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- EMDB-72189: Structure of the Borna Disease Virus 1 L and co-factor P Protein ... -

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Basic information

Entry
Database: EMDB / ID: EMD-72189
TitleStructure of the Borna Disease Virus 1 L and co-factor P Protein in an apo state
Map data
Sample
  • Complex: Borna Disease Virus 1 L and co-factor P Protein
    • Protein or peptide: Isoform p24 of Phosphoprotein
    • Protein or peptide: RNA-directed RNA polymerase L
  • Ligand: ZINC ION
KeywordsL Protein / Polymerase / NNS / Phosphoprotein / VIRAL PROTEIN / TRANSFERASE
Function / homology
Function and homology information


: / virion component / host cell cytoplasm / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / symbiont-mediated suppression of host innate immune response / RNA-directed RNA polymerase / RNA-directed RNA polymerase activity / host cell nucleus / 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
Phosphoprotein / RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesBorna disease virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 2.77 Å
AuthorsOgino T / Chakrapani S / Gibbs E / Ogino M
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21 AI176323 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI146172 United States
CitationJournal: Nucleic Acids Res / Year: 2026
Title: Structure and function of the RNA polymerase complex of Borna disease virus, a nuclear-replicating non-segmented negative-strand RNA virus.
Authors: Eric Gibbs / Minako Ogino / Takehiro Kanda / Dean Watkins / Kyle Whiddon / Keizo Tomonaga / Sudha Chakrapani / Tomoaki Ogino /
Abstract: Borna disease virus 1 (BoDV-1) is a non-segmented negative-strand (NNS) RNA virus that uniquely replicates in the nucleus of mammalian host cells, in contrast to most NNS RNA viruses that replicate ...Borna disease virus 1 (BoDV-1) is a non-segmented negative-strand (NNS) RNA virus that uniquely replicates in the nucleus of mammalian host cells, in contrast to most NNS RNA viruses that replicate in the cytoplasm. The mechanisms underlying nuclear replication of BoDV-1 and related bornaviruses with their RNA-dependent RNA polymerase (RdRp) complexes remain poorly understood. Here, we report the 2.8 Å cryo-EM structure of the BoDV-1 RdRp complex, comprising the large (L) protein and tetrameric phosphoprotein (P). The L protein features an N-terminal superdomain containing the RdRp and GDP polyribonucleotidyltransferase (PRNTase, mRNA-capping enzyme) domains, along with three C-terminal appendages, including a methyltransferase-like domain. The RdRp initiates de novo RNA synthesis internally at the genomic promoter, producing 5'-triphosphorylated transcripts corresponding to the 5' end of the anti-genome. P interacts with the fingers RdRp subdomain of L. Structure-guided mutagenesis shows that the residues involved in the L-P interaction are essential for efficient transcription initiation and, consequently, for viral gene expression. A flexible loop within the PRNTase domain, analogous to the rhabdovirus priming-capping loop, appears critical for transcription initiation. These findings provide the structural and functional insights into the BoDV-1 RdRp and support a shared evolutionary origin between nuclear and cytoplasmic NNS RNA viruses.
History
DepositionAug 18, 2025-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72189.png

Downloads & links

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Map

FileDownload / File: emd_72189.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 300 pix.
= 252. Å		0.84 Å/pix.
x 300 pix.
= 252. Å		0.84 Å/pix.
x 300 pix.
= 252. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.003
Minimum - Maximum-0.013090731 - 0.030778563
Average (Standard dev.)0.000025266932 (±0.00094213546)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 251.99998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_72189_msk_1.map
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Half map: #2

Fileemd_72189_half_map_1.map
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Half map: #1

Fileemd_72189_half_map_2.map
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Sample components

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Entire : Borna Disease Virus 1 L and co-factor P Protein

EntireName: Borna Disease Virus 1 L and co-factor P Protein
Components
  • Complex: Borna Disease Virus 1 L and co-factor P Protein
    • Protein or peptide: Isoform p24 of Phosphoprotein
    • Protein or peptide: RNA-directed RNA polymerase L
  • Ligand: ZINC ION

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Supramolecule #1: Borna Disease Virus 1 L and co-factor P Protein

SupramoleculeName: Borna Disease Virus 1 L and co-factor P Protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2, #1
Source (natural)Organism: Borna disease virus 1

