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- EMDB-50781: Cryo-EM structure of the Nipah virus polymerase (L) bound to the ... -

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Basic information

Entry
Database: EMDB / ID: EMD-50781
TitleCryo-EM structure of the Nipah virus polymerase (L) bound to the tetrameric phosphoprotein (P)
Map data
Sample
  • Complex: Nipah virus polymerase (L) bound to the tetrameric phosphoprotein (P)
    • Protein or peptide: RNA-directed RNA polymerase L
    • Protein or peptide: Phosphoprotein
  • Ligand: ZINC ION
KeywordsNipah virus L / Polymerase / Replicase / Transcriptase / VIRAL PROTEIN
Function / homology
Function and homology information


negative stranded viral RNA transcription / NNS virus cap methyltransferase / GDP polyribonucleotidyltransferase / negative stranded viral RNA replication / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / virion component / molecular adaptor activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / host cell cytoplasm / symbiont-mediated suppression of host innate immune response ...negative stranded viral RNA transcription / NNS virus cap methyltransferase / GDP polyribonucleotidyltransferase / negative stranded viral RNA replication / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / virion component / molecular adaptor activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / host cell cytoplasm / symbiont-mediated suppression of host innate immune response / RNA-directed RNA polymerase / RNA-directed RNA polymerase activity / GTPase 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: 2.49 Å
AuthorsBalikci E / Gunl F / Carrique L / Keown JR / Fodor E / Grimes JM
Funding support United States, 1 items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationINV-048922 United States
CitationJournal: EMBO J / Year: 2025
Title: Structure of the Nipah virus polymerase complex.
Authors: Esra Balıkçı / Franziska Günl / Loïc Carrique / Jeremy R Keown / Ervin Fodor / Jonathan M Grimes /
Abstract: Nipah virus is a highly virulent zoonotic paramyxovirus causing severe respiratory and neurological disease. Despite its lethality, there is no approved treatment for Nipah virus infection. The viral ...Nipah virus is a highly virulent zoonotic paramyxovirus causing severe respiratory and neurological disease. Despite its lethality, there is no approved treatment for Nipah virus infection. The viral polymerase complex, composed of the polymerase (L) and phosphoprotein (P), replicates and transcribes the viral RNA genome. Here, we describe structures of the Nipah virus L-P polymerase complex and the L-protein's Connecting Domain (CD). The cryo-electron microscopy L-P complex structure reveals the organization of the RNA-dependent RNA polymerase (RdRp) and polyribonucleotidyl transferase (PRNTase) domains of the L-protein, and shows how the P-protein, which forms a tetramer, interacts with the RdRp-domain of the L-protein. The crystal structure of the CD-domain alone reveals binding of three Mg ions. Modelling of this domain onto an AlphaFold 3 model of an RNA-L-P complex suggests a catalytic role for one Mg ion in mRNA capping. These findings offer insights into the structural details of the L-P polymerase complex and the molecular interactions between L-protein and P-protein, shedding light on the mechanisms of the replication machinery. This work will underpin efforts to develop antiviral drugs that target the polymerase complex of Nipah virus.
History
DepositionJun 26, 2024-
Header (metadata) releaseJan 8, 2025-
Map releaseJan 8, 2025-
UpdateJan 22, 2025-
Current statusJan 22, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50781.png

Downloads & links

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Map

FileDownload / File: emd_50781.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.73 Å/pix.
x 512 pix.
= 373.914 Å		0.73 Å/pix.
x 512 pix.
= 373.914 Å		0.73 Å/pix.
x 512 pix.
= 373.914 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.7303 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.0
Minimum - Maximum-54.750219999999999 - 66.063329999999993
Average (Standard dev.)-0.0007599686 (±0.9079539)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 373.9136 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Nipah virus polymerase (L) bound to the tetrameric phosphoprotein (P)

EntireName: Nipah virus polymerase (L) bound to the tetrameric phosphoprotein (P)
Components
  • Complex: Nipah virus polymerase (L) bound to the tetrameric phosphoprotein (P)
    • Protein or peptide: RNA-directed RNA polymerase L
    • Protein or peptide: Phosphoprotein
  • Ligand: ZINC ION

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Supramolecule #1: Nipah virus polymerase (L) bound to the tetrameric phosphoprotein (P)

