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- PDB-5m6s: folding intermediate of spectrin R16 -

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Basic information

Entry
Database: PDB / ID: 5m6s
Titlefolding intermediate of spectrin R16
Componentsspectrin
KeywordsSTRUCTURAL PROTEIN / spectrin / r16
Function / homology
Function and homology information


costamere / actin filament capping / cortical actin cytoskeleton / cell projection / actin filament binding / cell junction / actin cytoskeleton organization / calmodulin binding / calcium ion binding / plasma membrane
Similarity search - Function
Alpha Spectrin, SH3 domain / EF-hand, Ca insensitive / Ca2+ insensitive EF hand / Ca2+ insensitive EF hand / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Spectrin repeats / SH3 domain / EF-hand domain pair ...Alpha Spectrin, SH3 domain / EF-hand, Ca insensitive / Ca2+ insensitive EF hand / Ca2+ insensitive EF hand / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Spectrin repeats / SH3 domain / EF-hand domain pair / EF-hand, calcium binding motif / Src homology 3 domains / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
Spectrin alpha chain, non-erythrocytic 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.8 Å
AuthorsNilsson, O.B. / Nickson, A.A. / Clarke, J.
CitationJournal: 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
DepositionOct 25, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2017Group: Database references
Revision 1.2Feb 1, 2017Group: Database references
Revision 1.3Mar 15, 2017Group: Database references
Revision 1.4Aug 2, 2017Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.name / _em_software.version

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Assembly

Deposited unit
A: spectrin


Theoretical massNumber of molelcules
Total (without water)19,3711
Polymers19,3711
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6420 Å2
MethodPISA

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Components

#1: Protein spectrin /


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

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: spectrin folding intermediate bound to 70s ribosome / Type: RIBOSOME / Entity ID: all / Source: MULTIPLE SOURCES
Molecular weightValue: 2.5 MDa / Experimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R3/3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 2.4 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

EM software
IDNameVersionCategory
2EM-Toolsimage acquisition
4CTFFIND4CTF correction
9SPIDERinitial Euler assignment
10SPIDERfinal Euler assignment
11SPIDERclassification
12SPIDER3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 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 buildingProtocol: RIGID BODY FIT

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