+
Open data
-
Basic information
Entry | Database: PDB / ID: 5ydt | ||||||
---|---|---|---|---|---|---|---|
Title | Remodeled Utp30 in 90S pre-ribosome (Mtr4-depleted, Enp1-TAP) | ||||||
![]() |
| ||||||
![]() | RIBOSOME / ribosome assembly / 90S pre-ribosome | ||||||
Function / homology | ![]() 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / maturation of SSU-rRNA / small-subunit processome / ribosomal small subunit biogenesis / cytosolic large ribosomal subunit / nucleolus / RNA binding / nucleus Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å | ||||||
![]() | Ye, K. / Zhu, X. / Hu, J. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Structure and RNA recognition of ribosome assembly factor Utp30. Authors: Jianfei Hu / Xing Zhu / Keqiong Ye / ![]() Abstract: The 90S preribosomes are gigantic early assembly intermediates of small ribosomal subunits. Cryo-EM structures of 90S were recently determined, but many of its components have not been accurately ...The 90S preribosomes are gigantic early assembly intermediates of small ribosomal subunits. Cryo-EM structures of 90S were recently determined, but many of its components have not been accurately modeled. Here we determine the crystal structure of yeast Utp30, a ribosomal L1 domain-containing protein in 90S, at 2.65 Å resolution, revealing a classic two-domain fold. The structure of Utp30 fits well into the cryo-EM density of 90S, confirming its previously assigned location. Utp30 binds to the rearranged helix 41 of 18S rRNA and helix 4 of 5' external transcribed spacer in 90S. Comparison of RNA-binding modes of different L1 domains illustrates that they consistently recognize a short RNA duplex with the concaved surface of domain I, but are versatile in RNA recognition outside the core interface. Cic1 is a paralog of Utp30 associating with large subunit preribosomes. Utp30 and Cic1 share similar RNA-binding modes, suggesting that their distinct functions may be executed by a single protein in other organisms. Deletion of Utp30 does not affect the composition of 90S. The nonessential role of Utp30 could be ascribed to its peripheral localization and redundant interactions in 90S. | ||||||
History |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | Molecule: ![]() ![]() |
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 97.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 918.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 924.1 KB | Display | |
Data in XML | ![]() | 24.7 KB | Display | |
Data in CIF | ![]() | 35.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6696M ![]() 5yduC M: map data used to model this data C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
Components
#1: Protein | Mass: 31668.939 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P36144 |
---|---|
#2: RNA chain | Mass: 20614.229 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#3: RNA chain | Mass: 6031.593 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#4: Protein/peptide | Mass: 2911.580 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-
Sample preparation
Component | Name: 90S small subunit pre-ribosome (Mtr4-depleted, Enp1-TAP) Type: RIBOSOME / Entity ID: all / Source: NATURAL |
---|---|
Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K |
-
Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) |
-
Processing
EM software | Name: RELION / Version: 1.4 / Category: 3D reconstruction |
---|---|
CTF correction | Type: PHASE FLIPPING ONLY |
Symmetry | Point symmetry: C1 (asymmetric) |
3D reconstruction | Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 73543 / Symmetry type: POINT |
Atomic model building | Space: REAL |