SupramoleculeName: Nipah virus polymerase (L) bound to the tetrameric phosphoprotein (P)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Henipavirus nipahense
Molecular weightTheoretical: 570 KDa

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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: 257.433953 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: ADELSISDII YPECHLDSPI VSGKLISAIE YAQLRHNQPS DDKRLSENIR LNLHGKRKSL YILRQSKQGD YIRNNIKNLK EFMHIAYPE CNNILFSITS QGMTSKLDNI MKKSFKAYNI ISKKVIGMLQ NITRNLITQD RRDEIINIHE CRRLGDLGKN M SQSKWYEC ...String:
ADELSISDII YPECHLDSPI VSGKLISAIE YAQLRHNQPS DDKRLSENIR LNLHGKRKSL YILRQSKQGD YIRNNIKNLK EFMHIAYPE CNNILFSITS QGMTSKLDNI MKKSFKAYNI ISKKVIGMLQ NITRNLITQD RRDEIINIHE CRRLGDLGKN M SQSKWYEC FLFWFTIKTE MRAVIKNSQK PKFRSDSCII HMRDKSTEII LNPNLICIFK SDKTGKKCYY LTPEMVLMYC DV LEGRMMM ETTVKSDIKY QPLISRSNAL WGLIDPLFPV MGNRIYNIVS MIEPLVLALL QLKDEARILR GAFLHHCIKE MHQ ELSECG FTDQKIRSMF IDDLLSILNI DNIHLLAEFF SFFRTFGHPI LEAKVAAEKV REHMLADKVL EYAPIMKAHA IFCG TIING YRDRHGGAWP PLYLPAHASK HIIRLKNSGE SLTIDDCVKN WESFCGIQFD CFMELKLDSD LSMYMKDKAL SPIKD EWDS VYPREVLSYT PPKSTEPRRL VDVFVNDENF DPYNMLEYVL SGAYLEDEQF NVSYSLKEKE TKQAGRLFAK MTYKMR ACQ VIAEALIASG VGKYFKENGM VKDEHELLKT LFQLSISSVP RGNSQGNDPQ SINNIERDFQ YFKGVTTNVK DKKNNSF NK VKSALNNPCQ ADGVHHNMSP NTRNRYKCSN TSKSFLDYHT EFNPHNHYKS DNTEAAVLSR YEDNTGTKFD TVSAFLTT D LKKFCLNWRY ESMAIFAERL DEIYGLPGFF NWMHKRLERS VIYVADPNCP PNIDKHMELE KTPEDDIFIH YPKGGIEGY SQKTWTIATI PFLFLSAYET NTRIAAIVQG DNESIAITQK VHPNLPYKVK KEICAKQAQL YFERLRMNLR ALGHNLKATE TIISTHLFI YSKKIHYDGA VLSQALKSMS RCCFWSETLV DETRSACSNI STTIAKAIEN GLSRNVGYCI NILKVIQQLL I STEFSINE TLTLDVTSPI SNNLDWLITA ALIPAPIGGF NYLNLSRIFV RNIGDPVTAS LADLKRMIDH SIMTESVLQK VM NQEPGDA SFLDWASDPY SGNLPDSQSI TKTIKNITAR TILRNSPNPM LKGLFHDKSF DEDLELASFL MDRRVILPRA AHE ILDNSL TGAREEIAGL LDTTKGLIRS GLRKSGLQPK LVSRLSHHDY NQFLILNKLL SNRRQNDLIS SNTCSVDLAR ALRS HMWRE LALGRVIYGL EVPDALEAMV GRYITGSLEC QICEQGNTMY GWFFVPRDSQ LDQVDREHSS IRVPYVGSST DERSD IKLG NVKRPTKALR SAIRIATVYT WAYGDNEECW YEAWYLASQR VNIDLDVLKA ITPVSTSNNL SHRLRDKSTQ FKFAGS VLN RVSRYVNISN DNLDFRIEGE KVDTNLIYQQ AMLLGLSVLE GKFRLRLETD DYNGIYHLHV KDNCCVKEVA DVGQVDA EL PIPEYTEVDN NHLIYDPDPV SEIDCSRLSN QESKSRELDF PLWSTEELHD VLAKTVAQTV LEIITKADKD VLKQHLAI D SDDNINSLIT EFLIVDPELF ALYLGQSISI KWAFEIHHRR PRGRHTMVDL LSDLVSNTSK HTYKVLSNAL SHPRVFKRF VNCGLLLPTQ GPYLHQQDFE KLSQNLLVTS YMIYLMNWCD FKKSPFLIAE QDETVISLRE DIITSKHLCV IIDLYANHHK PPWIIDLNP QEKICVLRDF ISKSRHVDTS SRSWNTSDLD FVIFYASLTY LRRGIIKQLR IRQVTEVIDT TTMLRDNIIV E NPPIKTGV LDIRGCIIYN LEEILSMNTK SASKKIFNLN SRPSVENHKY RRIGLNSSSC YKALNLSPLI QRYLPSGAQR LF IGEGSGS MMLLYQSTLG QSISFYNSGI DGDYIPGQRE LKLFPSEYSI AEEDPSLTGK LKGLVVPLFN GRPETTWIGN LDS YEYIIN RTAGRSIGLV HSDMESGIDK NVEEILVEHS HLISIAINVM MEDGLLVSKI AYTPGFPISR LFNMYRSYFG LVLV CFPVY SNPDSTEVYL LCLQKTVKTI VPPQKVLEHS NLHDEVNDQG ITSVIFKIKN SQSKQFHDDL KKYYQIDQPF FVPTK ITSD EQVLLQAGLK LNGPEILKSE ISYDIGSDIN TLRDTIIIML NEAMNYFDDN RSPSHHLEPY PVLERTRIKT IMNCVT KKV IVYSLIKFKD TKSSELYHIK NNIRRKVLIL DFRSKLMTKT LPKGMQERRE KNGFKEVWIV DLSNREVKIW WKIIGYI SI I

