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- EMDB-29365: Co-structure of the Respiratory Syncytial Virus RNA-dependent RNA... -
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Open data
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Basic information
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Title | Co-structure of the Respiratory Syncytial Virus RNA-dependent RNA polymerase with MRK-1 | |||||||||
![]() | sharpened map used for model building and real space refinement | |||||||||
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![]() | RNA-BINDING PROTEIN / RSV / RDRP / RNA-DEPENDENT RNA POLYMERASE / PRNTASE / POLYRIBONUCLEOTIDYL TRANSFERASE / RNA CAPPING / VIRAL REPLICATION / VIRAL PROTEIN / REPLICATION | |||||||||
Function / homology | ![]() NNS virus cap methyltransferase / GDP polyribonucleotidyltransferase / Respiratory syncytial virus genome transcription / Translation of respiratory syncytial virus mRNAs / negative stranded viral RNA replication / Respiratory syncytial virus (RSV) attachment and entry / Respiratory syncytial virus genome replication / RSV-host interactions / Assembly and release of respiratory syncytial virus (RSV) virions / Maturation of hRSV A proteins ...NNS virus cap methyltransferase / GDP polyribonucleotidyltransferase / Respiratory syncytial virus genome transcription / Translation of respiratory syncytial virus mRNAs / negative stranded viral RNA replication / Respiratory syncytial virus (RSV) attachment and entry / Respiratory syncytial virus genome replication / RSV-host interactions / Assembly and release of respiratory syncytial virus (RSV) virions / Maturation of hRSV A proteins / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / viral life cycle / 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 / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.52 Å | |||||||||
![]() | Fischmann TO | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Conserved allosteric inhibitory site on the respiratory syncytial virus and human metapneumovirus RNA-dependent RNA polymerases. Authors: Victoria A Kleiner / Thierry O Fischmann / John A Howe / Douglas C Beshore / Michael J Eddins / Yan Hou / Todd Mayhood / Daniel Klein / Debbie D Nahas / Bob J Lucas / He Xi / Edward Murray / ...Authors: Victoria A Kleiner / Thierry O Fischmann / John A Howe / Douglas C Beshore / Michael J Eddins / Yan Hou / Todd Mayhood / Daniel Klein / Debbie D Nahas / Bob J Lucas / He Xi / Edward Murray / Daphne Y Ma / Krista Getty / Rachel Fearns / ![]() Abstract: Respiratory syncytial virus (RSV) and human metapneumovirus (HMPV) are related RNA viruses responsible for severe respiratory infections and resulting disease in infants, elderly, and ...Respiratory syncytial virus (RSV) and human metapneumovirus (HMPV) are related RNA viruses responsible for severe respiratory infections and resulting disease in infants, elderly, and immunocompromised adults. Therapeutic small molecule inhibitors that bind to the RSV polymerase and inhibit viral replication are being developed, but their binding sites and molecular mechanisms of action remain largely unknown. Here we report a conserved allosteric inhibitory site identified on the L polymerase proteins of RSV and HMPV that can be targeted by a dual-specificity, non-nucleoside inhibitor, termed MRK-1. Cryo-EM structures of the inhibitor in complexes with truncated RSV and full-length HMPV polymerase proteins provide a structural understanding of how MRK-1 is active against both viruses. Functional analyses indicate that MRK-1 inhibits conformational changes necessary for the polymerase to engage in RNA synthesis initiation and to transition into an elongation mode. Competition studies reveal that the MRK-1 binding pocket is distinct from that of a capping inhibitor with an overlapping resistance profile, suggesting that the polymerase conformation bound by MRK-1 may be distinct from that involved in mRNA capping. These findings should facilitate optimization of dual RSV and HMPV replication inhibitors and provide insights into the molecular mechanisms underlying their polymerase activities. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 28.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17.6 KB 17.6 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 6.6 KB | Display | ![]() |
Images | ![]() | 130.1 KB | ||
Filedesc metadata | ![]() | 6.8 KB | ||
Others | ![]() ![]() | 28.4 MB 28.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 815 KB | Display | ![]() |
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Full document | ![]() | 814.6 KB | Display | |
Data in XML | ![]() | 14.2 KB | Display | |
Data in CIF | ![]() | 18.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8fpiMC ![]() 8fpjC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | sharpened map used for model building and real space refinement | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: half map
File | emd_29365_half_map_1.map | ||||||||||||
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Annotation | half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map
File | emd_29365_half_map_2.map | ||||||||||||
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Annotation | half map | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : RESPIRATORY SYNCYTIAL VIRUS POLYMERASE (L) PROTEIN BOUND BY THE T...
Entire | Name: RESPIRATORY SYNCYTIAL VIRUS POLYMERASE (L) PROTEIN BOUND BY THE TETRAMERIC PHOSPHOPROTEIN (P) AND COMPLEXED WITH MRK-1 |
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Components |
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-Supramolecule #1: RESPIRATORY SYNCYTIAL VIRUS POLYMERASE (L) PROTEIN BOUND BY THE T...
