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- EMDB-21096: Parainfluenza virus 5 L-P complex with an alternate conformation ... -

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Basic information

Entry
Database: EMDB / ID: EMD-21096
TitleParainfluenza virus 5 L-P complex with an alternate conformation of the CD-MTase-CTD module
Map data
Sample
  • Complex: L-P complex
    • Complex: L protein
      • Protein or peptide: RNA-directed RNA polymerase L
    • Complex: P protein
      • Protein or peptide: Phosphoprotein
  • Ligand: ZINC ION
KeywordsVIRAL PROTEIN / POLYMERASE / METHYLTRANSFERASE / POLY-RIBONUCLEOTIDYLTRANSFERASE
Function / homology
Function and homology information


NNS virus cap methyltransferase / GDP polyribonucleotidyltransferase / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / virion component / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / host cell cytoplasm / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / GTPase activity / ATP binding
Similarity search - Function
RNA-directed RNA polymerase, paramyxovirus / Phosphoprotein P soyouz module / N-terminal region of Paramyxovirinae phosphoprotein (P) / 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 ...RNA-directed RNA polymerase, paramyxovirus / Phosphoprotein P soyouz module / N-terminal region of Paramyxovirinae phosphoprotein (P) / 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.
Similarity search - Domain/homology
Phosphoprotein / RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesSimian virus 5 (strain W3)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.63 Å
AuthorsAbdella R / He Y
Funding support United States, 5 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Cancer Institute (NIH/NCI)U54-CA193419 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P01-CA092584 United States
American Cancer SocietyIRG-15-173-21 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32-GM008382 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2020
Title: Structure of a paramyxovirus polymerase complex reveals a unique methyltransferase-CTD conformation.
Authors: Ryan Abdella / Megha Aggarwal / Takashi Okura / Robert A Lamb / Yuan He /
Abstract: Paramyxoviruses are enveloped, nonsegmented, negative-strand RNA viruses that cause a wide spectrum of human and animal diseases. The viral genome, packaged by the nucleoprotein (N), serves as a ...Paramyxoviruses are enveloped, nonsegmented, negative-strand RNA viruses that cause a wide spectrum of human and animal diseases. The viral genome, packaged by the nucleoprotein (N), serves as a template for the polymerase complex, composed of the large protein (L) and the homo-tetrameric phosphoprotein (P). The ∼250-kDa L possesses all enzymatic activities necessary for its function but requires P in vivo. Structural information is available for individual P domains from different paramyxoviruses, but how P interacts with L and how that affects the activity of L is largely unknown due to the lack of high-resolution structures of this complex in this viral family. In this study we determined the structure of the L-P complex from parainfluenza virus 5 (PIV5) at 4.3-Å resolution using cryoelectron microscopy, as well as the oligomerization domain (OD) of P at 1.4-Å resolution using X-ray crystallography. P-OD associates with the RNA-dependent RNA polymerase domain of L and protrudes away from it, while the X domain of one chain of P is bound near the L nucleotide entry site. The methyltransferase (MTase) domain and the C-terminal domain (CTD) of L adopt a unique conformation, positioning the MTase active site immediately above the poly-ribonucleotidyltransferase domain and near the likely exit site for the product RNA 5' end. Our study reveals a potential mechanism that mononegavirus polymerases may employ to switch between transcription and genome replication. This knowledge will assist in the design and development of antivirals against paramyxoviruses.
History
DepositionDec 10, 2019-
Header (metadata) releaseJan 1, 2020-
Map releaseFeb 19, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.027
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.027
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6v86
  • Surface level: 0.027
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21096.png

Downloads & links

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Map

FileDownload / File: emd_21096.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.12 Å
Density
Contour LevelBy AUTHOR: 0.027 / Movie #1: 0.027
Minimum - Maximum-0.038610402 - 0.083207324
Average (Standard dev.)0.0001567096 (±0.0019646622)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 403.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.121.121.12
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z403.200403.200403.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.0390.0830.000

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Supplemental data

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Sample components

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Entire : L-P complex

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

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Supramolecule #1: L-P complex

SupramoleculeName: L-P complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Simian virus 5 (strain W3)
Molecular weightTheoretical: 170 KDa

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Supramolecule #2: L protein

SupramoleculeName: L protein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Simian virus 5 (strain W3)

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Supramolecule #3: P protein

SupramoleculeName: P protein / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 / Details: homo-tetramer
Source (natural)Organism: Simian virus 5 (strain W3)

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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: Simian virus 5 (strain W3) / Strain: W3
Molecular weightTheoretical: 256.195672 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAGSREILLP EVHLNSPIVK HKLYYYILLG NLPNEIDLDD LGPLHNQNWN QIAHEESNLA QRLVNVRNFL ITHIPDLRKG HWQEYVNVI LWPRILPLIP DFKINDQLPL LKNWDKLVKE SCSVINAGTS QCIQNLSYGL TGRGNLFTRS RELSGDRRDI D LKTVVAAW ...String:
MAGSREILLP EVHLNSPIVK HKLYYYILLG NLPNEIDLDD LGPLHNQNWN QIAHEESNLA QRLVNVRNFL ITHIPDLRKG HWQEYVNVI LWPRILPLIP DFKINDQLPL LKNWDKLVKE SCSVINAGTS QCIQNLSYGL TGRGNLFTRS RELSGDRRDI D LKTVVAAW HDSDWKRISD FWIMIKFQMR QLIVRQTDHN DSDLITYIEN REGIIIITPE LVALFNTENH TLTYMTFEIV LM VSDMYEG RHNILSLCTV STYLNPLKKR ITYLLSLVDN LAFQIGDAVY NIIALLESFV YAQLQMSDPI PELRGQFHAF VCS EILDAL RGTNSFTQDE LRTVTTNLIS PFQDLTPDLT AELLCIMRLW GHPMLTASQA AGKVRESMCA GKVLDFPTIM KTLA FFHTI LINGYRRKHH GVWPPLNLPG NASKGLTELM NDNTEISYEF TLKHWKEVSL IKFKKCFDAD AGEELSIFMK DKAIS APKQ DWMSVFRRSL IKQRHQHHQV PLPNPFNRRL LLNFLGDDKF DPNVELQYVT SGEYLHDDTF CASYSLKEKE IKPDGR IFA KLTKRMRSCQ VIAESLLANH AGKLMKENGV VMNQLSLTKS LLTMSQIGII SEKARKSTRD NINQPGFQNI QRNKSHH SK QVNQRDPSDD FELAASFLTT DLKKYCLQWR YQTIIPFAQS LNRMYGYPHL FEWIHLRLMR STLYVGDPFN PPADTSQF D LDKVINGDIF IVSPRGGIEG LCQKAWTMIS IAVIILSATE SGTRVMSMVQ GDNQAIAVTT RVPRSLPTLE KKTIAFRSC NLFFERLKCN NFGLGHHLKE QETIISSHFF VYSKRIFYQG RILTQALKNA SKLCLTADVL GECTQSSCSN LATTVMRLTE NGVEKDICF YLNIYMTIKQ LSYDIIFPQV SIPGDQITLE YINNPHLVSR LALLPSQLGG LNYLSCSRLF NRNIGDPVVS A VADLKRLI KSGCMDYWIL YNLLGRKPGN GSWATLAADP YSINIEYQYP PTTALKRHTQ QALMELSTNP MLRGIFSDNA QA EENNLAR FLLDREVIFP RVAHIIIEQT SVGRRKQIQG YLDSTRSIMR KSLEIKPLSN RKLNEILDYN INYLAYNLAL LKN AIEPPT YLKAMTLETC SIDIARNLRK LSWAPLLGGR NLEGLETPDP IEITAGALIV GSGYCEQCAA GDNRFTWFFL PSGI EIGGD PRDNPPIRVP YIGSRTDERR VASMAYIRGA SSSLKAVLRL AGVYIWAFGD TLENWIDALD LSHTRVNITL EQLQS LTPL PTSANLTHRL DDGTTTLKFT PASSYTFSSF THISNDEQYL TINDKTADSN IIYQQLMITG LGILETWNNP PINRTF EES TLHLHTGASC CVRPVDSCIL SEALTVKPHI TVPYSNKFVF DEDPLSEYET AKLESLSFQA QLGNIDAVDM TGKLTLL SQ FTARQIINAI TGLDESVSLT NDAIVASDYV SNWISECMYT KLDELFMYCG WELLLELSYQ MYYLRVVGWS NIVDYSYM I LRRIPGAALN NLASTLSHPK LFRRAINLDI VAPLNAPHFA SLDYIKMSVD AILWGCKRVI NVLSNGGDLE LVVTSEDSL ILSDRSMNLI ARKLTLLSLI HHNGLELPKI KGFSPDEKCF ALTEFLRKVV NSGLSSIENL SNFMYNVENP RLAAFASNNY YLTRKLLNS IRDTESGQVA VTSYYESLEY IDSLKLTPHV PGTSCIEDDS LCTNDYIIWI IESNANLEKY PIPNSPEDDS N FHNFKLNA PSHHTLRPLG LSSTAWYKGI SCCRYLERLK LPQGDHLYIA EGSGASMTII EYLFPGRKIY YNSLFSSGDN PP QRNYAPM PTQFIESVPY KLWQAHTDQY PEIFEDFIPL WNGNAAMTDI GMTACVEFII NRVGPRTCSL VHVDLESSAS LNQ QCLSKP IINAIITATT VLCPHGVLIL KYSWLPFTRF STLITFLWCY FERITVLRST YSDPANHEVY LICILANNFA FQTV SQATG MAMTLTDQGF TLISPERINQ YWDGHLKQER IVAEAIDKVV LGENALFNSS DNELILKCGG TPNARNLIDI EPVAT FIEF EQLICTMLTT HLKEIIDITR SGTQDYESLL LTPYNLGLLG KISTIVRLLT ERILNHTIRN WLILPPSLRM IVKQDL EFG IFRITSILNS DRFLKLSPNR KYLIAQLTAG YIRKLIEGDC NIDLTRPIQK QIWKALGCVV YCHDPMDQRE STEFIDI NI NEEIDRGIDG EEI

