[English] 日本語
![](img/lk-miru.gif)
- EMDB-17869: Tilapia Lake Virus polymerase in cRNA pre-initiation state mode A... -
+
Open data
-
Basic information
Entry | ![]() | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Tilapia Lake Virus polymerase in cRNA pre-initiation state mode A (core-endo only) | |||||||||
![]() | ||||||||||
![]() |
| |||||||||
![]() | Viral polymerase / VIRAL PROTEIN | |||||||||
Function / homology | RNA-dependent RNA polymerase activity / DNA/RNA polymerase superfamily / Uncharacterized protein / Putative PB1 / RNA-dependent RNA polymerase![]() | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||
![]() | Arragain B / Cusack S | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Structural and functional analysis of the minimal orthomyxovirus-like polymerase of Tilapia Lake Virus from the highly diverged Amnoonviridae family. Authors: Benoit Arragain / Martin Pelosse / Albert Thompson / Stephen Cusack / ![]() ![]() Abstract: Tilapia Lake Virus (TiLV), a recently discovered pathogen of tilapia fish, belongs to the Amnoonviridae family from the Articulavirales order. Its ten genome segments have characteristic conserved ...Tilapia Lake Virus (TiLV), a recently discovered pathogen of tilapia fish, belongs to the Amnoonviridae family from the Articulavirales order. Its ten genome segments have characteristic conserved ends and encode proteins with no known homologues, apart from the segment 1, which encodes an orthomyxo-like RNA-dependent-RNA polymerase core subunit. Here we show that segments 1-3 encode respectively the PB1, PB2 and PA-like subunits of an active heterotrimeric polymerase that maintains all domains found in the distantly related influenza polymerase, despite an unprecedented overall size reduction of 40%. Multiple high-resolution cryo-EM structures of TiLV polymerase in pre-initiation, initiation and active elongation states, show how it binds the vRNA and cRNA promoters and performs RNA synthesis, with both transcriptase and replicase configurations being characterised. However, the highly truncated endonuclease-like domain appears inactive and the putative cap-binding domain is autoinhibited, emphasising that many functional aspects of TiLV polymerase remain to be elucidated. | |||||||||
History |
|
-
Structure visualization
Supplemental images |
---|
-
Downloads & links
-EMDB archive
Map data | ![]() | 8.2 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 20.5 KB 20.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.7 KB | Display | ![]() |
Images | ![]() | 62.7 KB | ||
Masks | ![]() | 103 MB | ![]() | |
Filedesc metadata | ![]() | 6.7 KB | ||
Others | ![]() ![]() ![]() | 80.7 MB 80.8 MB 80.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8pt7MC ![]() 8psnC ![]() 8psoC ![]() 8psqC ![]() 8pssC ![]() 8psuC ![]() 8psxC ![]() 8pszC ![]() 8pt2C ![]() 8pt6C ![]() 8pthC ![]() 8ptjC ![]() 8qz8C M: atomic model generated by this map C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
EMDB pages | ![]() ![]() |
---|
-
Map
File | ![]() | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 0.84 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Mask #1
File | ![]() | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: #1
File | emd_17869_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #2
File | emd_17869_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_17869_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-
Sample components
-Entire : Tilapia lake virus polymerase
Entire | Name: Tilapia lake virus polymerase |
---|---|
Components |
|
-Supramolecule #1: Tilapia lake virus polymerase
Supramolecule | Name: Tilapia lake virus polymerase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
