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- EMDB-51765: Structure of the borna disease virus 1 replication complex -

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Basic information

Entry
Database: EMDB / ID: EMD-51765
TitleStructure of the borna disease virus 1 replication complex
Map dataUnsharpened map
Sample
  • Complex: BoDV-1 Replication complex
    • Protein or peptide: RNA-directed RNA polymerase L
    • Protein or peptide: Phosphoprotein
  • Ligand: ZINC ION
Keywordspolymerase / phosphoprotein / bornavirus / RdRp / VIRAL PROTEIN
Function / homology
Function and homology information


exit of virus from host cell nucleus through nuclear pore / 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 / host cell cytoplasm / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / 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: 3.07 Å
AuthorsKeown JR / Carrique L / Grimes JM
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust200835/Z/16/Z United Kingdom
CitationJournal: To Be Published
Title: Structure of the borna disease virus 1 replication complex
Authors: Keown JR / Carrique L / Grimes JM
History
DepositionOct 9, 2024-
Header (metadata) releaseAug 20, 2025-
Map releaseAug 20, 2025-
UpdateAug 20, 2025-
Current statusAug 20, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51765.png

Downloads & links

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Map

FileDownload / File: emd_51765.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 300 pix.
= 279. Å		0.93 Å/pix.
x 300 pix.
= 279. Å		0.93 Å/pix.
x 300 pix.
= 279. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0332
Minimum - Maximum-0.096587315 - 0.21099702
Average (Standard dev.)0.0004506798 (±0.0060475976)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 279.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: DeepEMhancer -wideTarget -no halfmaps

Fileemd_51765_additional_1.map
AnnotationDeepEMhancer -wideTarget -no halfmaps
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: cryoSparc default Sharpened

Fileemd_51765_additional_2.map
AnnotationcryoSparc default Sharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_51765_half_map_1.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_51765_half_map_2.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : BoDV-1 Replication complex

EntireName: BoDV-1 Replication complex
Components
  • Complex: BoDV-1 Replication complex
    • Protein or peptide: RNA-directed RNA polymerase L
    • Protein or peptide: Phosphoprotein
  • Ligand: ZINC ION

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Supramolecule #1: BoDV-1 Replication complex

