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Yorodumi- PDB-4v6m: Structure of the ribosome-SecYE complex in the membrane environment -
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-Basic information
Entry | Database: PDB / ID: 4v6m | |||||||||
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Title | Structure of the ribosome-SecYE complex in the membrane environment | |||||||||
Components |
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Keywords | RIBOSOME/RIBOSOMAL PROTEIN / RIBOSOMAL PROTEIN / RIBONUCLEOPROTEIN / NUCLEOTIDE-BINDING / PROTEIN BIOSYNTHESIS / TRANSLATION / ZINC-FINGER / 70S RIBOSOME / RIBOSOME / TRANSLOCON / SECYEG / NANODISC / RIBOSOME-RIBOSOMAL PROTEIN complex | |||||||||
Function / homology | Function and homology information cell septum assembly / cellular response to lipoprotein particle stimulus / Defective ABCA1 causes TGD / high-density lipoprotein particle receptor binding / Scavenging by Class B Receptors / HDL clearance / spherical high-density lipoprotein particle / regulation of intestinal cholesterol absorption / positive regulation of hydrolase activity / negative regulation of response to cytokine stimulus ...cell septum assembly / cellular response to lipoprotein particle stimulus / Defective ABCA1 causes TGD / high-density lipoprotein particle receptor binding / Scavenging by Class B Receptors / HDL clearance / spherical high-density lipoprotein particle / regulation of intestinal cholesterol absorption / positive regulation of hydrolase activity / negative regulation of response to cytokine stimulus / protein oxidation / vitamin transport / cholesterol import / high-density lipoprotein particle binding / HDL assembly / negative regulation of heterotypic cell-cell adhesion / protein transport by the Sec complex / intracellular protein transmembrane transport / apolipoprotein receptor binding / blood vessel endothelial cell migration / ABC transporters in lipid homeostasis / apolipoprotein A-I receptor binding / negative regulation of cell adhesion molecule production / negative regulation of cytokine production involved in immune response / negative regulation of very-low-density lipoprotein particle remodeling / peptidyl-methionine modification / phosphatidylcholine biosynthetic process / protein-transporting ATPase activity / glucocorticoid metabolic process / acylglycerol homeostasis / Chylomicron remodeling / phosphatidylcholine-sterol O-acyltransferase activator activity / positive regulation of phospholipid efflux / Chylomicron assembly / positive regulation of cholesterol metabolic process / lipid storage / high-density lipoprotein particle clearance / chylomicron / phospholipid homeostasis / high-density lipoprotein particle remodeling / phospholipid efflux / chemorepellent activity / cholesterol transfer activity / reverse cholesterol transport / high-density lipoprotein particle assembly / cholesterol transport / very-low-density lipoprotein particle / low-density lipoprotein particle / positive regulation of CoA-transferase activity / lipoprotein biosynthetic process / high-density lipoprotein particle / FtsZ-dependent cytokinesis / regulation of Cdc42 protein signal transduction / triglyceride homeostasis / HDL remodeling / endothelial cell proliferation / cholesterol efflux / Scavenging by Class A Receptors / negative regulation of interleukin-1 beta production / positive regulation of Rho protein signal transduction / adrenal gland development / negative chemotaxis / cholesterol binding / cell division site / stringent response / cholesterol biosynthetic process / plasma membrane => GO:0005886 / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / endocytic vesicle / misfolded RNA binding / Group I intron splicing / RNA folding / protein secretion / negative regulation of tumor necrosis factor-mediated signaling pathway / transcriptional attenuation / positive regulation of cholesterol efflux / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / protein targeting / negative regulation of cytoplasmic translation / Scavenging of heme from plasma / translational termination / Retinoid metabolism and transport / four-way junction DNA binding / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of phagocytosis / DnaA-L2 complex / translation repressor activity / negative regulation of translational initiation / positive regulation of stress fiber assembly / endocytic vesicle lumen / heat shock protein binding / negative regulation of DNA-templated DNA replication initiation / regulation of mRNA stability / cholesterol metabolic process / mRNA regulatory element binding translation repressor activity / ribosome assembly / positive regulation of RNA splicing Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) Escherichia coli DH1 (bacteria) Escherichia coli O157:H7 (bacteria) Escherichia coli K-12 (bacteria) Escherichia coli 536 (bacteria) Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.1 Å | |||||||||
Authors | Frauenfeld, J. / Gumbart, J. / van der Sluis, E.O. / Funes, S. / Gartmann, M. / Beatrix, B. / Mielke, T. / Berninghausen, O. / Becker, T. / Schulten, K. / Beckmann, R. | |||||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2011 Title: Cryo-EM structure of the ribosome-SecYE complex in the membrane environment. Authors: Jens Frauenfeld / James Gumbart / Eli O van der Sluis / Soledad Funes / Marco Gartmann / Birgitta Beatrix / Thorsten Mielke / Otto Berninghausen / Thomas Becker / Klaus Schulten / Roland Beckmann / Abstract: The ubiquitous SecY-Sec61 complex translocates nascent secretory proteins across cellular membranes and integrates membrane proteins into lipid bilayers. Several structures of mostly detergent- ...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. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 4v6m.cif.gz | 3.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4v6m.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 4v6m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4v6m_validation.pdf.gz | 3.8 MB | Display | wwPDB validaton report |