Supramolecule | Name: RESPIRATORY SYNCYTIAL VIRUS POLYMERASE (L) PROTEIN BOUND BY THE TETRAMERIC PHOSPHOPROTEIN (P) AND COMPLEXED WITH MRK-1 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: RNA-directed RNA polymerase L
Macromolecule | Name: RNA-directed RNA polymerase L / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA-directed RNA polymerase |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 173.267922 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MGSDYKDHDG DYKDHDIDYK DDDDKGSGSL EVLFQGPMDP IINGNSANVY LTDSYLKGVI SFSECNALGS YIFNGPYLKN DYTNLISRQ NPLIEHMNLK KLNITQSLIS KYHKGEIKLE EPTYFQSLLM TYKSMTSSEQ IATTNLLKKI IRRAIEISDV K VYAILNKL ...String: MGSDYKDHDG DYKDHDIDYK DDDDKGSGSL EVLFQGPMDP IINGNSANVY LTDSYLKGVI SFSECNALGS YIFNGPYLKN DYTNLISRQ NPLIEHMNLK KLNITQSLIS KYHKGEIKLE EPTYFQSLLM TYKSMTSSEQ IATTNLLKKI IRRAIEISDV K VYAILNKL GLKEKDKIKS NNGQDEDNSV ITTIIKDDIL SAVKDNQSHL KADKNHSTKQ KDTIKTTLLK KLMCSMQHPP SW LIHWFNL YTKLNNILTQ YRSNEVKNHG FTLIDNQTLS GFQFILNQYG CIVYHKELKR ITVTTYNQFL TWKDISLSRL NVC LITWIS NCLNTLNKSL GLRCGFNNVI LTQLFLYGDC ILKLFHNEGF YIIKEVEGFI MSLILNITEE DQFRKRFYNS MLNN ITDAA NKAQKNLLSR VCHTLLDKTV SDNIINGRWI ILLSKFLKLI KLAGDNNLNN LSELYFLFRI FGHPMVDERQ AMDAV KINC NETKFYLLSS LSMLRGAFIY RIIKGFVNNY NRWPTLRNAI VLPLRWLTYY KLNTYPSLLE LTERDLIVLS GLRFYR EFR LPKKVDLEMI INDKAISPPK NLIWTSFPRN YMPSHIQNYI EHEKLKFSES DKSRRVLEYY LRDNKFNECD LYNCVVN QS YLNNPNHVVS LTGKERELSV GRMFAMQPGM FRQVQILAEK MIAENILQFF PESLTRYGDL ELQKILELKA GISNKSNR Y NDNYNNYISK CSIITDLSKF NQAFRYETSC ICSDVLDELH GVQSLFSWLH LTIPHVTIIC TYRHAPPYIG DHIVDLNNV DEQSGLYRYH MGGIEGWCQK LWTIEAISLL DLISLKGKFS ITALINGDNQ SIDISKPIRL MEGQTHAQAD YLLALNSLKL LYKEYAGIG HKLKGTETYI SRDMQFMSKT IQHNGVYYPA SIKKVLRVGP WINTILDDFK VSLESIGSLT QELEYRGESL L CSLIFRNV WLYNQIALQL KNHALCNNKL YLDILKVLKH LKTFFNLDNI DTALTLYMNL PMLFGGGDPN LLYRSFYRRT PD FLTEAIV HSVFILSYYT NHDLKDKLQD LSDDRLNKFL TCIITFDKNP NAEFVTLMRD PQALGSERQA KITSEINRLA VTE VLSTAP NKIFSKSAQH YTTTEIDLND IMQNIEPTYP HGLRVVYESL PFYKAEKIVN LISGTKSITN ILEKTSAIDL TDID RATEM MRKNITLLIR ILPLDCNRDK REILSMENLS ITELSKYVRE RSWSLSNIVG VTSPSIMYTM DIKYTTSTIS SGIII EKYN VNSLTRGERG PTKPWVGSST QEKKTMPVYN RQVLTKKQRD QIDLLAKLDW VYASIDNKDE FMEELSIGTL GLTYEK AKK LFPQYLSVNY LHRLTVSSRP CEFPASIPAY RTTNYHFDTS PINRILTEKY GDEDIDIVFQ NCISFGLSLM SVVEQFT NV CPNRIILIPK LNEIHLMKPP IFTGDVDIHK LKQVIQKQHM FLPDKISLTQ YVELF UniProtKB: RNA-directed RNA polymerase L |
-Macromolecule #2: Phosphoprotein
Macromolecule | Name: Phosphoprotein / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 29.062895 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MEKFAPEFHG EDANNRATKF LESIKGKFTS PKDPKKKDSI ISVNSIDIEV TKESPITSNS TIINPTNETD DTAGNKPNYQ RKPLVSFKE DPTPSDNPFS KLYKETIETF DNNEEESSYS YEEINDQTND NITARLDRID EKLSEILGML HTLVVASAGP T SARDGIRD ...String: MEKFAPEFHG EDANNRATKF LESIKGKFTS PKDPKKKDSI ISVNSIDIEV TKESPITSNS TIINPTNETD DTAGNKPNYQ RKPLVSFKE DPTPSDNPFS KLYKETIETF DNNEEESSYS YEEINDQTND NITARLDRID EKLSEILGML HTLVVASAGP T SARDGIRD AMIGLREEMI EKIRTEALMT NDRLEAMARL RNEESEKMAK DTSDEVSLNP TSEKLNNLLE GNDSDNDLSL ED FKGENKY FQGHHHHHH UniProtKB: Phosphoprotein |
-Macromolecule #3: 4-(2-aminopropan-2-yl)-N'-[4-(cyclopropyloxy)-3-methoxybenzoyl]-6...
Macromolecule | Name: 4-(2-aminopropan-2-yl)-N'-[4-(cyclopropyloxy)-3-methoxybenzoyl]-6-(4-fluorophenyl)pyridine-2-carbohydrazide type: ligand / ID: 3 / Number of copies: 1 / Formula: Y6L |
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Molecular weight | Theoretical: 478.515 Da |
Chemical component information | ![]() ChemComp-Y6L: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.6 mg/mL |
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Buffer | pH: 7.4 |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 34.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL |
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Output model | ![]() PDB-8fpi: |