SupramoleculeName: BoDV-1 Replication complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
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: 196.999156 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MWSHPQFEKG GGSGGGSGGS SAWSHPQFEK HHHHHHHHEN LYFQGMSFHA SLLREEETPR PVAGINRTDQ SLKNPLLGTE VSFCLKSSS LPHHVRALGQ IKARNLASCD YYLLFRQVVL PPEVYPIGVL IRAAEAILTV IVSAWKLDHM TKTLYSSVRY A LTNPRVRA ...String:
MWSHPQFEKG GGSGGGSGGS SAWSHPQFEK HHHHHHHHEN LYFQGMSFHA SLLREEETPR PVAGINRTDQ SLKNPLLGTE VSFCLKSSS LPHHVRALGQ IKARNLASCD YYLLFRQVVL PPEVYPIGVL IRAAEAILTV IVSAWKLDHM TKTLYSSVRY A LTNPRVRA QLELHIAYQR IVGQVSYSRE ADIGPKRLGN MSLQFIQSLV IATIDTTSCL MTYNHFLAAA DTAKSRCHLL IA SVVQGAL WEQGSFLDHI INMIDIIDSI NLPHDDYFTI IKSIFPYSQG LVMGRHNVSV SSDFASVFAI PELCPQLDSL LKK LLQLDP VLLLMVSSVQ KSWYFPEIRM VDGSREQLHK MRVELETPQA LLSYGHTLLS IFRAEFIKGY VSKNAKWPPV HLLP GCDKS IKNARELGRW SPAFDRRWQL FEKVVILRIA DLDMDPDFND IVSDKAIISS RRDWVFEYNA AAFWKKYGER LERPP ARSG PSRLVNALID GRLDNIPALL EPFYRGAVEF EDRLTVLVPK EKELKVKGRF FSKQTLAIRI YQVVAEAALK NEVMPY LKT HSMTMSSTAL THLLNRLSHT ITKGDSFVIN LDYSSWCNGF RPELQAPICR QLDQMFNCGY FFRTGCTLPC FTTFIIQ DR FNPPYSLSGE PVEDGVTCAV GTKTMGEGMR QKLWTILTSC WEIIALREIN VTFNILGQGD NQTIIIHKSA SQNNQLLA E RALGALYKHA RLAGHNLKVE ECWVSDCLYE YGKKLFFRGV PVPGCLKQLS RVTDSTGELF PNLYSKLACL TSSCLSAAM ADTSPWVALA TGVCLYLIEL YVELPPAIIQ DESLLTTLCL VGPSIGGLPT PATLPSVFFR GMSDPLPFQL ALLQTLIKTT GVTCSLVNR VVKLRIAPYP DWLSLVTDPT SLNIAQVYRP ERQIRRWIEE AIATSSHSSR IATFFQQPLT EMAQLLARDL S TMMPLRPR DMSALFALSN VAYGLSIIDL FQKSSTVVSA SQAVHIEDVA LESVRYKESI IQGLLDTTEG YNMQPYLEGC TY LAAKQLR RLTWGRDLVG VTMPFVAEQF HPHSSVGAKA ELYLDAIIYC PQETLRSHHL TTRGDQPLYL GSNTAVKVQR GEI TGLAKS RAANLVKDTL VLHQWYKVRK VTDPHLNTLM ARFLLEKGYT SDARPSIQGG TLTHRLPSRG DSRQGLTGYV NILS TWLRF SSDYLHSFSK SSDDYTIHFQ HVFTYGCLYA DSVIRSGGVI STPYLLSASC KTCFEKIDSE EFVLACEPQY RGAEW LISK PVTVPEQITD AEVEFDPCVS ASYCLGILIG KSFLVDIRAS GHDIMEQRTW ANLERFSVSD MQKLPWSIVI RSLWRF LIG ARLLQFEKAG LIRMLYAATG PTFSFLMKVF QDSALLMDCA PLDRLSPRIN FHSRGDLVAK LVLLPFINPG IVEIEVS GI NSKYHAVSEA NMDLYIAAAK SVGVKPTQFV EETNDFTARG HHHGCYSLSW SKSRNQSQVL KMVVRKLKLC VLYIYPTV D PAVALDLCHL PALTIILVLG GDPAYYERLL EMDLCGAVSS RVDIPHSLAA RTHRGFAVGP DAGPGVIRLD RLESVCYAH PCLEELEFNA YLDSELVDIS DMCCLPLATP CKALFRPIYR SLQSFRLALM DNYSFVMDLI MIRGLDIRPH LEEFDELLVV GQHILGQPV LVEVVYYVGV VRKRPVLARH PWSADLKRIT VGGRAPCPSA ARLRDEDCQG SLLVGLPAGL TQLLIID

UniProtKB: RNA-directed RNA polymerase L

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Macromolecule #2: Phosphoprotein

MacromoleculeName: Phosphoprotein / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Borna disease virus 1
Molecular weightTheoretical: 24.603912 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MHHHHHHHHE NLYFQGMATR PSSLVDSLED EEDPQTLRRE RPGSPRPRKV PRNALTQPVD QLLKDLRKNP SMISDPDQRT GREQLSNDE LIKKLVTELA ENSMIEAEEV RGTLGDISAR IEAGFESLSA LQVETIQTAQ RCDHSDSIRI LGENIKILDR S MKTMMETM ...String:
MHHHHHHHHE NLYFQGMATR PSSLVDSLED EEDPQTLRRE RPGSPRPRKV PRNALTQPVD QLLKDLRKNP SMISDPDQRT GREQLSNDE LIKKLVTELA ENSMIEAEEV RGTLGDISAR IEAGFESLSA LQVETIQTAQ RCDHSDSIRI LGENIKILDR S MKTMMETM KLMMEKVDLL YASTAVGTSA PMLPSHPAPP RIYPQLPSAP TTDEWDIIP

UniProtKB: Phosphoprotein

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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

Concentration0.33 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMHEPEShepes
250.0 mMNaClsodium chloride
0.5 mMDTTdithiothreitol
5.0 % w/vGlycerolglycerol
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.4000000000000001 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: Alphafold 2
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 152965
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
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-9h1g:
Structure of the borna disease virus 1 replication complex

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