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- EMDB-51403: Structure of replicating Nipah Virus RNA Polymerase Complex - RNA... -

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Basic information

Entry
Database: EMDB / ID: EMD-51403
TitleStructure of replicating Nipah Virus RNA Polymerase Complex - RNA-bound state
Map dataComposite map
Sample
  • Complex: Nipah Virus RdRp Complex in actively replicating state.
    • Complex: Nipah Virus RdRp Complex
      • Protein or peptide: Phosphoprotein
      • Protein or peptide: RNA-directed RNA polymerase L
    • Complex: RNA
      • RNA: RNA (5'-R(P*AP*CP*CP*AP*AP*AP*CP*AP*A)-3')
      • RNA: RNA (5'-R(P*CP*CP*CP*UP*UP*GP*UP*UP*UP*GP*GP*U)-3')
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
KeywordsRNA Polymerase / Nipah Virus / negative strand RNA Virus / 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 / host cell cytoplasm / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / 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 / 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 / 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 / Mononegavirus L protein 2-O-ribose methyltransferase ...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 / Mononegavirus L protein 2-O-ribose methyltransferase / RNA-directed RNA polymerase L, C-terminal / Mononegavirus L protein 2'-O-ribose methyltransferase domain profile. / 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. / 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: 2.8 Å
AuthorsSala F / Ditter K / Dybkov O / Urlaub H / Hillen HS
Funding support Germany, 2 items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB1565 Germany
German Research Foundation (DFG)SFB1190 Germany
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionAug 22, 2024-
Header (metadata) releaseMar 5, 2025-
Map releaseMar 5, 2025-
UpdateMar 19, 2025-
Current statusMar 19, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51403.png

Downloads & links

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Map

FileDownload / File: emd_51403.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 480 pix.
= 400.32 Å		0.83 Å/pix.
x 480 pix.
= 400.32 Å		0.83 Å/pix.
x 480 pix.
= 400.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.834 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00578
Minimum - Maximum-0.0031530913 - 0.04150228
Average (Standard dev.)0.000037105106 (±0.0006126362)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 400.32 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 RdRp Complex in actively replicating state.

EntireName: Nipah Virus RdRp Complex in actively replicating state.
Components
  • Complex: Nipah Virus RdRp Complex in actively replicating state.
    • Complex: Nipah Virus RdRp Complex
      • Protein or peptide: Phosphoprotein
      • Protein or peptide: RNA-directed RNA polymerase L
    • Complex: RNA
      • RNA: RNA (5'-R(P*AP*CP*CP*AP*AP*AP*CP*AP*A)-3')
      • RNA: RNA (5'-R(P*CP*CP*CP*UP*UP*GP*UP*UP*UP*GP*GP*U)-3')
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Nipah Virus RdRp Complex in actively replicating state.

SupramoleculeName: Nipah Virus RdRp Complex in actively replicating state.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Molecular weightTheoretical: 570 KDa

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Supramolecule #2: Nipah Virus RdRp Complex

SupramoleculeName: Nipah Virus RdRp Complex / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1, #4
Source (natural)Organism: Henipavirus nipahense

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Supramolecule #3: RNA

SupramoleculeName: RNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Henipavirus nipahense

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Macromolecule #1: Phosphoprotein

MacromoleculeName: Phosphoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Henipavirus nipahense
Molecular weightTheoretical: 78.39032 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MDKLELVNDG LNIIDFIQKN QKEIQKTYGR SSIQQPSIKD QTKAWEDFLQ CTSGESEQVE GGMSKDDGDV ERRNLEDLSS TSPTDGTIG KRVSNTRDWA EGSDDIQLDP VVTDVVYHDH GGECTGYGFT SSPERGWSDY TSGANNGNVC LVSDAKMLSY A PEIAVSKE ...String:
MDKLELVNDG LNIIDFIQKN QKEIQKTYGR SSIQQPSIKD QTKAWEDFLQ CTSGESEQVE GGMSKDDGDV ERRNLEDLSS TSPTDGTIG KRVSNTRDWA EGSDDIQLDP VVTDVVYHDH GGECTGYGFT SSPERGWSDY TSGANNGNVC LVSDAKMLSY A PEIAVSKE DRETDLVHLE NKLSTTGLNP TAVPFTLRNL SDPAKDSPVI AEHYYGLGVK EQNVGPQTSR NVNLDSIKLY TS DDEEADQ LEFEDEFAGS SSEVIVGISP EDEEPSSVGG KPNESIGRTI EGQSIRDNLQ AKDNKSTDVP GAGPKDSAVK EEP PQKRLP MLAEEFECSG SEDPIIRELL KENSLINCQQ GKDAQPPYHW SIERSISPDK TEIVNGAVQT ADRQRPGTPM PKSR GIPIK KGTDAKYPSA GTENVPGSKS GATRHVRGSP PYQEGKSVNA ENVQLNASTA VKETDKSEVN PVDDNDSLDD KYIMP SDDF SNTFFPHDTD RLNYHADHLG DYDLETLCEE SVLMGVINSI KLINLDMRLN HIEEQVKEIP KIINKLESID RVLAKT NTA LSTIEGHLVS MMIMIPGKGK GERKGKNNPE LKPVIGRDIL EQQSLFSFDN VKNFRDGSLT NEPYGAAVQL REDLILP EL NFEETNASQF VPMADDSSRD VIKTLIRTHI KDRELRSELI GYLNKAENDE EIQEIANTVN DIIDGNI

