+Open data
-Basic information
Entry | Database: PDB / ID: 7ot5 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | CspA-70 cotranslational folding intermediate 1 | ||||||||||||
Components |
| ||||||||||||
Keywords | RIBOSOME / cotranslational folding / CspA70-1 | ||||||||||||
Function / homology | Function and homology information transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / negative regulation of cytoplasmic translation / DnaA-L2 complex / translation repressor activity / negative regulation of DNA-templated DNA replication initiation / ribosome assembly / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly ...transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / negative regulation of cytoplasmic translation / DnaA-L2 complex / translation repressor activity / negative regulation of DNA-templated DNA replication initiation / ribosome assembly / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / ribosomal large subunit assembly / DNA-templated transcription termination / response to radiation / mRNA 5'-UTR binding / large ribosomal subunit / ribosomal small subunit assembly / small ribosomal subunit / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / DNA binding / RNA binding / zinc ion binding / membrane / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | Escherichia coli (E. coli) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å | ||||||||||||
Authors | Agirrezabala, X. / Samatova, E. / Macher, M. / Liutkute, M. / Gil-Carton, D. / Novacek, J. / Valle, M. / Rodnina, M.V. | ||||||||||||
Funding support | Spain, European Union, 3items
| ||||||||||||
Citation | Journal: EMBO J / Year: 2022 Title: A switch from α-helical to β-strand conformation during co-translational protein folding. Authors: Xabier Agirrezabala / Ekaterina Samatova / Meline Macher / Marija Liutkute / Manisankar Maiti / David Gil-Carton / Jiri Novacek / Mikel Valle / Marina V Rodnina / Abstract: Cellular proteins begin to fold as they emerge from the ribosome. The folding landscape of nascent chains is not only shaped by their amino acid sequence but also by the interactions with the ...Cellular proteins begin to fold as they emerge from the ribosome. The folding landscape of nascent chains is not only shaped by their amino acid sequence but also by the interactions with the ribosome. Here, we combine biophysical methods with cryo-EM structure determination to show that folding of a β-barrel protein begins with formation of a dynamic α-helix inside the ribosome. As the growing peptide reaches the end of the tunnel, the N-terminal part of the nascent chain refolds to a β-hairpin structure that remains dynamic until its release from the ribosome. Contacts with the ribosome and structure of the peptidyl transferase center depend on nascent chain conformation. These results indicate that proteins may start out as α-helices inside the tunnel and switch into their native folds only as they emerge from the ribosome. Moreover, the correlation of nascent chain conformations with reorientation of key residues of the ribosomal peptidyl-transferase center suggest that protein folding could modulate ribosome activity. | ||||||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7ot5.cif.gz | 3.2 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7ot5.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7ot5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ot5_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Data in XML | 7ot5_validation.xml.gz | 208.2 KB | Display | |
Data in CIF | 7ot5_validation.cif.gz | 364.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ot/7ot5 ftp://data.pdbj.org/pub/pdb/validation_reports/ot/7ot5 | HTTPS FTP |
-Related structure data
Related structure data | 13055MC 7nwwC 7oifC 7oigC 7oiiC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-RNA chain , 5 types, 5 molecules 1234z
#1: RNA chain | Mass: 941526.438 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) |
---|---|
#2: RNA chain | Mass: 497404.969 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) |
#3: RNA chain | Mass: 38790.090 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: GenBank: CP035706.1 |
#53: RNA chain | Mass: 1813.109 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) |
#54: RNA chain | Mass: 27609.617 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) |
+50S ribosomal protein ... , 28 types, 28 molecules CDEFGHIJKLMNOPQRSUVWXYZabcde
-Ribosomal protein ... , 2 types, 2 molecules Tw
#21: Protein | Mass: 11208.054 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7U9B0M1 |
---|---|
#50: Protein | Mass: 9421.018 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7U9ARG2 |
-30S ribosomal protein ... , 19 types, 19 molecules fghijklmnopqrstuvxy
#33: Protein | Mass: 25072.867 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6C9U5I4 |
---|---|
#34: Protein | Mass: 23248.994 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsC, G4V09_06545, NCTC9094_00425 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A376HTV6 |
#35: Protein | Mass: 23383.002 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsD / Production host: Escherichia coli (E. coli) / References: UniProt: V0YKB3 |
#36: Protein | Mass: 16475.037 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: V6G0C0 |
#37: Protein | Mass: 12125.993 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: D9J60_11985 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7J9U446 |
#38: Protein | Mass: 16861.523 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsG / Production host: Escherichia coli (E. coli) / References: UniProt: P02359 |
#39: Protein | Mass: 14015.361 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsH / Production host: Escherichia coli (E. coli) / References: UniProt: H4JDM0 |
#40: Protein | Mass: 14554.882 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsI / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6L7FQ03 |
#41: Protein | Mass: 11254.041 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: L4V303 |
#42: Protein | Mass: 12487.200 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsK / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5I5F5V9 |
#43: Protein | Mass: 13683.053 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli #1/H766 / References: UniProt: A0A1X3IFC8 |
#44: Protein | Mass: 12868.091 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: B7LHZ5 |
#45: Protein | Mass: 11475.364 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsN / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1X3K3H0 |
#46: Protein | Mass: 10159.621 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsO / Production host: Escherichia coli (E. coli) / References: UniProt: E9YUR8 |
#47: Protein | Mass: 9207.572 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsP / Production host: Escherichia coli (E. coli) / References: UniProt: C3SYP2 |
#48: Protein | Mass: 9263.946 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsQ / Production host: Escherichia coli (E. coli) / References: UniProt: T6LV72 |
#49: Protein | Mass: 7734.896 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsR / Production host: Escherichia coli (E. coli) / References: UniProt: I2SQR9 |
#51: Protein | Mass: 9577.268 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsT / Production host: Escherichia coli (E. coli) / References: UniProt: I4T5W9 |
#52: Protein | Mass: 8392.844 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsU / Production host: Escherichia coli (E. coli) / References: UniProt: E9TH65 |
-Protein , 1 types, 1 molecules B
#55: Protein | Mass: 7036.796 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7U8W1U7 |
---|
-Non-polymers , 2 types, 396 molecules
#56: Chemical | ChemComp-MG / #57: Chemical | |
---|
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: 70S-CspA70-1 / Type: RIBOSOME / Entity ID: #1-#55 / Source: MULTIPLE SOURCES |
---|---|
Molecular weight | Value: 2.5 MDa / Experimental value: NO |
Buffer solution | pH: 7.5 Details: 50 mM Tris-HCl, 70 mM NH4Cl, 30 mM KCl, 3.5 mM MgCl2, 8 mM putrescine, 0.5 mM spermidine, 1 mM DTT, 1 mM GTP, pH 7.5 |
Specimen | Conc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1 |
Vitrification | Cryogen name: ETHANE / Humidity: 99 % / Chamber temperature: 278 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 75000 X / Nominal defocus max: -2200 nm / Nominal defocus min: -500 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 2.2 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
EM software |
| ||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: NONE | ||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 26765 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL Details: The software LocScale for model-based local density sharpening was used as implemented in the CCP-EM suite, version 1.3.0 | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6ORE Accession code: 6ORE / Source name: PDB / Type: experimental model |