UniProtKB: RNA-directed RNA polymerase L

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Macromolecule #2: Phosphoprotein

MacromoleculeName: Phosphoprotein / type: protein_or_peptide / ID: 2
Details: Chain F belongs to the same peptide as one of B, C, D or E, but the density is not well resolved enough to determine which chain it should associate with.
Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Simian virus 5 (strain W3) / Strain: W3
Molecular weightTheoretical: 42.155152 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDPTDLSFSP DEINKLIETG LNTVEYFTSQ QVTGTSSLGK NTIPPGVTGL LTNAAEAKIQ ESTNHQKGSV GGGAKPKKPR PKIAIVPAD DKTVPGKPIP NPLLGLDSTP STQTVLDLSG KTLPSGSYKG VKLAKFGKEN LMTRFIEEPR ENPIATSSPI D FKRGAGIP ...String:
MDPTDLSFSP DEINKLIETG LNTVEYFTSQ QVTGTSSLGK NTIPPGVTGL LTNAAEAKIQ ESTNHQKGSV GGGAKPKKPR PKIAIVPAD DKTVPGKPIP NPLLGLDSTP STQTVLDLSG KTLPSGSYKG VKLAKFGKEN LMTRFIEEPR ENPIATSSPI D FKRGAGIP AGSIEGSTQS DGWEMKSRSL SGAIHPVLQS PLQQGDLNAL VTSVQSLALN VNEILNTVRN LDSRMNQLET KV DRILSSQ SLIQTIKNDI VGLKAGMATL EGMITTVKIM DPGVPSNVTV EDVRKTLSNH AVVVPESFND SFLTQSEDVI SLD ELARPT ATSVKKIVRK VPPQKDLTGL KITLEQLAKD CISKPKMREE YLLKINQASS EAQLIDLKKA IIRSAI

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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL 3200FS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 80.8 e/Å2

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Image processing

Particle selectionNumber selected: 717008
Startup modelType of model: OTHER / Details: Negative stain density
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2)
Final 3D classificationNumber classes: 5 / Avg.num./class: 143000 / Software - Name: RELION (ver. 2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.63 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 78547
FSC plot (resolution estimation)

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