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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: Borna disease virus 1
Molecular weightTheoretical: 193.155938 KDa
Recombinant expressionOrganism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
SequenceString: MSFHASLLRE EETPRPVAGI NRTDQSLKNP LLGTEVSFCL KSSSLPHHVR ALGQIKAKNL ASCDYYLLFR QVVLPPEVYP IGVLIRAAE AILTVIVSAW KLDHMTKTLY SSVRYALTNP RVRAQLELHI AYQRIVGQVS YSREADIGPK RLGNMSLQFI Q SLVIATID ...String:
MSFHASLLRE EETPRPVAGI NRTDQSLKNP LLGTEVSFCL KSSSLPHHVR ALGQIKAKNL ASCDYYLLFR QVVLPPEVYP IGVLIRAAE AILTVIVSAW KLDHMTKTLY SSVRYALTNP RVRAQLELHI AYQRIVGQVS YSREADIGPK RLGNMSLQFI Q SLVIATID TTSCLMTYNH FLAAADTAKS RCHLLIASVV QGALWEQGSF LDHIINMIDT IDSINLPHDD YFTIIKSISP YS QGLVMGR HNVSVSSDFA SVFTIPESCP QLDSLLKKLL QLDPVLLLMV SSVQKSWYFP EIRMVDGSRE QLHKMRVELE TPQ ALLSYG HTLLSIFRAE FIKGYVSKNA KWPPVHLLPG CDKSIKNARE LGRWSPVFDR RWQLFAKVVI LRIADLDMDP DFND IVSDK AIISSRRDWV FEYNAAAFWK KYGERLERPP ARSGPSRLVN ALIDGRLDNI PALLEPFYRG AVEFEDRLTV LVPKE KELK VKGRFFSKQT LAIRIYQVVA EAALKNEVMP YLKTHSMTMS STALTHLLNR LSHTITKGDS FVINLDYSSW CNGFRP ELQ APLCRQLDQM FNCGYFFRTG CTLPCFTTFI IQDRFNPPYS FRGEPVEDGV TCAVGTKTMG EGMRQKLWTI LTSCWEI IA LREINVTFNI LGQGDNQTII VHKSASQNNQ 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 NTLMARFLRE KGY TSDARP SIQGGTLTHR LPSRGDSRQG LTGYVNILST WLRFSSDYLH SFSKSSDDYT IHFQHVFTYG CLYADSVIRS GGVI STPYL LSASCKTCFE KIDSEEFVLA CEPQYRGAEW LISKPVTVPE QIIDAEVEFD PCVSASYCLG ILIGKSFLVD IRASG HDIM EQRTWANLER FSVSDMQKLP WSIVIRSLWR FLIGARLLQF EKAGLIRMLY AATGPTFSFL MKVFQDSALL MDCAPL DRL SPRINFHSRG DLVAKLVLLP FINPGIVEIE VSRIDSKYHA VSEANMDLYI AAAKSVGVKP TQFVEETNDF TARGHHH GC YSLSWSKSRN QSQVLKMVVR KLKLCVLYIY PTVDPAVALD LCHLPALTII LVLGGDPAYY ERLLEMDLCG AVSSRVDI P HSLAARTHRG FTIGPDAGPG VIRLDKLESV CYAHPCLEEL EFNAYLDSEL VDISDMCCLP LATPCKALFR PVYRSLQSF RLALMDNYSF VMDLITIRGL DIRPHLEEFD ELLVVGQHIL GQPVLVEVVY YVGVVGKRPV LARHPWSADL KRITVGGRAP CPSAAGLRD EDCRGSLLVG LPAGLTQLLV VDGTHHHHHH HH

UniProtKB: RNA-directed RNA polymerase L

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Macromolecule #2: Isoform p24 of Phosphoprotein

MacromoleculeName: Isoform p24 of Phosphoprotein / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Borna disease virus 1
Molecular weightTheoretical: 22.489598 KDa
Recombinant expressionOrganism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
SequenceString: MATRPSSLVD SLEDEEDPQT LRRERSGSPR PRKIPRNALT QPVDQLLKDL RKNPSMISDP DQRTGREQLS NDELIKKLVT ELAENSMIE AEEVRGTLGD ISARIEAGFE SLSALQVETI QTAQRCDHSD SIRILGENIK ILDRSMKTMM ETMKLMMEKV D LLYASTAV ...String:
MATRPSSLVD SLEDEEDPQT LRRERSGSPR PRKIPRNALT QPVDQLLKDL RKNPSMISDP DQRTGREQLS NDELIKKLVT ELAENSMIE AEEVRGTLGD ISARIEAGFE SLSALQVETI QTAQRCDHSD SIRILGENIK ILDRSMKTMM ETMKLMMEKV D LLYASTAV GTSAPMLPSH PAPPRIYPQL PSAPTADEWD IIP

UniProtKB: Phosphoprotein

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 16.0 µm / Nominal defocus min: 8.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: AlphaFold3 Generated Model
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.77 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Number images used: 224617
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2) / Details: Ab Initio
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0) / Details: Blush Maximization
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
Output model

PDB-9q3a:
Structure of the Borna Disease Virus 1 L and co-factor P Protein in an apo state

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