TCAVGTKTMG EGMRQKLWTI LTSCWEI IA LREINVTFNI LGQGDNQTII IHKSASQNNQ LLAERALGAL YKHARLAGHN LKVEECWVSD CLYEYGKKLF FRGVPVPG C LKQLSRVTDS TGELFPNLYS KLACLTSSCL SAAMADTSPW VALATGVCLY LIELYVELPP AIMQDESLLT TLCLVGPSI GGLPTPATLP SVFFRGMSDP LPFQLALLQT LIKTTGVTCS LVNRVVKLRI APYPDWLSLV TDPTSLNIAQ VYRPERQIRR WIEEAIATS SHSSRIATFF QQPLTEMAQL LARDLSTMMP LRPRDMSALF ALSNVAYGLS IIDLFQKSST VVSASQAVHI E DVALESVR YKESIIQGLL DTTEGYNMQP YLEGCTYLAA KQLRRLTWGR DLVGVTMPFV AEQFHPHSSV GAKAELYLDA II YCPQETL RSHHLTTRGD QPLYLGSNTA VKVQRGEITG LTKSRAANLV KDTLVLHQWY KVRKVTDPHL NTLMARFLLE KGY TSDARP SIQGGTLTHR LPSRGDSRQG LTGYVNILST WLRFSSDYLH SFSKSSDDYT IHFQHVFTYG CLYADSVIRS GGVI STPYL LSASCKTCFE KIDSEEFVLA CEPQYRGAEW LITKPVTVPE QIIDAEVEFD PCVSASYCLG ILIGKSFLVD IRASG QDIM EQRTWANLER FSISDMQKLP WSIVIRSLWR FLIGARLLQF EKAGLIRMLY AATGPTFSFL MKVFQDSALL MDCAPL DRL SPRINFHSRG DLVAKLVLLP FINPGIVEIE VSGINSKYHA VSEANMDLYI AAAKSVGVKP TQFVEETNDF TARGHHH GC YSLSWSKSRN QSQVLKMVVR KLKLCVLYIY PTVDPAVALD LCHLPALTII LVLGGDPAYY ERLLEMDLCG AVSSRVDI P HSLAARTHKG FTIGPDTGPG VIRLDKLESV CYAHPCLEEL EFNAYLDSEL VDISDMCCLP LATPCKALFR PIYRSLQSF RLALMDNYSF VMDLILIRGL DIRPHLEEFD ELLVVGQHIL GQPVLVEVVY YVGVVGKRPV LARHPWSADL KRITVGGRAP CPSAARLRD EDCQGSLLVG LPAGLTQLLI ID

UniProtKB: RNA-directed RNA polymerase

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Macromolecule #2: P protein

MacromoleculeName: P protein / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Orthobornavirus
Molecular weightTheoretical: 22.45957 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAARPSSLVD SLEDEEDPQT LRRERSGSPR PRKIPRNALT QPVDQLLKDL RKNPSMISDP DQRTGREQLS NDELIKKLVT ELAENSMIE AEEVRGTLGD ISARIEAGFE SLSALQVETI QTAQRCDHSD SIRILGENIK ILDRSMKTMM ETMKLMMEKV D LLYASTAV ...String:
MAARPSSLVD SLEDEEDPQT LRRERSGSPR PRKIPRNALT QPVDQLLKDL RKNPSMISDP DQRTGREQLS NDELIKKLVT ELAENSMIE AEEVRGTLGD ISARIEAGFE SLSALQVETI QTAQRCDHSD SIRILGENIK ILDRSMKTMM ETMKLMMEKV D LLYASTAV GTSAPMLPSH PAPPRIYPQL PSAPTADEWD IIP

UniProtKB: P protein

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Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 2 / 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: 8
Details: 50 mM Tris-HCl pH 8.0, 250 mM NaCl, 5% glycerol, 1 mM TCEP, and 4 mM MgCl2
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
TemperatureMin: 63.0 K / Max: 77.0 K
SoftwareName: EPU
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 5562 / Average exposure time: 1.7 sec. / Average electron dose: 50.4 e/Å2
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: 2.0 µm / Nominal defocus min: 1.0 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: 3933494
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: SIMULTANEOUS ITERATIVE (SIRT) / Resolution.type: BY AUTHOR / Resolution: 3.09 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 214250
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 / Protocol: OTHER / Overall B value: 73.5
Output model

PDB-9n0q:
3.09A Bornavirus L-P complex (without incubation with RNA/NTP) (state 1)

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