Cryo-EM structure of the ribosome–SecYE complex in the membrane environment

A cryo-EM structure of the bacterial ribosome–SecYEG complex in a so-called Nanodisc allows for the molecular interpretation of the SecYEG complex in its natural lipid bilayer environment. Molecular dynamics simulations based on the structure reveal stable interactions between ribosomal RNA and the...

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Published inNature structural & molecular biology Vol. 18; no. 5; pp. 614 - 621
Main Authors Frauenfeld, Jens, Gumbart, James, Sluis, Eli O van der, Funes, Soledad, Gartmann, Marco, Beatrix, Birgitta, Mielke, Thorsten, Berninghausen, Otto, Becker, Thomas, Schulten, Klaus, Beckmann, Roland
Format Journal Article
LanguageEnglish
Published New York Nature Publishing Group US 01.05.2011
Nature Publishing Group
Subjects
631/337/574/1789
631/45/612/1237
631/535/1258/1259
Biochemistry
Biological Microscopy
Biomedical and Life Sciences
Cell Membrane - metabolism
Cryoelectron Microscopy
Crystal structure
Escherichia coli
Escherichia coli Proteins - chemistry
Escherichia coli Proteins - metabolism
Life Sciences
Lipids
Lipoproteins, HDL - chemistry
Lipoproteins, HDL - metabolism
Medicin och hälsovetenskap
Membrane Biology
Membrane proteins
Membrane Proteins - chemistry
Membrane Proteins - metabolism
Membranes
Models, Molecular
Molecular biology
Physiological aspects
Polypeptides
Protein Structure
Protein Transport
Proteins
Ribonucleic acid
Ribosomes
Ribosomes - chemistry
RNA
SEC Translocation Channels
Signal Recognition Particle - physiology
Structure
United States
Germany
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Abstract A cryo-EM structure of the bacterial ribosome–SecYEG complex in a so-called Nanodisc allows for the molecular interpretation of the SecYEG complex in its natural lipid bilayer environment. Molecular dynamics simulations based on the structure reveal stable interactions between ribosomal RNA and the membrane that may contribute to the insertase activity of the protein-conducting channel. The ubiquitous SecY–Sec61 complex translocates nascent secretory proteins across cellular membranes and integrates membrane proteins into lipid bilayers. Several structures of mostly detergent-solubilized Sec complexes have been reported. Here we present a single-particle cryo-EM structure of the SecYEG complex in a membrane environment, bound to a translating ribosome, at subnanometer resolution. Using the SecYEG complex reconstituted in a so-called Nanodisc, we could trace the nascent polypeptide chain from the peptidyltransferase center into the membrane. The reconstruction allowed for the identification of ribosome–lipid interactions. The rRNA helix 59 (H59) directly contacts the lipid surface and appears to modulate the membrane in immediate vicinity to the proposed lateral gate of the protein-conducting channel (PCC). On the basis of our map and molecular dynamics simulations, we present a model of a signal anchor–gated PCC in the membrane.
AbstractList A cryo-EM structure of the bacterial ribosome–SecYEG complex in a so-called Nanodisc allows for the molecular interpretation of the SecYEG complex in its natural lipid bilayer environment. Molecular dynamics simulations based on the structure reveal stable interactions between ribosomal RNA and the membrane that may contribute to the insertase activity of the protein-conducting channel. The ubiquitous SecY–Sec61 complex translocates nascent secretory proteins across cellular membranes and integrates membrane proteins into lipid bilayers. Several structures of mostly detergent-solubilized Sec complexes have been reported. Here we present a single-particle cryo-EM structure of the SecYEG complex in a membrane environment, bound to a translating ribosome, at subnanometer resolution. Using the SecYEG complex reconstituted in a so-called Nanodisc, we could trace the nascent polypeptide chain from the peptidyltransferase center into the membrane. The reconstruction allowed for the identification of ribosome–lipid interactions. The rRNA helix 59 (H59) directly contacts the lipid surface and appears to modulate the membrane in immediate vicinity to the proposed lateral gate of the protein-conducting channel (PCC). On the basis of our map and molecular dynamics simulations, we present a model of a signal anchor–gated PCC in the membrane.
