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- PDB-5a7u: Single-particle cryo-EM of co-translational folded adr1 domain in... -

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Basic information

Entry
Database: PDB / ID: 5a7u
TitleSingle-particle cryo-EM of co-translational folded adr1 domain inside the E. coli ribosome exit tunnel.
ComponentsREGULATORY PROTEIN ADR1
KeywordsTRANSLATION / PROTEIN FOLDING / RIBOSOME / ZINC FINGER / SECM / TRANSLATIONAL ARREST PEPTIDE / CRYO-EM / SINGLE- MOLECULE STUDIES
Function / homology
Function and homology information


positive regulation of transcription from RNA polymerase II promoter by oleic acid / 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 / RNA polymerase II-specific DNA-binding transcription factor binding ...positive regulation of transcription from RNA polymerase II promoter by oleic acid / 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 / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / nucleic acid binding / transcription coactivator activity / molecular adaptor activity / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin / regulation of transcription by RNA polymerase II / 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 speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.8 Å
AuthorsNilsson, O.B. / Hedman, R. / Marino, J. / Wickles, S. / Bischoff, L. / Johansson, M. / Muller-Lucks, A. / Trovato, F. / Puglisi, J.D. / O'Brien, E. ...Nilsson, O.B. / Hedman, R. / Marino, J. / Wickles, S. / Bischoff, L. / Johansson, M. / Muller-Lucks, A. / Trovato, F. / Puglisi, J.D. / 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 10, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2015Group: Database references
Revision 1.2Aug 23, 2017Group: Data collection / Category: em_software
Item: _em_software.fitting_id / _em_software.image_processing_id
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Assembly

Deposited unit
A: REGULATORY PROTEIN ADR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,4712
Polymers3,4061
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

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Components

#1: Protein/peptide REGULATORY PROTEIN ADR1 / ADR1


Mass: 3406.024 Da / Num. of mol.: 1 / Fragment: RESIDUES 130-158
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P07248
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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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: ADR1 DOMAIN COTRANSLATIONALLY FOLDED INSIDE THE E. COLI RIBOSOME EXIT TUNNEL
Type: RIBOSOME
Buffer solutionName: 20 MM HEPES PH 7.2 , 50 MM KOAC, 5 MM MG OAC2, 0.03% DDM, 50 MICROM ZNCL2, 125 MM SUCROSE.
pH: 7.2
Details: 20 MM HEPES PH 7.2 , 50 MM KOAC, 5 MM MG OAC2, 0.03% DDM, 50 MICROM ZNCL2, 125 MM SUCROSE.
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: CARBON
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE
Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, INSTRUMENT- FEI VITROBOT MARK IV,

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Apr 13, 2015
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3200 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 5 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)
Image scansNum. digital images: 2000
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1UCSF Chimeramodel fitting
2SPIDER3D reconstruction
CTF correctionDetails: MICROGRAPH
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.8 Å / Num. of particles: 151900 / Nominal pixel size: 3.7 Å / Actual pixel size: 3.7 Å
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3079. (DEPOSITION ID: 13581).
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Details: METHOD--RIGID BODY REFINEMENT PROTOCOL--NMR
Atomic model buildingPDB-ID: 2ADR

2adr


Accession code: 2ADR / Source name: PDB / Type: experimental model
RefinementHighest resolution: 4.8 Å
Refinement stepCycle: LAST / Highest resolution: 4.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms223 0 1 0 224

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