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Yorodumi- EMDB-9063: Cryo-EM structure of the essential ribosome assembly AAA-ATPase Rix7 -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9063 | |||||||||
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Title | Cryo-EM structure of the essential ribosome assembly AAA-ATPase Rix7 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | AAA-ATPase / RIBOSOMAL PROTEIN | |||||||||
Function / homology | Function and homology information preribosome binding / ribosome biogenesis / ATP hydrolysis activity / RNA binding / ATP binding / nucleus Similarity search - Function | |||||||||
Biological species | Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) / Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.5 Å | |||||||||
Authors | Lo YH / Sobhany M / Hsu AL / Ford BL / Krahn JM / Borgnia MJ / Stanley RE | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Commun / Year: 2019 Title: Cryo-EM structure of the essential ribosome assembly AAA-ATPase Rix7. Authors: Yu-Hua Lo / Mack Sobhany / Allen L Hsu / Brittany L Ford / Juno M Krahn / Mario J Borgnia / Robin E Stanley / Abstract: Rix7 is an essential type II AAA-ATPase required for the formation of the large ribosomal subunit. Rix7 has been proposed to utilize the power of ATP hydrolysis to drive the removal of assembly ...Rix7 is an essential type II AAA-ATPase required for the formation of the large ribosomal subunit. Rix7 has been proposed to utilize the power of ATP hydrolysis to drive the removal of assembly factors from pre-60S particles, but the mechanism of release is unknown. Rix7's mammalian homolog, NVL2 has been linked to cancer and mental illness disorders, highlighting the need to understand the molecular mechanisms of this essential machine. Here we report the cryo-EM reconstruction of the tandem AAA domains of Rix7 which form an asymmetric stacked homohexameric ring. We trapped Rix7 with a polypeptide in the central channel, revealing Rix7's role as a molecular unfoldase. The structure establishes that type II AAA-ATPases lacking the aromatic-hydrophobic motif within the first AAA domain can engage a substrate throughout the entire central channel. The structure also reveals that Rix7 contains unique post-α7 insertions within both AAA domains important for Rix7 function. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_9063.map.gz | 25.2 MB | EMDB map data format | |
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Header (meta data) | emd-9063-v30.xml emd-9063.xml | 12.6 KB 12.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_9063_fsc.xml | 6.9 KB | Display | FSC data file |
Images | emd_9063.png | 110.1 KB | ||
Filedesc metadata | emd-9063.cif.gz | 6.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9063 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9063 | HTTPS FTP |
-Validation report
Summary document | emd_9063_validation.pdf.gz | 620.8 KB | Display | EMDB validaton report |
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Full document | emd_9063_full_validation.pdf.gz | 620.4 KB | Display | |
Data in XML | emd_9063_validation.xml.gz | 9.4 KB | Display | |
Data in CIF | emd_9063_validation.cif.gz | 11.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9063 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9063 | HTTPS FTP |
-Related structure data
Related structure data | 6matMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_9063.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.39 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : AAA-ATPase Rix7
Entire | Name: AAA-ATPase Rix7 |
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Components |
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-Supramolecule #1: AAA-ATPase Rix7
Supramolecule | Name: AAA-ATPase Rix7 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) |
-Macromolecule #1: Rix7 mutant
Macromolecule | Name: Rix7 mutant / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 |
Molecular weight | Theoretical: 89.418266 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MSRRPTLRLG LDRDVYNIVL NLEQQGTDEN GKRPRLTVDY VYDTIKRSNS SLARQKKRML EDSIERVLAV RKEQAKAEEE TDSDDLIEA QERERERQKA AQAQRDANLL NRQIAKSWGF ASSPGAKAAD GEKGTDTGSI ATPAPATPAV AENMAADTPT T STGPVLPA ...String: MSRRPTLRLG LDRDVYNIVL NLEQQGTDEN GKRPRLTVDY VYDTIKRSNS SLARQKKRML EDSIERVLAV RKEQAKAEEE TDSDDLIEA QERERERQKA AQAQRDANLL NRQIAKSWGF ASSPGAKAAD GEKGTDTGSI ATPAPATPAV AENMAADTPT T STGPVLPA SSTDRQPNGE PRPKKRKAAP KEIDRTPPTK VSILDIAGVD DTLQRLLKEV WFPLRGGEAC EKMGYRYDNG VL LHGPSGC GKTTLAHAIA GSIGVAFIPV SAPSVIGGTS GESEKNIRDV FDEAIRLAPC LIFLDQIDAI AGRRESANKG MES RIVAEI MNGMDRIRQN TPLGKNVVVL AATNRPEFLD PAIRRRFSVE IDMGMPSERA REQILRSLTR DLSLADDINF KELA KMTPG YVGSDLQYVV KAAVSESFQA NIDSLLAQAR AKHPADHLAN VSQPQRDWLL LEAHRDEEVS WPSTKITMEQ FRKAV SLVQ PASKREGFST IPDTTWSHVG ALEDVRKKLE MSIIGPIKNP ELFTRVGIKP AAGILLWGPP GCGKTLVAKA VANESK ANF ISIKGPELLN KYVGESERAV RQLFSRAKSS APCILFFDQM DALVPRRDDS LSDASARVVN TLLTELDGVG DRSGIYV IG ATNRPDMIDE AIRRPGRLGT SIYVGLPSAE DRVKILKTLY RNTVKAPKKR EGTNGEDVDM TDAAAEQQHQ GTTDADLE K VALDLRCTGF SGADLGNLMQ AAAQACLERV YTQRQQKRKE GGSVAEEEEI EPVITMEDWE KALNEVKPSV KDPEKYMHS GFAAALEHHH HHH UniProtKB: AAA+ ATPase domain-containing protein |
-Macromolecule #2: unknown protein
Macromolecule | Name: unknown protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 |
Molecular weight | Theoretical: 2.315846 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) |
-Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 11 / Formula: ATP |
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Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ChemComp-ATP: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Grid | Model: C-flat-1.2/1.3 4C / Material: COPPER |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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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: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: -2.7 µm / Nominal defocus min: -1.2 µm / Nominal magnification: 59000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |