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- EMDB-3451: Folding intermediate of spectrin R16 bound to 70s ribosome -

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Basic information

Entry
Database: EMDB / ID: EMD-3451
TitleFolding intermediate of spectrin R16 bound to 70s ribosome
Map dataFolding intermediate of spectrin R16 bound to 70s ribosome
Sample
  • Complex: Folding intermediate of spectrin R16 bound to 70s ribosome
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.8 Å
AuthorsNilsson OB / Nickson AA / 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, 2016-
Header (metadata) releaseNov 23, 2016-
Map releaseJan 11, 2017-
UpdateJul 26, 2017-
Current statusJul 26, 2017Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.000296
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.000296
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5m6s
  • Surface level: 0.000296
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5m6s
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3451.png

Downloads & links

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Map

FileDownload / File: emd_3451.map.gz / Format: CCP4 / Size: 190.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFolding intermediate of spectrin R16 bound to 70s ribosome
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 368 pix.
= 398.912 Å		1.08 Å/pix.
x 368 pix.
= 398.912 Å		1.08 Å/pix.
x 368 pix.
= 398.912 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.084 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.000296 / Movie #1: 0.000296
Minimum - Maximum-0.0007037198 - 0.0017035634
Average (Standard dev.)-0.0000038463795 (±0.000127588)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions368368368
Spacing368368368
CellA=B=C: 398.912 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0841.0841.084
M x/y/z368368368
origin x/y/z0.0000.0000.000
length x/y/z398.912398.912398.912
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS368368368
D min/max/mean-0.0010.002-0.000

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Supplemental data

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Sample components

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Entire : Folding intermediate of spectrin R16 bound to 70s ribosome

EntireName: Folding intermediate of spectrin R16 bound to 70s ribosome
Components
  • Complex: Folding intermediate of spectrin R16 bound to 70s ribosome

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Supramolecule #1: Folding intermediate of spectrin R16 bound to 70s ribosome

SupramoleculeName: Folding intermediate of spectrin R16 bound to 70s ribosome
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 2.5 MDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
Component:
ConcentrationNameFormula
50.0 mMTris
100.0 mMPotassium acetateKOAc
5.0 mMMagnesium acetateMgOAc
GridModel: Quantifoil R3/3 / Material: COPPER/PALLADIUM / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2.0 nm / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV
DetailsFolding intermediate of spectrin R16 bound to 70s ribosome

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Electron microscopy

MicroscopeFEI TITAN
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: FEI FALCON II (4k x 4k) / #0 - Average electron dose: 2.4 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: FEI FALCON II (4k x 4k) / #1 - Average electron dose: 2.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus min: 0.8 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

Image recording ID1
CTF correctionSoftware - Name: CTFFIND (ver. 4)
Details: CTF correction was done following 3D reconstruction.
Startup modelType of model: OTHER / Details: 70S ribosome
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: SPIDER (ver. 09.03)
Details: To exclude potential overfitting, the data were processed using a frequency limited refinement protocol by truncating high frequencies (low-pass filter at 8A)
Number images used: 46067
Initial angle assignmentType: PROJECTION MATCHING
Projection matching processing - Number reference projections: 83
Software - Name: SPIDER (ver. 09.03)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: SPIDER (ver. 09.03)
Final 3D classificationSoftware - Name: SPIDER (ver. 09.03)

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Atomic model buiding 1

RefinementProtocol: BACKBONE TRACE
Output model

PDB-5m6s:
folding intermediate of spectrin R16

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