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- EMDB-3079: Single-particle cryo-EM of co-translational folded adr1 domain in... -

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Basic information

Entry
Database: EMDB / ID: EMD-3079
TitleSingle-particle cryo-EM of co-translational folded adr1 domain inside the E. coli ribosome exit tunnel.
Map dataAdr1 domain inside the ribosome exit tunnel
Sample
  • Sample: adr1 domain cotranslationally folded inside the E. coli ribosome exit tunnel
  • Complex: 70s ribosome
  • Protein or peptide: adr1 domain
Keywordsprotein folding / translation / ribosome / zinc finger / SecM / translational arrest peptide / cryo-EM / single-molecule studies
Function / homology
Function and homology information


positive regulation of peroxisome organization / positive regulation of ethanol catabolic process / peroxisome organization / positive regulation of fatty acid beta-oxidation / cellular response to ethanol / TFIID-class transcription factor complex binding / TFIIB-class transcription factor binding / chromatin organization / molecular adaptor activity / RNA polymerase II-specific DNA-binding transcription factor binding ...positive regulation of peroxisome organization / positive regulation of ethanol catabolic process / peroxisome organization / positive regulation of fatty acid beta-oxidation / cellular response to ethanol / TFIID-class transcription factor complex binding / TFIIB-class transcription factor binding / chromatin organization / molecular adaptor activity / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / transcription coactivator activity / nucleic acid binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / chromatin / positive regulation of transcription by RNA polymerase II / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
: / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type
Similarity search - Domain/homology
Regulatory protein ADR1
Similarity search - Component
Biological speciesEscherichia coli (E. coli) / Saccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.8 Å
AuthorsNilsson OB / Hedman R / Marino J / Wickles S / Bischoff L / Johansson M / Muller-Lucks A / Trovato F / Puglisi JD / O'Brien E ...Nilsson OB / Hedman R / Marino J / Wickles S / Bischoff L / Johansson M / Muller-Lucks A / Trovato F / Puglisi JD / O'Brien E / Beckmann R / von Heijne G
CitationJournal: Cell Rep / Year: 2015
Title: Cotranslational Protein Folding inside the Ribosome Exit Tunnel.
Authors: Ola B Nilsson / Rickard Hedman / Jacopo Marino / Stephan Wickles / Lukas Bischoff / Magnus Johansson / Annika Müller-Lucks / Fabio Trovato / Joseph D Puglisi / Edward P O'Brien / Roland ...Authors: Ola B Nilsson / Rickard Hedman / Jacopo Marino / Stephan Wickles / Lukas Bischoff / Magnus Johansson / Annika Müller-Lucks / Fabio Trovato / Joseph D Puglisi / Edward P O'Brien / Roland Beckmann / Gunnar von Heijne /
Abstract: At what point during translation do proteins fold? It is well established that proteins can fold cotranslationally outside the ribosome exit tunnel, whereas studies of folding inside the exit tunnel ...At what point during translation do proteins fold? It is well established that proteins can fold cotranslationally outside the ribosome exit tunnel, whereas studies of folding inside the exit tunnel have so far detected only the formation of helical secondary structure and collapsed or partially structured folding intermediates. Here, using a combination of cotranslational nascent chain force measurements, inter-subunit fluorescence resonance energy transfer studies on single translating ribosomes, molecular dynamics simulations, and cryoelectron microscopy, we show that a small zinc-finger domain protein can fold deep inside the vestibule of the ribosome exit tunnel. Thus, for small protein domains, the ribosome itself can provide the kind of sheltered folding environment that chaperones provide for larger proteins.
History
DepositionJul 8, 2015-
Header (metadata) releaseAug 12, 2015-
Map releaseSep 9, 2015-
UpdateSep 23, 2015-
Current statusSep 23, 2015Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.00085
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.00085
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5a7u
  • Surface level: 0.00085
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-5a7u
  • Surface level: 0.00085
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5a7u
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-3079.tif

Downloads & links

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Map

FileDownload / File: emd_3079.map.gz / Format: CCP4 / Size: 185.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAdr1 domain inside the ribosome exit tunnel
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.37 Å/pix.
x 368 pix.
= 504.16 Å		1.37 Å/pix.
x 368 pix.
= 504.16 Å		1.37 Å/pix.
x 368 pix.
= 504.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.37 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00085 / Movie #1: 0.00085
Minimum - Maximum-0.00153911 - 0.00393142
Average (Standard dev.)-0.00001018 (±0.00019531)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions368368368
Spacing368368368
CellA=B=C: 504.16 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.371.371.37
M x/y/z368368368
origin x/y/z0.0000.0000.000
length x/y/z504.160504.160504.160
α/β/γ90.00090.00090.000
start NX/NY/NZ-21-120
NX/NY/NZ432573
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS368368368
D min/max/mean-0.0020.004-0.000

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Supplemental data

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Sample components

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Entire : adr1 domain cotranslationally folded inside the E. coli ribosome ...

EntireName: adr1 domain cotranslationally folded inside the E. coli ribosome exit tunnel
Components
  • Sample: adr1 domain cotranslationally folded inside the E. coli ribosome exit tunnel
  • Complex: 70s ribosome
  • Protein or peptide: adr1 domain

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Supramolecule #1000: adr1 domain cotranslationally folded inside the E. coli ribosome ...

SupramoleculeName: adr1 domain cotranslationally folded inside the E. coli ribosome exit tunnel
type: sample / ID: 1000 / Oligomeric state: One monomer of adr1 domain with ribosome / Number unique components: 2

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Supramolecule #1: 70s ribosome

SupramoleculeName: 70s ribosome / type: complex / ID: 1 / Recombinant expression: No / Ribosome-details: ribosome-prokaryote: ALL
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: adr1 domain

MacromoleculeName: adr1 domain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's Yeast
Molecular weightTheoretical: 151 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceUniProtKB: Regulatory protein ADR1

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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: 7.2
Details: 20 mM Hepes pH 7.2 , 50 mM KOAc, 5 mM Mg[OAc]2, 0.03% DDM, 50 microM ZnCl2, 125 mM sucrose.
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
DateApr 13, 2015
Image recordingCategory: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 3308 / Average electron dose: 5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: -3.2 µm / Nominal defocus min: -1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Micrograph
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.8 Å / Resolution method: OTHER / Software - Name: Spider / Number images used: 151900

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Atomic model buiding 1

Initial modelPDB ID:

2adr

SoftwareName: Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-5a7u:
Single-particle cryo-EM of co-translational folded adr1 domain inside the E. coli ribosome exit tunnel.

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