+
Open data
-
Basic information
Entry | Database: EMDB / ID: EMD-20041 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Precursor ribosomal RNA processing complex, State 1. | |||||||||
![]() | ||||||||||
![]() |
| |||||||||
![]() | Complex / Ribonuclease / Polynucleotide kinase / RNA BINDING PROTEIN | |||||||||
Function / homology | ![]() polynucleotide 5'-hydroxyl-kinase activity / Las1 complex / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of 5.8S rRNA / preribosome, large subunit precursor / maturation of LSU-rRNA / endonuclease activity / ATP binding / nucleus Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
![]() | Pillon MC / Hsu AL | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Cryo-EM reveals active site coordination within a multienzyme pre-rRNA processing complex. Authors: Monica C Pillon / Allen L Hsu / Juno M Krahn / Jason G Williams / Kevin H Goslen / Mack Sobhany / Mario J Borgnia / Robin E Stanley / ![]() Abstract: Ribosome assembly is a complex process reliant on the coordination of trans-acting enzymes to produce functional ribosomal subunits and secure the translational capacity of cells. The ...Ribosome assembly is a complex process reliant on the coordination of trans-acting enzymes to produce functional ribosomal subunits and secure the translational capacity of cells. The endoribonuclease (RNase) Las1 and the polynucleotide kinase (PNK) Grc3 assemble into a multienzyme complex, herein designated RNase PNK, to orchestrate processing of precursor ribosomal RNA (rRNA). RNase PNK belongs to the functionally diverse HEPN nuclease superfamily, whose members rely on distinct cues for nuclease activation. To establish how RNase PNK coordinates its dual enzymatic activities, we solved a series of cryo-EM structures of Chaetomium thermophilum RNase PNK in multiple conformational states. The structures reveal that RNase PNK adopts a butterfly-like architecture, harboring a composite HEPN nuclease active site flanked by discrete RNA kinase sites. We identify two molecular switches that coordinate nuclease and kinase function. Together, our structures and corresponding functional studies establish a new mechanism of HEPN nuclease activation essential for ribosome production. | |||||||||
History |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
-
Downloads & links
-EMDB archive
Map data | ![]() | 39.2 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 12.1 KB 12.1 KB | Display Display | ![]() |
Images | ![]() | 85.1 KB | ||
Filedesc metadata | ![]() | 5.8 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6of3MC ![]() 6of2C ![]() 6of4C M: atomic model generated by this map C: citing same article ( |
---|---|
Similar structure data |
-
Links
EMDB pages | ![]() ![]() |
---|
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-
Sample components
-Entire : Precursor Ribosomal RNA Processing Complex
Entire | Name: Precursor Ribosomal RNA Processing Complex |
---|---|
Components |
|
-Supramolecule #1: Precursor Ribosomal RNA Processing Complex
Supramolecule | Name: Precursor Ribosomal RNA Processing Complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 Details: Precursor Ribosomal RNA Processing Complex coordinates removal of a transcribed spacer. |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 234 KDa |
-Macromolecule #1: Ribonuclease
Macromolecule | Name: Ribonuclease / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() Strain: DSM 1495 / CBS 144.50 / IMI 039719 |
Molecular weight | Theoretical: 43.842871 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MSYYHHHHHH DYDIPTTENL YFQGAMGSMV QYIFTPWRNR AELLAVRAQF YPEHTSKTHL KKHHQSTFQD DEHIRSEKQK AVARVSMWM QRGGCPHMVE STALLVAAIL SDEAQGSGAA GGYAVRAAYS AAFSRFVTGL LDSHQDKQRK QSMYDVAKAV G LPAAFVEL ...String: MSYYHHHHHH DYDIPTTENL YFQGAMGSMV QYIFTPWRNR AELLAVRAQF YPEHTSKTHL KKHHQSTFQD DEHIRSEKQK AVARVSMWM QRGGCPHMVE STALLVAAIL SDEAQGSGAA GGYAVRAAYS AAFSRFVTGL LDSHQDKQRK QSMYDVAKAV G LPAAFVEL RHQATHEQLP SLTRLRSAAR RALEWIWWYY WKGLGPVDMV QRGVNGKGVA GVGDTSESEE KDVGEEGGDA AA RCREGVV RLLESDVRVG GEAINGPGKE ELLAEFGEAL VLTTLDAAAG NTRDVGVLRR AIGLMREIVN GGDEDCMQLE NGK GNRDVE KLKEELKKGW EEIKRLAQEK EDSGDDQTED EDVDMEAEEE DKKEQQSGWV LYDEKEWVPK PIGIV UniProtKB: Uncharacterized protein |
-Macromolecule #2: CLP1_P domain-containing protein
Macromolecule | Name: CLP1_P domain-containing protein / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() Strain: DSM 1495 / CBS 144.50 / IMI 039719 |
Molecular weight | Theoretical: 69.660539 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MHHSSFQPNN SNFQRKAGGR LVLSTPDVER FVILGNYGVK VHQGEVTIAG ATLTPIDDVQ WVHAPHCHAL PVLRTANDTV IELLPCPTA QGLRELARLN PLFGRLWNET SDTFQIIYTS ADAPKRTSLR ELASHPAWNK KISELLTSTR RKPSPILFIC G PKSSGKST ...String: MHHSSFQPNN SNFQRKAGGR LVLSTPDVER FVILGNYGVK VHQGEVTIAG ATLTPIDDVQ WVHAPHCHAL PVLRTANDTV IELLPCPTA QGLRELARLN PLFGRLWNET SDTFQIIYTS ADAPKRTSLR ELASHPAWNK KISELLTSTR RKPSPILFIC G PKSSGKST FGRLLTNRLM TDRAGHKSRS WKPVMVLDLD PGQPEFSPPG VVSLTKLRRP NLAPPFCHPG LSFGEKGLDG GN EGMTTVR MHAIASVTPA LDPAHFIACA RDLFAYYRRS ASQENIPLVV NTPGWIQGTG LDLLAELIAV LRPTEVLYMS EDG PEETVS ALREACASSS TIPFTMLPSQ PNSSGEGGGG GAASWTPATL RSMAMQSYFH LSPFSRDQQG GPGCEWNPTP LTHL CPWRV RLAGRPDERG VLGIVCYDHQ YAPELVSDAI NGMVMGLVRI EKKEALRGLA VPGDTSLSFT SSTSQGGCDD ELDSD SNSS SAPSFTSSSP SHLNSTPLLP LIPNPTGSPL SPQYTSLVGL VLIRGVSLTA SNPELHLLTP VPPSVLHSFR GDELVL VAG KFDAPTWAYV EGLYWKSNSK AAKRVDEERE DEDREESGGV EEEEEQDEVP WVEMLHGSAG RDVGSRVWRV RRDLGRS UniProtKB: Polynucleotide 5'-hydroxyl-kinase GRC3 |
-Macromolecule #3: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
Macromolecule | Name: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 3 / Number of copies: 2 / Formula: AGS |
---|---|
Molecular weight | Theoretical: 523.247 Da |
Chemical component information | ![]() ChemComp-AGS: |
-Macromolecule #4: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 2 / 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: NITROGEN |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
-
Image processing
Startup model | Type of model: INSILICO MODEL |
---|---|
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 74582 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |