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- EMDB-45968: Cryo EM structure of Nipah virus L-P polymerase complex -

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Basic information

Entry
Database: EMDB / ID: EMD-45968
TitleCryo EM structure of Nipah virus L-P polymerase complex
Map data
Sample
  • Complex: L-P polymerase complex
    • Protein or peptide: RNA-directed RNA polymerase L
    • Protein or peptide: Phosphoprotein
KeywordsNipah / virus / RNA polymerase. / VIRAL PROTEIN
Function / homology
Function and homology information


GDP polyribonucleotidyltransferase / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / Transferases; Transferring one-carbon groups; Methyltransferases / virion component / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / host cell cytoplasm / hydrolase activity / RNA-directed RNA polymerase / RNA-directed RNA polymerase activity / ATP binding
Similarity search - Function
Phosphoprotein P region PNT disordered / Phosphoprotein P region PNT disordered / Paramyxovirus structural protein P/V, N-terminal domain / Paramyxovirus structural protein V/P N-terminus / Phosphoprotein P soyouz module / N-terminal region of Paramyxovirinae phosphoprotein (P) / RNA-directed RNA polymerase, paramyxovirus / P/V phosphoprotein, paramyxoviral / Paramyxovirus P/V phosphoprotein C-terminal / Mononegavirales RNA-directed RNA polymerase catalytic domain ...Phosphoprotein P region PNT disordered / Phosphoprotein P region PNT disordered / Paramyxovirus structural protein P/V, N-terminal domain / Paramyxovirus structural protein V/P N-terminus / Phosphoprotein P soyouz module / N-terminal region of Paramyxovirinae phosphoprotein (P) / RNA-directed RNA polymerase, paramyxovirus / P/V phosphoprotein, paramyxoviral / Paramyxovirus P/V phosphoprotein C-terminal / Mononegavirales RNA-directed RNA polymerase catalytic domain / Mononegavirus L protein 2-O-ribose methyltransferase / Mononegavirales mRNA-capping domain V / RNA-directed RNA polymerase L, C-terminal / Mononegavirales RNA dependent RNA polymerase / Mononegavirales mRNA-capping region V / RdRp of negative ssRNA viruses with non-segmented genomes catalytic domain profile. / Mononegavirus L protein 2'-O-ribose methyltransferase domain profile. / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase
Similarity search - Domain/homology
RNA-directed RNA polymerase L / Phosphoprotein
Similarity search - Component
Biological speciesHenipavirus nipahense
Methodsingle particle reconstruction / cryo EM / Resolution: 3.43 Å
AuthorsDeniston C / Buffalo C / Rohaim A
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19AI171413 United States
CitationJournal: To Be Published
Title: Cryo EM structure of Nipah virus L-P polymerase complex
Authors: Deniston C / Buffalo C / Rohaim A
History
DepositionJul 29, 2024-
Header (metadata) releaseJul 30, 2025-
Map releaseJul 30, 2025-
UpdateJul 30, 2025-
Current statusJul 30, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45968.png

Downloads & links

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Map

FileDownload / File: emd_45968.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 416 pix.
= 357.76 Å		0.86 Å/pix.
x 416 pix.
= 357.76 Å		0.86 Å/pix.
x 416 pix.
= 357.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.7
Minimum - Maximum-4.6079535 - 6.1642785
Average (Standard dev.)0.00019318995 (±0.08472493)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 357.76 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_45968_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_45968_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_45968_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : L-P polymerase complex

EntireName: L-P polymerase complex
Components
  • Complex: L-P polymerase complex
    • Protein or peptide: RNA-directed RNA polymerase L
    • Protein or peptide: Phosphoprotein

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Supramolecule #1: L-P polymerase complex

SupramoleculeName: L-P polymerase complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Henipavirus nipahense