---|---|
Source (natural) | Organism: ![]() |
-Macromolecule #1: Polymerase acidic protein (PA-like)
Macromolecule | Name: Polymerase acidic protein (PA-like) / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 47.780508 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MDSRFAQLTG VFCDDFTYSE GSRRFLSSYS TVERRPGVPV EGDCYDCLKN KWIAFELEGQ PRKFPKATVR CILNNDATYV CSEQEYQQI CKVQFKDYLE IDGVVKVGHK ASYDAELRER LLELPHPKSG PKPRIEWVAP PRLADISKET AELKRQYGFF E CSKFLACG ...String: MDSRFAQLTG VFCDDFTYSE GSRRFLSSYS TVERRPGVPV EGDCYDCLKN KWIAFELEGQ PRKFPKATVR CILNNDATYV CSEQEYQQI CKVQFKDYLE IDGVVKVGHK ASYDAELRER LLELPHPKSG PKPRIEWVAP PRLADISKET AELKRQYGFF E CSKFLACG EECGLDQEAR ELILNEYARD REFEFRNGGW IQRYTVASHK PATQKILPLP ASAPLARELL MLIARSTTQA GK VLHSDNT SILAVPVMRD SGKHSKRRPT ASTHHLVVGL SKPGCEHDFE FDGYRAAVHV MHLDPKQSAN IGEQDFVSTR EIY KLDMLE LPPISRKGDL DRASGLETRW DVILLLECLD STRVSQAVAQ HFNRHRLALS VCKDEFRKGY QLASEIRGTI PLSS LYYSL CAVRLRMTVH PFAR UniProtKB: Uncharacterized protein |
-Macromolecule #2: Putative PB1
Macromolecule | Name: Putative PB1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 57.179375 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MWAFQEGVCK GNLLSGPTSM KAPDSAARES IDRASEIMTG KSYNAVHTGD LSKLPNQGES PLRIVDSDLY SERSCCWVIE KEGRVVCKS TTLTRGMTSL LNTTKCSSPS ELICKVLTVE SLSEKIGDTS VEELLSHGRY FKCALRDQER GKPKSRAIFL S HPFFRLLS ...String: MWAFQEGVCK GNLLSGPTSM KAPDSAARES IDRASEIMTG KSYNAVHTGD LSKLPNQGES PLRIVDSDLY SERSCCWVIE KEGRVVCKS TTLTRGMTSL LNTTKCSSPS ELICKVLTVE SLSEKIGDTS VEELLSHGRY FKCALRDQER GKPKSRAIFL S HPFFRLLS SVVETHARSV LSKVSAVYTA TASAEQRAMM AAQVVESRKH VLNGDCTKYN EAIDADTLLK VWDAIGMGSI GV MLAYMVR RKCVLIKDTL VECPGGMLMG MFNATATLAL QGTTDRFLSF SDDFITSFNS PAELREIEDL LFASCHNLSL KKS YISVAS LEINSCTLTR DGDLATGLGC TAGVPFRGPL VTLKQTAAML SGAVDSGVMP FHSAERLFQI KQQECAYRYN NPTY TTRNE DFLPTCLGGK TVISFQSLLT WDCHPFWYQV HPDGPDTIDQ KVLSVLASKT RRRRTRLEAL SDLDPLVPHR LLVSE SDVS KIRAARQAHL KSLGLEQPTN FNYAIYKAVQ PTAGC UniProtKB: Putative PB1 |
-Macromolecule #3: RNA-dependent RNA polymerase
Macromolecule | Name: RNA-dependent RNA polymerase / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 53.782141 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MSQFGKSFKG RTEVTITEYR SHTVKDVHRS LLTADKSLRK SFCFRNALNQ FLDKDLPLLP IRPKLESRVA VKKSKLRSQL SFRPGLTQE EAIDLYNKGY DGDSVSGALQ DRVVNEPVAY SSADNDKFHR GLAALGYTLA DRAFDTCESG FVRAIPTTPC G FICCGPGS ...String: MSQFGKSFKG RTEVTITEYR SHTVKDVHRS LLTADKSLRK SFCFRNALNQ FLDKDLPLLP IRPKLESRVA VKKSKLRSQL SFRPGLTQE EAIDLYNKGY DGDSVSGALQ DRVVNEPVAY SSADNDKFHR GLAALGYTLA DRAFDTCESG FVRAIPTTPC G FICCGPGS FKDSLGFVIK IGEFWHMYDG FQHFVAVEDA KFLASKSPSF WLAKRLAKRL NLVPKEDPSV AAAECPCKKV WE ASFARAP TALDPFGGRA FCDQGWVYHR DVGYATANHI SQETLFQQAL SVRNLGPQGS ANVSGSIHTA LDRLRAAYSR GTP ASRSIL QGLANLITPV GENFECDLDK RKLNIKALRS PERYITIEGL VVNLDDVVRG FYLDKAKVTV LSRSKWMGYE DLPQ KPPNG TFYCRKRKAM LLISCSPGTY AKKRKVAVQE DRFKDMRVEN FREVAENMDL NQGSGSENLY FQGHHHHHHH HHH UniProtKB: RNA-dependent RNA polymerase |
-Macromolecule #4: 5'/3' cRNA ends - cRNA loop (40-mer)
Macromolecule | Name: 5'/3' cRNA ends - cRNA loop (40-mer) / type: rna / ID: 4 / Number of copies: 2 |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 12.82868 KDa |
Sequence | String: CCAAAUUUUA CUCACAAGUC AGGACGUGAG AAAGAUUUGC |
-Macromolecule #5: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: ZN |
---|---|
Molecular weight | Theoretical: 65.409 Da |
-Macromolecule #6: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: MG |
---|---|
Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Buffer | pH: 8 |
---|---|
Vitrification | Cryogen name: ETHANE |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
+
Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
---|---|
Output model | ![]() PDB-8pt7: |