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: 78.259109 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DKLELVNDGL NIIDFIQKNQ KEIQKTYGRS SIQQPSIKDQ TKAWEDFLQC TSGESEQVEG GMSKDDGDVE RRNLEDLSST SPTDGTIGK RVSNTRDWAE GSDDIQLDPV VTDVVYHDHG GECTGYGFTS SPERGWSDYT SGANNGNVCL VSDAKMLSYA P EIAVSKED ...String:
DKLELVNDGL NIIDFIQKNQ KEIQKTYGRS SIQQPSIKDQ TKAWEDFLQC TSGESEQVEG GMSKDDGDVE RRNLEDLSST SPTDGTIGK RVSNTRDWAE GSDDIQLDPV VTDVVYHDHG GECTGYGFTS SPERGWSDYT SGANNGNVCL VSDAKMLSYA P EIAVSKED RETDLVHLEN KLSTTGLNPT AVPFTLRNLS DPAKDSPVIA EHYYGLGVKE QNVGPQTSRN VNLDSIKLYT SD DEEADQL EFEDEFAGSS SEVIVGISPE DEEPSSVGGK PNESIGRTIE GQSIRDNLQA KDNKSTDVPG AGPKDSAVKE EPP QKRLPM LAEEFECSGS EDPIIRELLK ENSLINCQQG KDAQPPYHWS IERSISPDKT EIVNGAVQTA DRQRPGTPMP KSRG IPIKK GTDAKYPSAG TENVPGSKSG ATRHVRGSPP YQEGKSVNAE NVQLNASTAV KETDKSEVNP VDDNDSLDDK YIMPS DDFS NTFFPHDTDR LNYHADHLGD YDLETLCEES VLMGVINSIK LINLDMRLNH IEEQVKEIPK IINKLESIDR VLAKTN TAL STIEGHLVSM MIMIPGKGKG ERKGKNNPEL KPVIGRDILE QQSLFSFDNV KNFRDGSLTN EPYGAAVQLR EDLILPE LN FEETNASQFV PMADDSSRDV IKTLIRTHIK DRELRSELIG YLNKAENDEE IQEIANTVND IIDGNI

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

Concentration0.5 mg/mL
BufferpH: 7.4
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: TFS FALCON 4i (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: 2.4 µm / Nominal defocus min: 1.4000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 6748913
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.49 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. V4.4.1) / Number images used: 490675
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. V4.4.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. V4.4.1)
Final 3D classificationNumber classes: 3 / Avg.num./class: 50000 / Software - Name: cryoSPARC (ver. V4.4.1)

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Atomic model buiding 1

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

PDB-9fux:
Cryo-EM structure of the Nipah virus polymerase (L) bound to the tetrameric phosphoprotein (P)

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