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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: Henipavirus nipahense
Molecular weightTheoretical: 185.001125 KDa
Recombinant expressionOrganism: Baculovirus expression vector pFastBac1-HM
SequenceString: MASHHHHHHH HHHAQHDEAV DNKFNKEQQN AFYEILHLPN LNEEQRNAFI QSLKDDPSQS ANRRAEAKKL NDAQAPKVDN KFNKEQQNA FYEILHLPNL NEEQRNAFIQ SLKDDPSQSA NLLAEAKKLN DAQAPKVDAN GGGGSGGGGS LEVLFQGPAD E LSISDIIY ...String:
MASHHHHHHH HHHAQHDEAV DNKFNKEQQN AFYEILHLPN LNEEQRNAFI QSLKDDPSQS ANRRAEAKKL NDAQAPKVDN KFNKEQQNA FYEILHLPNL NEEQRNAFIQ SLKDDPSQSA NLLAEAKKLN DAQAPKVDAN GGGGSGGGGS LEVLFQGPAD E LSISDIIY PECHLDSPIV SGKLISAIEY AQLKHNQPSD DKRLSENIRL NLHGKRKSLY ILRQSKQGNY IRNNVKNLKE FM HIAYPEC NNTLFSITSQ GMTSKLDNIM RKSFKAYNII SKKVIGMLQN ITRNLITQDR RDEIINIHEC RRLGDLGKNM SQS KWYECF LFWFTIKTEM RAVIKNSQKP KFRSDSCIIH MRDKSTEIIL NPNLICIFKS DKTGKKCYYL TPEMVLMYCD VLEG RMMME TTIKSDIKYQ PLISRSNALW GLIDPLFPVM GNRIYNIVSM IEPLVLALLQ LKDEARILRG AFLHHCIKEM HQELS ECGF TDQKIRSMFI DDLLSILNID NIHLLAEFFS FFRTFGHPIL EAKVAAEKVR EHMLADKVLE YAPIMKAHAI FCGTII NGY RDRHGGAWPP LYLPAHASKH IIRLKNSGES LTIDDCVKNW ESFCGIQFDC FMELKLDSDL SMYMKDKALS PIKDEWD SV YPREVLSYTP PKSTEPRRLV DVFVNDENFD PYNMLEYVLS GAYLEDDQFN VSYSLKEKET KQAGRLFAKM TYKMRACQ V IAEALIASGV GKYFKENGMV KDEHELLKTL FQLSISSVPR GNSQGNDPQS INNIEKDFQC FKGVTTSVKD KKNDPFYKV KSALNNPCQA DGVYHNMSPN IRNRYKCSNT SKSFLDYHTE FNPHNHYKSD NTEAAVLSKY EDNTGTKFDT VSAFLTTDLK KFCLNWRYE SMAIFAERLD EIYGLPGFFN WMHKRLERSV IYVADPNCPP NIDKHMELEE TPEDDIFIHY PKGGIEGYSQ K TWTIATIP FLFLSAYETN TRIAAIVQGD NESIAITQKV HPNLPYKVKK EICAKQAQLY FERLRMNLRA LGHNLKATET II STHLFVY SKKIHYDGAV LSQALKSMSR CCFWSETLVD ETRSACSNIS TTIAKAIENG LSRNVGYCIN ILKVIQQLLI STE FSINET LTLDVTSPIS NNLDWLITAA LIPAPIGGFN YLNLSRIFVR NIGDPVTASL ADLKRMIDHS IMTESVLQKV MNQE PGDAS FLDWASDPYS GNLPDSQSIT KTIKNITART ILRNSPNPML KGLFHDKSFD EDLELASFLM DRRVILPRAA HEILD NSLT GAREEIAGLL DTTKGLIRSG LRKSGIQPRL VSRLSHHDYN QFLILNKLLS NRKQNDLISS NTCSVDLARA LRSHMW REL ALGRVIYGLE VPDALEAMVG RYITGSLECQ ICEQGNTMYG WFFVPRDSQL DQVDKEHSSI RVPYVGSSTD ERSDIKL GN VKRPTKALRS AIRIATVYTW AYGDNEECWY EAWYLASQRV NIDLDVLKAI TPVSTSNNLS HRLRDKSTQF KFAGSVLN R VSRYVNISND NLDFRIEGEK VDTNLIYQQA MLLGLSVLEG KFRLRLETDD YNGIYHLHVK DNCCVKEVAD VGQVDAELP IPEYTEVDNN HLIYDPDPV

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: Henipavirus nipahense
Molecular weightTheoretical: 79.183242 KDa
Recombinant expressionOrganism: Baculovirus expression vector pFastBac1-HM
SequenceString: MDKLELVNDG LNIIDFIQKN QKEIQKTYGR SSIQQPSIKD RTKAWEDFLQ CTSGESEQVE GGMSKDDGGV ERRSLEDLSS TSPTDGTIG KRVSNTRDWA EGSDDIQLDP VVTDVVYHDH GGECTGYGFT SSPERGWSDH SSGANNGDVC LVSDAKVLSY A PEIAVSKE ...String:
MDKLELVNDG LNIIDFIQKN QKEIQKTYGR SSIQQPSIKD RTKAWEDFLQ CTSGESEQVE GGMSKDDGGV ERRSLEDLSS TSPTDGTIG KRVSNTRDWA EGSDDIQLDP VVTDVVYHDH GGECTGYGFT SSPERGWSDH SSGANNGDVC LVSDAKVLSY A PEIAVSKE DRETDLVHLE DKLSATGLNP TAIPFTPKNL SVPAKDSPVI AEHYYGLGVR EQNVDPQTNR NVNLDSIKLY TS DDEEADQ LEFEDEFAGS SSEVIVGISP EEEEPSSAGR KPIESVGHII EGQSTRDSLQ IKGNKPADAP GAGPKDSAVK EKS PQKRLP MLAEEFECSG SEDPIIQELL KENSFINSQQ GKDAQPLYYR GIEGSRSPDK TEITSDAVQT ANKQRPGTPM PKSR GIPIK KGTDEKYPSA GTENVPGSKS GATRHVRGSP PYQEGKSVNA ENVQLNVPTV VKETDKSEAN PADDNDSLDD KYIMP SDDF SNTFFPHDTD RLNYHADHLG DYDLETLCEE SVLMGVINSI KLINLDMRLN HIEEQVKEIP KIINKLESID RVLAKT NTA LSTIEGHLVS MMIMIPGKGK GERKGKSNPE LKPVIGRDVL EQQSLFSFDN VKNFRDGSLT NEPYGAAVQL RGDLILP EL NFEETNASQF VPMADDSSRD VVKTLIRTHI KDRELRSELI GYLNRAENDE EIQEIANTVN DIIDGNIWSH PQFEK

UniProtKB: Phosphoprotein

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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 GLACIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 1.2 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.43 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 335177
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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