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Full document | 4v6m_full_validation.pdf.gz | 5.2 MB | Display | |
Data in XML | 4v6m_validation.xml.gz | 356.8 KB | Display | |
Data in CIF | 4v6m_validation.cif.gz | 580.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v6/4v6m ftp://data.pdbj.org/pub/pdb/validation_reports/v6/4v6m | HTTPS FTP |
-Related structure data
Related structure data | 1858MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-RNA chain , 5 types, 5 molecules AAAXAVB7B8
#1: RNA chain | Mass: 499690.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: J01695 |
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#2: RNA chain | Mass: 3442.106 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) |
#3: RNA chain | Mass: 24876.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli DH1 (bacteria) / References: GenBank: AP012030 |
#26: RNA chain | Mass: 38790.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli DH1 (bacteria) / References: GenBank: AP012030 |
#27: RNA chain | Mass: 941612.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli DH1 (bacteria) / References: GenBank: AP012030 |
-Protein , 2 types, 3 molecules AZA0A1
#4: Protein | Mass: 11085.822 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli O157:H7 (bacteria) / References: UniProt: Q8X9Y5 |
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#5: Protein | Mass: 23309.361 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: nanodiscs derived from human Apo-A1 / Source: (synth.) Homo sapiens (human) / References: UniProt: P02647 |
-30S ribosomal protein ... , 20 types, 20 molecules ABACADAEAFAGAHAIAJAKALAMANAOAPAQARASATAU
#6: Protein | Mass: 26650.475 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0A7V0 |
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#7: Protein | Mass: 25900.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0A7V3 |
#8: Protein | Mass: 23383.002 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0A7V8 |
#9: Protein | Mass: 17498.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0A7W1 |
#10: Protein | Mass: 15727.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P02358 |
#11: Protein | Mass: 19923.959 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P02359 |
#12: Protein | Mass: 14015.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0A7W7 |
#13: Protein | Mass: 14755.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0A7X3 |
#14: Protein | Mass: 11755.597 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0A7R5 |
#15: Protein | Mass: 13739.778 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0A7R9 |
#16: Protein | Mass: 13636.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0A7S3 |
#17: Protein | Mass: 12997.271 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0ADZ4 |
#18: Protein | Mass: 11475.364 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0AG59 |
#19: Protein | Mass: 10188.687 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0A7S3 |
#20: Protein | Mass: 9207.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0A7T3 |
#21: Protein | Mass: 9593.296 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0AG63 |
#22: Protein | Mass: 8874.276 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0A7T7 |
#23: Protein | Mass: 10324.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0A7U3 |
#24: Protein | Mass: 9577.268 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0A7U7 |
#25: Protein | Mass: 8392.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P68679 |
-Preprotein translocase ... , 2 types, 2 molecules BABB
#28: Protein | Mass: 47669.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli 536 (bacteria) / Strain: UTI89 / UPEC / References: UniProt: Q0TCG1, UniProt: A0A454A8B1*PLUS |
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#29: Protein | Mass: 12623.296 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli 536 (bacteria) / Strain: UTI89 / UPEC / References: UniProt: Q0TA84, UniProt: A0A454AA55*PLUS |
+50S ribosomal protein ... , 30 types, 30 molecules B5B6BDBEBFBGBHBIBJBKBLBMBNBOBPBQBRBSBTBUBVBWBXBYBZB0B1B2B3B4
-Non-polymers , 2 types, 133 molecules
#60: Chemical | ChemComp-PEV / ( #61: Chemical | ChemComp-PGV / ( |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: An active E. coli SecYEG complex embedded in a lipid bilayer (Nanodisc), bound to a translating E. coli ribosome Type: RIBOSOME Details: The heterotrimeric SecYEG complex was embedded in a lipid bilayer (nascent HDL, Nanodisc) |
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Buffer solution | Name: 20 mM Hepes (pH 7.2), 100 mM KOAc, 10 mM Mg(OAc)2, 1 mM DTT, 250 microg/ml chloramphenicol pH: 7.2 Details: 20 mM Hepes (pH 7.2), 100 mM KOAc, 10 mM Mg(OAc)2, 1 mM DTT, 250 microg/ml chloramphenicol |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE / Details: liquid ethane was used as a cryogen |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
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Microscopy | Model: FEI POLARA 300 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 39000 X / Calibrated magnification: 38000 X / Nominal defocus max: 4500 nm / Nominal defocus min: 1000 nm / Cs: 2.26 mm |
Image recording | Electron dose: 22 e/Å2 / Film or detector model: KODAK SO-163 FILM |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software |
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CTF correction | Details: DEFOCUS GROUP VOLUMES | ||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||
3D reconstruction | Resolution: 7.1 Å / Num. of particles: 85664 / Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL / Details: REFINEMENT PROTOCOL--flexible fitting | ||||||||||||
Refinement step | Cycle: LAST
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