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- PDB-6em3: State A architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing th... -
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Basic information
Entry | Database: PDB / ID: 6em3 | ||||||
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Title | State A architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes | ||||||
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![]() | RIBOSOME / Large Subunit Biogenesis Nucleolus | ||||||
Function / homology | ![]() snoRNA release from pre-rRNA / nuclear division / exonucleolytic trimming to generate mature 5'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / PeBoW complex / rRNA primary transcript binding / ATP-dependent activity, acting on RNA / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / preribosome, small subunit precursor ...snoRNA release from pre-rRNA / nuclear division / exonucleolytic trimming to generate mature 5'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / PeBoW complex / rRNA primary transcript binding / ATP-dependent activity, acting on RNA / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / preribosome, small subunit precursor / proteasome binding / maturation of 5.8S rRNA / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / L13a-mediated translational silencing of Ceruloplasmin expression / preribosome, large subunit precursor / ribosomal large subunit export from nucleus / ribonucleoprotein complex binding / proteasome complex / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear periphery / maturation of LSU-rRNA / ribosomal large subunit biogenesis / maturation of SSU-rRNA / small-subunit processome / macroautophagy / protein catabolic process / ribosomal large subunit assembly / rRNA processing / protein-macromolecule adaptor activity / nuclear envelope / ribosomal small subunit biogenesis / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / RNA helicase activity / rRNA binding / negative regulation of translation / ribosome / RNA helicase / structural constituent of ribosome / cell cycle / mRNA binding / nucleolus / ATP hydrolysis activity / DNA binding / RNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||
![]() | Kater, L. / Cheng, J. / Barrio-Garcia, C. / Hurt, E. / Beckmann, R. | ||||||
![]() | ![]() Title: Visualizing the Assembly Pathway of Nucleolar Pre-60S Ribosomes. Authors: Lukas Kater / Matthias Thoms / Clara Barrio-Garcia / Jingdong Cheng / Sherif Ismail / Yasar Luqman Ahmed / Gert Bange / Dieter Kressler / Otto Berninghausen / Irmgard Sinning / Ed Hurt / Roland Beckmann / ![]() Abstract: Eukaryotic 60S ribosomal subunits are comprised of three rRNAs and ∼50 ribosomal proteins. The initial steps of their formation take place in the nucleolus, but, owing to a lack of structural ...Eukaryotic 60S ribosomal subunits are comprised of three rRNAs and ∼50 ribosomal proteins. The initial steps of their formation take place in the nucleolus, but, owing to a lack of structural information, this process is poorly understood. Using cryo-EM, we solved structures of early 60S biogenesis intermediates at 3.3 Å to 4.5 Å resolution, thereby providing insights into their sequential folding and assembly pathway. Besides revealing distinct immature rRNA conformations, we map 25 assembly factors in six different assembly states. Notably, the Nsa1-Rrp1-Rpf1-Mak16 module stabilizes the solvent side of the 60S subunit, and the Erb1-Ytm1-Nop7 complex organizes and connects through Erb1's meandering N-terminal extension, eight assembly factors, three ribosomal proteins, and three 25S rRNA domains. Our structural snapshots reveal the order of integration and compaction of the six major 60S domains within early nucleolar 60S particles developing stepwise from the solvent side around the exit tunnel to the central protuberance. | ||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 1.3 MB | Display | ![]() |
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-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 126.7 KB | Display | |
Data in CIF | ![]() | 229.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3888MC ![]() 3889C ![]() 3890C ![]() 3891C ![]() 3892C ![]() 3893C ![]() 6elzC ![]() 6em1C ![]() 6em4C ![]() 6em5C ![]() 6emfC ![]() 6emgC ![]() 6en7C M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Protein , 8 types, 8 molecules x34JvDKn
#1: Protein | Mass: 35184.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Backbone model Source: (natural) ![]() ![]() References: UniProt: P38805 |
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#3: Protein | Mass: 35754.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Backbone model Source: (natural) ![]() ![]() References: UniProt: P10962 |
#4: Protein | Mass: 33250.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Backbone model Source: (natural) ![]() ![]() References: UniProt: P35178 |
#7: Protein | Mass: 49842.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Backbone model Source: (natural) ![]() ![]() References: UniProt: P36049 |
#8: Protein | Mass: 26954.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Backbone model Source: (natural) ![]() ![]() References: UniProt: P40007 |
#27: Protein | Mass: 56798.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Backbone model Source: (natural) ![]() ![]() References: UniProt: Q03532, RNA helicase |