UniProtKB: Phosphoprotein

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Macromolecule #4: RNA-directed RNA polymerase L

MacromoleculeName: RNA-directed RNA polymerase L / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA-directed RNA polymerase
Source (natural)Organism: Henipavirus nipahense
Molecular weightTheoretical: 257.706219 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: SNAADELSIS DIIYPECHLD SPIVSGKLIS AIEYAQLRHN QPSDDKRLSE NIRLNLHGKR KSLYILRQSK QGDYIRNNIK NLKEFMHIA YPECNNILFS ITSQGMTSKL DNIMKKSFKA YNIISKKVIG MLQNITRNLI TQDRRDEIIN IHECRRLGDL G KNMSQSKW ...String:
SNAADELSIS DIIYPECHLD SPIVSGKLIS AIEYAQLRHN QPSDDKRLSE NIRLNLHGKR KSLYILRQSK QGDYIRNNIK NLKEFMHIA YPECNNILFS ITSQGMTSKL DNIMKKSFKA YNIISKKVIG MLQNITRNLI TQDRRDEIIN IHECRRLGDL G KNMSQSKW YECFLFWFTI KTEMRAVIKN SQKPKFRSDS CIIHMRDKST EIILNPNLIC IFKSDKTGKK CYYLTPEMVL MY CDVLEGR MMMETTVKSD IKYQPLISRS NALWGLIDPL FPVMGNRIYN IVSMIEPLVL ALLQLKDEAR ILRGAFLHHC IKE MHQELS ECGFTDQKIR SMFIDDLLSI LNIDNIHLLA EFFSFFRTFG HPILEAKVAA EKVREHMLAD KVLEYAPIMK AHAI FCGTI INGYRDRHGG AWPPLYLPAH ASKHIIRLKN SGESLTIDDC VKNWESFCGI QFDCFMELKL DSDLSMYMKD KALSP IKDE WDSVYPREVL SYTPPKSTEP RRLVDVFVND ENFDPYNMLE YVLSGAYLED EQFNVSYSLK EKETKQAGRL FAKMTY KMR ACQVIAEALI ASGVGKYFKE NGMVKDEHEL LKTLFQLSIS SVPRGNSQGN DPQSINNIER DFQYFKGVTT NVKDKKN NS FNKVKSALNN PCQADGVHHN MSPNTRNRYK CSNTSKSFLD YHTEFNPHNH YKSDNTEAAV LSRYEDNTGT KFDTVSAF L TTDLKKFCLN WRYESMAIFA ERLDEIYGLP GFFNWMHKRL ERSVIYVADP NCPPNIDKHM ELEKTPEDDI FIHYPKGGI EGYSQKTWTI ATIPFLFLSA YETNTRIAAI VQGDNESIAI TQKVHPNLPY KVKKEICAKQ AQLYFERLRM NLRALGHNLK ATETIISTH LFIYSKKIHY DGAVLSQALK SMSRCCFWSE TLVDETRSAC SNISTTIAKA IENGLSRNVG YCINILKVIQ Q LLISTEFS INETLTLDVT SPISNNLDWL ITAALIPAPI GGFNYLNLSR IFVRNIGDPV TASLADLKRM IDHSIMTESV LQ KVMNQEP GDASFLDWAS DPYSGNLPDS QSITKTIKNI TARTILRNSP NPMLKGLFHD KSFDEDLELA SFLMDRRVIL PRA AHEILD NSLTGAREEI AGLLDTTKGL IRSGLRKSGL QPKLVSRLSH HDYNQFLILN KLLSNRRQND LISSNTCSVD LARA LRSHM WRELALGRVI YGLEVPDALE AMVGRYITGS LECQICEQGN TMYGWFFVPR DSQLDQVDRE HSSIRVPYVG SSTDE RSDI KLGNVKRPTK ALRSAIRIAT VYTWAYGDNE ECWYEAWYLA SQRVNIDLDV LKAITPVSTS NNLSHRLRDK STQFKF AGS VLNRVSRYVN ISNDNLDFRI EGEKVDTNLI YQQAMLLGLS VLEGKFRLRL ETDDYNGIYH LHVKDNCCVK EVADVGQ VD AELPIPEYTE VDNNHLIYDP DPVSEIDCSR LSNQESKSRE LDFPLWSTEE LHDVLAKTVA QTVLEIITKA DKDVLKQH L AIDSDDNINS LITEFLIVDP ELFALYLGQS ISIKWAFEIH HRRPRGRHTM VDLLSDLVSN TSKHTYKVLS NALSHPRVF KRFVNCGLLL PTQGPYLHQQ DFEKLSQNLL VTSYMIYLMN WCDFKKSPFL IAEQDETVIS LREDIITSKH LCVIIDLYAN HHKPPWIID LNPQEKICVL RDFISKSRHV DTSSRSWNTS DLDFVIFYAS LTYLRRGIIK QLRIRQVTEV IDTTTMLRDN I IVENPPIK TGVLDIRGCI IYNLEEILSM NTKSASKKIF NLNSRPSVEN HKYRRIGLNS SSCYKALNLS PLIQRYLPSG AQ RLFIGEG SGSMMLLYQS TLGQSISFYN SGIDGDYIPG QRELKLFPSE YSIAEEDPSL TGKLKGLVVP LFNGRPETTW IGN LDSYEY IINRTAGRSI GLVHSDMESG IDKNVEEILV EHSHLISIAI NVMMEDGLLV SKIAYTPGFP ISRLFNMYRS YFGL VLVCF PVYSNPDSTE VYLLCLQKTV KTIVPPQKVL EHSNLHDEVN DQGITSVIFK IKNSQSKQFH DDLKKYYQID QPFFV PTKI TSDEQVLLQA GLKLNGPEIL KSEISYDIGS DINTLRDTII IMLNEAMNYF DDNRSPSHHL EPYPVLERTR IKTIMN CVT KKVIVYSLIK FKDTKSSELY HIKNNIRRKV LILDFRSKLM TKTLPKGMQE RREKNGFKEV WIVDLSNREV KIWWKII GY ISII