The ubiquitous SecY-Sec61 complex translocates nascent secretory proteins across cellular membranes and integrates membrane proteins into lipid bilayers. Several structures of mostly detergent-solubilized Sec complexes have been reported. Here we present a single-particle cryo-EM structure of the SecYEG complex in a membrane environment, bound to a translating ribosome, at subnanometer resolution. Using the SecYEG complex reconstituted in a so-called Nanodisc, we could trace the nascent polypeptide chain from the peptidyltransferase center into the membrane. The reconstruction allowed for the identification of ribosome-lipid interactions. The rRNA helix 59 (H59) directly contacts the lipid surface and appears to modulate the membrane in immediate vicinity to the proposed lateral gate of the protein-conducting channel (PCC). On the basis of our map and molecular dynamics simulations, we present a model of a signal anchor-gated PCC in the membrane.
The ubiquitous SecY/Sec61–complex translocates nascent secretory proteins across cellular membranes and integrates membrane proteins into lipid bilayers. Several structures of mostly detergent solubilized Sec–complexes have been reported. Here, we present a single–particle cryo–electron microscopy structure of the SecYEG complex in a membrane environment at sub–nanometer resolution, bound to a translating ribosome. Using the SecYEG complex reconstituted in a so–called Nanodisc, we could trace the nascent polypeptide chain from the peptidyl transferase center into the membrane. The reconstruction allowed for the identification of ribosome–lipid interactions. The rRNA helix 59 (H59) directly contacts the lipid surface and appears to modulate the membrane in immediate vicinity to the proposed lateral gate of the PCC. Based on our map and molecular dynamics simulations we present a model of a signal anchor–gated PCC in the membrane.
The ubiquitous SecY-Sec61 complex translocates nascent secretory proteins across cellular membranes and integrates membrane proteins into lipid bilayers. Several structures of mostly detergent-solubilized Sec complexes have been reported. Here we present a single-particle cryo-EM structure of the SecYEG complex in a membrane environment, bound to a translating ribosome, at subnanometer resolution. Using the SecYEG complex reconstituted in a so-called Nanodisc, we could trace the nascent polypeptide chain from the peptidyltransferase center into the membrane. The reconstruction allowed for the identification of ribosome-lipid interactions. The rRNA helix 59 (H59) directly contacts the lipid surface and appears to modulate the membrane in immediate vicinity to the proposed lateral gate of the protein-conducting channel (PCC). On the basis of our map and molecular dynamics simulations, we present a model of a signal anchor-gated PCC in the membrane. [PUBLICATION ABSTRACT]
Audience Academic
Author Beatrix, Birgitta
Berninghausen, Otto
Schulten, Klaus
Sluis, Eli O van der
Gartmann, Marco
Beckmann, Roland
Gumbart, James
Funes, Soledad
Mielke, Thorsten
Becker, Thomas
Frauenfeld, Jens
AuthorAffiliation 3 Department of Physics, Beckman Institute, University of Illinois at Urbana–Champaign, Urbana, IL, 61801, USA
1 Gene Center, Department for Biochemistry, University of Munich, Feodor–Lynen–Str. 25, 81377 Munich, Germany
2 Munich Center For Integrated Protein Science (CIPSM), Department of Chemistry and Biochemistry, Butenandtstr. 5–13, 81377 Munich, Germany
5 Ultrastrukturnetzwerk, Max Planck Institute for Molecular Genetics, Ihnestr. 63–73, 14195 Berlin, Institut für Medizinische Physik und Biophysik, Charite–Universitätsmedizin Berlin, Ziegelstrasse 5–9, 10117–Berlin, Germany
4 Departamento de Genética Molecular, Instituto de Fisiología Celular, Circuito Exterior S/N, Ciudad Universitaria, Universidad Nacional Autónoma de México, Mexico, D.F., 04510, Mexico
AuthorAffiliation_xml – name: 1 Gene Center, Department for Biochemistry, University of Munich, Feodor–Lynen–Str. 25, 81377 Munich, Germany
– name: 2 Munich Center For Integrated Protein Science (CIPSM), Department of Chemistry and Biochemistry, Butenandtstr. 5–13, 81377 Munich, Germany
– name: 3 Department of Physics, Beckman Institute, University of Illinois at Urbana–Champaign, Urbana, IL, 61801, USA
– name: 5 Ultrastrukturnetzwerk, Max Planck Institute for Molecular Genetics, Ihnestr. 63–73, 14195 Berlin, Institut für Medizinische Physik und Biophysik, Charite–Universitätsmedizin Berlin, Ziegelstrasse 5–9, 10117–Berlin, Germany
– name: 4 Departamento de Genética Molecular, Instituto de Fisiología Celular, Circuito Exterior S/N, Ciudad Universitaria, Universidad Nacional Autónoma de México, Mexico, D.F., 04510, Mexico
Author_xml – sequence: 1
  givenname: Jens
  surname: Frauenfeld
  fullname: Frauenfeld, Jens
  organization: Department for Biochemistry, Gene Center, University of Munich, Department of Chemistry and Biochemistry, Munich Center for Integrated Protein Science (CIPSM)
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  surname: Gumbart
  fullname: Gumbart, James
  organization: Department of Physics, Beckman Institute, University of Illinois at Urbana–Champaign
– sequence: 3
  givenname: Eli O van der
  surname: Sluis
  fullname: Sluis, Eli O van der
  organization: Department for Biochemistry, Gene Center, University of Munich, Department of Chemistry and Biochemistry, Munich Center for Integrated Protein Science (CIPSM)
– sequence: 4
  givenname: Soledad
  surname: Funes
  fullname: Funes, Soledad
  organization: Departamento de Genética Molecular, Instituto de Fisiología Celular, Circuito Exterior S/N, Ciudad Universitaria, Universidad Nacional Autónoma de México
– sequence: 5
  givenname: Marco
  surname: Gartmann
  fullname: Gartmann, Marco
  organization: Department for Biochemistry, Gene Center, University of Munich, Department of Chemistry and Biochemistry, Munich Center for Integrated Protein Science (CIPSM)
– sequence: 6
  givenname: Birgitta
  surname: Beatrix
  fullname: Beatrix, Birgitta
  organization: Department for Biochemistry, Gene Center, University of Munich, Department of Chemistry and Biochemistry, Munich Center for Integrated Protein Science (CIPSM)
– sequence: 7
  givenname: Thorsten
  surname: Mielke
  fullname: Mielke, Thorsten
  organization: Ultrastrukturnetzwerk, Max Planck Institute for Molecular Genetics, Institut für Medizinische Physik und Biophysik, Charite–Universitätsmedizin Berlin
– sequence: 8
  givenname: Otto
  surname: Berninghausen
  fullname: Berninghausen, Otto
  organization: Department for Biochemistry, Gene Center, University of Munich, Department of Chemistry and Biochemistry, Munich Center for Integrated Protein Science (CIPSM)
– sequence: 9
  givenname: Thomas
  surname: Becker
  fullname: Becker, Thomas
  organization: Department for Biochemistry, Gene Center, University of Munich, Department of Chemistry and Biochemistry, Munich Center for Integrated Protein Science (CIPSM)
– sequence: 10
  givenname: Klaus
  surname: Schulten
  fullname: Schulten, Klaus
  organization: Department of Physics, Beckman Institute, University of Illinois at Urbana–Champaign
– sequence: 11
  givenname: Roland
  surname: Beckmann
  fullname: Beckmann, Roland
  email: beckmann@lmb.uni-muenchen.de
  organization: Department for Biochemistry, Gene Center, University of Munich, Department of Chemistry and Biochemistry, Munich Center for Integrated Protein Science (CIPSM)
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Snippet A cryo-EM structure of the bacterial ribosome–SecYEG complex in a so-called Nanodisc allows for the molecular interpretation of the SecYEG complex in its...
The ubiquitous SecY-Sec61 complex translocates nascent secretory proteins across cellular membranes and integrates membrane proteins into lipid bilayers....
The ubiquitous SecY/Sec61–complex translocates nascent secretory proteins across cellular membranes and integrates membrane proteins into lipid bilayers....
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StartPage 614
SubjectTerms 631/337/574/1789
631/45/612/1237
631/535/1258/1259
Biochemistry
Biological Microscopy
Biomedical and Life Sciences
Cell Membrane - metabolism
Cryoelectron Microscopy
Crystal structure
Escherichia coli
Escherichia coli Proteins - chemistry
Escherichia coli Proteins - metabolism
Life Sciences
Lipids
Lipoproteins, HDL - chemistry
Lipoproteins, HDL - metabolism
Medicin och hälsovetenskap
Membrane Biology
Membrane proteins
Membrane Proteins - chemistry
Membrane Proteins - metabolism
Membranes
Models, Molecular
Molecular biology
Physiological aspects
Polypeptides
Protein Structure
Protein Transport
Proteins
Ribonucleic acid
Ribosomes
Ribosomes - chemistry
RNA
SEC Translocation Channels
Signal Recognition Particle - physiology
Structure
Title Cryo-EM structure of the ribosome–SecYE complex in the membrane environment
URI https://link.springer.com/article/10.1038/nsmb.2026
https://www.ncbi.nlm.nih.gov/pubmed/21499241
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https://pubmed.ncbi.nlm.nih.gov/PMC3412285
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