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- PDB-6em1: State C (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway o... -
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Basic information
Entry | Database: PDB / ID: 6em1 | ||||||
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Title | State C (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 / positive regulation of ATP-dependent activity / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear-transcribed mRNA catabolic process ...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 / positive regulation of ATP-dependent activity / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear-transcribed mRNA catabolic process / 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 / ribosomal large subunit binding / 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) / ATPase activator activity / L13a-mediated translational silencing of Ceruloplasmin expression / preribosome, large subunit precursor / ribosomal large subunit export from nucleus / ribonucleoprotein complex binding / ribosomal subunit export from nucleus / translation initiation factor activity / proteasome complex / nuclear periphery / 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) / assembly of large subunit precursor of preribosome / maturation of LSU-rRNA / cytosolic ribosome assembly / ribosomal large subunit biogenesis / maturation of SSU-rRNA / macroautophagy / small-subunit processome / maintenance of translational fidelity / protein catabolic process / ribosomal large subunit assembly / rRNA processing / protein transport / protein-macromolecule adaptor activity / nuclear envelope / ribosomal small subunit biogenesis / ATPase binding / 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 / translation / cell cycle / GTPase activity / mRNA binding / nucleolus / GTP binding / 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: 3.6 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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-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 194.7 KB | Display | |
Data in CIF | ![]() | 330.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3893MC ![]() 3888C ![]() 3889C ![]() 3890C ![]() 3891C ![]() 3892C ![]() 6elzC ![]() 6em3C ![]() 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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Assembly
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Components
-Protein , 13 types, 13 molecules x34bJsvWyzKDn
#1: Protein | Mass: 35184.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P38805 |
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#3: Protein | Mass: 35754.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P10962 |
#4: Protein | Mass: 33250.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P35178 |
#7: Protein | Mass: 74531.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q02892 |
#8: Protein | Mass: 49842.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#10: Protein | Mass: 57798.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#12: Protein | Mass: 26954.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P40007 |
#13: Protein | Mass: 27098.012 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#14: Protein | Mass: 26476.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q12522 |
#15: Protein | Mass: 12435.429 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P38202 |
#38: Protein | Mass: 42596.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Rigid body fit based on 6ELZ Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P38779 |
#40: Protein | Mass: 56798.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Rigid body fit based on 6ELZ Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q03532, RNA helicase |
#42: Protein | Mass: 69984.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Rigid body fit based on 6ELZ Source: (natural) ![]() ![]() Strain: YJM789 / References: UniProt: A6ZV85, UniProt: P53261*PLUS |
-60S ribosomal protein ... , 20 types, 20 molecules FBCeEfGhHijLMNOPQSVY
#2: Protein | Mass: 27686.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P05737 |
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#16: Protein | Mass: 43850.793 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P14126 |
#17: Protein | Mass: 39159.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P10664 |
#18: Protein | Mass: 14809.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P38061 |
#19: Protein | Mass: 20000.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q02326 |
#20: Protein | Mass: 12177.130 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P05744 |
#21: Protein | Mass: 28175.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P17076 |
#22: Protein | Mass: 13942.640 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P0CX84 |
#23: Protein | Mass: 21605.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P05738 |
#24: Protein | Mass: 11162.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: O14455 |
#25: Protein | Mass: 9877.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P49166 |
#26: Protein | Mass: 22604.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q12690 |
#27: Protein | Mass: 15195.066 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P36105 |
#28: Protein | Mass: 24482.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P05748 |
#29: Protein | Mass: 22247.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P26784 |
#30: Protein | Mass: 20589.518 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P05740 |
#31: Protein | Mass: 20609.252 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P0CX49 |
#32: Protein | Mass: 20478.852 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P0CX23 |
#33: Protein | Mass: 14493.950 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P0CX41 |
#34: Protein | Mass: 14265.784 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P05743 |
-Ribosome biogenesis protein ... , 7 types, 7 molecules 5Arumot
#5: Protein | Mass: 51982.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P53136 |
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#6: Protein | Mass: 33585.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#9: Protein | Mass: 29786.783 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#11: Protein | Mass: 24027.650 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#39: Protein | Mass: 91830.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Rigid body fit based on 6ELZ Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q04660 |
#41: Protein | Mass: 25499.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Rigid body fit based on 6ELZ Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P53927 |
#43: Protein | Mass: 36621.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Rigid body fit based on 6ELZ Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P40693 |
-5.8S ribosomal ... , 2 types, 2 molecules 26
#36: RNA chain | Mass: 50682.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: GenBank: 1214879358 |
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#37: RNA chain | Mass: 74308.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Rigid body fit based on 6ELZ Source: (natural) ![]() ![]() References: GenBank: 1102641490 |
-RNA chain / Non-polymers , 2 types, 3 molecules 1![](data/chem/img/ZN.gif)
![](data/chem/img/ZN.gif)
#35: RNA chain | Mass: 1097493.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: GenBank: 834774822 |
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#44: Chemical |
-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 intermediates purified via Nsa1-TAP Flag-Ytm1 Entity ID: #1-#43 / 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: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 156937 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: RECIPROCAL / Target criteria: AVERAGE FSC Details: Due to low local resolution, Chains 6 (ITS2), t (Rlp7), o (Nop15), n (Nop7), m (Erb1), K (Cic1) and D (Has1) of the "Foot" were rigid body docked into the EM-Map as a rigid assembly. These ...Details: Due to low local resolution, Chains 6 (ITS2), t (Rlp7), o (Nop15), n (Nop7), m (Erb1), K (Cic1) and D (Has1) of the "Foot" were rigid body docked into the EM-Map as a rigid assembly. These Chains were taken from pdb 6ELZ |