UniProtKB: RNA-directed RNA polymerase L

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Macromolecule #2: RNA (5'-R(P*AP*CP*CP*AP*AP*AP*CP*AP*A)-3')

MacromoleculeName: RNA (5'-R(P*AP*CP*CP*AP*AP*AP*CP*AP*A)-3') / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Henipavirus nipahense
Molecular weightTheoretical: 2.845823 KDa
SequenceString:
ACCAAACAA

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Macromolecule #3: RNA (5'-R(P*CP*CP*CP*UP*UP*GP*UP*UP*UP*GP*GP*U)-3')

MacromoleculeName: RNA (5'-R(P*CP*CP*CP*UP*UP*GP*UP*UP*UP*GP*GP*U)-3') / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: Henipavirus nipahense
Molecular weightTheoretical: 3.7432 KDa
SequenceString:
CCCUUGUUUG GU

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Macromolecule #5: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / type: ligand / ID: 5 / Number of copies: 1 / Formula: GNP
Molecular weightTheoretical: 522.196 Da
Chemical component information

ChemComp-GNP:
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GppNHp, GMPPNP, energy-carrying molecule analogue*YM

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Macromolecule #6: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 6 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #7: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 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 HEPES pH 8.0, 150 mM NaCl, 6 mM MgCl2, 10% glycerol, 5 mM DTT, 0.01% Tween 20
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 2.14 sec. / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000
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: 9886170
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Number images used: 330750
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0)
Final 3D classificationNumber classes: 4 / Avg.num./class: 600000 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

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

PDB-9gju:
Structure of replicating Nipah Virus RNA Polymerase Complex - RNA-bound state

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