#28: Protein | Mass: 42596.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Backbone model Source: (natural) ![]() ![]() References: UniProt: P38779 |
#29: Protein | Mass: 69984.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Backbone model Source: (natural) ![]() ![]() References: UniProt: P53261 |
-60S ribosomal protein ... , 17 types, 17 molecules FCeEfGhijLMNOPQSY
#2: Protein | Mass: 27686.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Backbone model Source: (natural) ![]() ![]() References: UniProt: P05737 |
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#9: Protein | Mass: 39159.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Backbone model Source: (natural) ![]() ![]() References: UniProt: P10664 |
#10: Protein | Mass: 14809.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Backbone model Source: (natural) ![]() ![]() References: UniProt: P38061 |
#11: Protein | Mass: 20000.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Backbone model Source: (natural) ![]() ![]() References: UniProt: Q02326 |
#12: Protein | Mass: 12177.130 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Backbone model Source: (natural) ![]() ![]() References: UniProt: P05744 |
#13: Protein | Mass: 28175.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Backbone model Source: (natural) ![]() ![]() References: UniProt: P17076 |
#14: Protein | Mass: 13942.640 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Backbone model Source: (natural) ![]() ![]() References: UniProt: P0CX84 |
#15: Protein | Mass: 11162.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Backbone model Source: (natural) ![]() ![]() References: UniProt: O14455 |
#16: Protein | Mass: 9877.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Backbone model Source: (natural) ![]() ![]() References: UniProt: P49166 |
#17: Protein | Mass: 22604.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Backbone model Source: (natural) ![]() ![]() References: UniProt: Q12690 |
#18: Protein | Mass: 15195.066 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Backbone model Source: (natural) ![]() ![]() References: UniProt: P36105 |
#19: Protein | Mass: 24482.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Backbone model Source: (natural) ![]() ![]() References: UniProt: P05748 |
#20: Protein | Mass: 22247.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Backbone model Source: (natural) ![]() ![]() References: UniProt: P26784 |
#21: Protein | Mass: 20589.518 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Backbone model Source: (natural) ![]() ![]() References: UniProt: P05740 |
#22: Protein | Mass: 20609.252 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Backbone model Source: (natural) ![]() ![]() References: UniProt: P0CX49 |
#23: Protein | Mass: 20478.852 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Backbone model Source: (natural) ![]() ![]() References: UniProt: P0CX23 |
#24: Protein | Mass: 14265.784 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Backbone model Source: (natural) ![]() ![]() References: UniProt: P05743 |
-Ribosome biogenesis protein ... , 5 types, 5 molecules 5AotB
#5: Protein | Mass: 51982.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Backbone model Source: (natural) ![]() ![]() References: UniProt: P53136 |
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#6: Protein | Mass: 33585.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Backbone model Source: (natural) ![]() ![]() References: UniProt: Q08235 |
#30: Protein | Mass: 25499.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Backbone model Source: (natural) ![]() ![]() References: UniProt: P53927 |
#31: Protein | Mass: 36621.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Backbone model Source: (natural) ![]() ![]() References: UniProt: P40693 |
#33: Protein | Mass: 91830.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Backbone model Source: (natural) ![]() ![]() References: UniProt: Q04660 |
-RNA chain , 1 types, 1 molecules 1
#25: RNA chain | Mass: 1097493.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Backbone model Source: (natural) ![]() ![]() References: GenBank: 834774822 |
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-5.8S ribosomal ... , 2 types, 2 molecules 26
#26: RNA chain | Mass: 50682.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Backbone model Source: (natural) ![]() ![]() References: GenBank: 1214879358 |
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#32: RNA chain | Mass: 74308.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Backbone model Source: (natural) ![]() ![]() References: GenBank: 1102641490 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Nsa1-TAP Flag-Ytm1 / Type: RIBOSOME Details: Pre-60S assembly intermediates purified via Nsa1-TAP Flag-Ytm1 Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 27 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) |
Image scans | Sampling size: 14 µm / Width: 4096 / Height: 4096 / Movie frames/image: 10 / Used frames/image: 1-6 |
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Processing
EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 34453 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL / Details: Backbone model |