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- EMDB-48793: 3.37A Bornavirus L-P complex (after incubation with RNA/NTP) (state 3) -

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Basic information

Entry
Database: EMDB / ID: EMD-48793
Title3.37A Bornavirus L-P complex (after incubation with RNA/NTP) (state 3)
Map data3.37A Bornavirus L-P complex (after incubation with RNA/NTP) (state 3)
Sample
  • Complex: Bornavirus L-P complex (after incubation with RNA/NTP) (state 3)
    • 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 / host cell / 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: 3.37 Å
AuthorsLiu B / Yang G / Wang D
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of the Bornavirus polymerase (L) protein in complex with the tetrameric phosphoprotein (P) - (after incubation with RNA/NTP) (state 3)
Authors: Liu B / Yang G / Wang D
History
DepositionJan 24, 2025-
Header (metadata) releaseSep 10, 2025-
Map releaseSep 10, 2025-
UpdateSep 10, 2025-
Current statusSep 10, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48793.png

Downloads & links

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Map

FileDownload / File: emd_48793.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3.37A Bornavirus L-P complex (after incubation with RNA/NTP) (state 3)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 254 pix.
= 255.016 Å		1 Å/pix.
x 254 pix.
= 255.016 Å		1 Å/pix.
x 254 pix.
= 255.016 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.004 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.0005666861 - 0.28504404
Average (Standard dev.)0.00047666839 (±0.0060165543)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions254254254
Spacing254254254
CellA=B=C: 255.01599 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map B

Fileemd_48793_half_map_1.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_48793_half_map_2.map
Annotationhalf map A
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 (after incubation with RNA/NTP) (state 3)

EntireName: Bornavirus L-P complex (after incubation with RNA/NTP) (state 3)
Components
  • Complex: Bornavirus L-P complex (after incubation with RNA/NTP) (state 3)
    • 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 (after incubation with RNA/NTP) (state 3)

SupramoleculeName: Bornavirus L-P complex (after incubation with RNA/NTP) (state 3)
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 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
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
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: 12867 / Average exposure time: 1.7 sec. / Average electron dose: 50.5 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: 9320492
CTF correctionType: 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: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 107976
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: OTHER / Overall B value: 73.5
Output model

PDB-9n0t:
3.37A Bornavirus L-P complex (after incubation with RNA/NTP) (state 3)

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