+Open data
-Basic information
Entry | Database: PDB / ID: 5m6s | ||||||
---|---|---|---|---|---|---|---|
Title | folding intermediate of spectrin R16 | ||||||
Components | spectrin | ||||||
Keywords | STRUCTURAL PROTEIN / spectrin / r16 | ||||||
Function / homology | Function and homology information actin filament capping / costamere / cortical actin cytoskeleton / cell projection / actin filament binding / cell junction / actin cytoskeleton organization / calmodulin binding / calcium ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.8 Å | ||||||
Authors | Nilsson, O.B. / Nickson, A.A. / Clarke, J. | ||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2017 Title: Cotranslational folding of spectrin domains via partially structured states. Authors: Ola B Nilsson / Adrian A Nickson / Jeffrey J Hollins / Stephan Wickles / Annette Steward / Roland Beckmann / Gunnar von Heijne / Jane Clarke / Abstract: How do the key features of protein folding, elucidated from studies on native, isolated proteins, manifest in cotranslational folding on the ribosome? Using a well-characterized family of homologous ...How do the key features of protein folding, elucidated from studies on native, isolated proteins, manifest in cotranslational folding on the ribosome? Using a well-characterized family of homologous α-helical proteins with a range of biophysical properties, we show that spectrin domains can fold vectorially on the ribosome and may do so via a pathway different from that of the isolated domain. We use cryo-EM to reveal a folded or partially folded structure, formed in the vestibule of the ribosome. Our results reveal that it is not possible to predict which domains will fold within the ribosome on the basis of the folding behavior of isolated domains; instead, we propose that a complex balance of the rate of folding, the rate of translation and the lifetime of folded or partly folded states will determine whether folding occurs cotranslationally on actively translating ribosomes. | ||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5m6s.cif.gz | 47.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5m6s.ent.gz | 33.7 KB | Display | PDB format |
PDBx/mmJSON format | 5m6s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5m6s_validation.pdf.gz | 797.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5m6s_full_validation.pdf.gz | 803 KB | Display | |
Data in XML | 5m6s_validation.xml.gz | 11.7 KB | Display | |
Data in CIF | 5m6s_validation.cif.gz | 15.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m6/5m6s ftp://data.pdbj.org/pub/pdb/validation_reports/m6/5m6s | HTTPS FTP |
-Related structure data
Related structure data | 3451MC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 19370.596 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pET19b / Production host: Escherichia coli (E. coli) / References: UniProt: P07751*PLUS |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: spectrin folding intermediate bound to 70s ribosome / Type: RIBOSOME / Entity ID: all / Source: MULTIPLE SOURCES |
---|---|
Molecular weight | Value: 2.5 MDa / Experimental value: NO |
Source (natural) | Organism: Escherichia coli (E. coli) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid type: Quantifoil R3/3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE |
-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: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 2.4 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
-Processing
EM software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: NONE | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 46067 Details: To exclude potential overfitting, the data were processed using a frequency limited refinement protocol by truncating high frequencies (low-pass filter at 8 A) Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT |