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- EMDB-1858: Structure of the ribosome-SecYE complex in the membrane environment -

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Basic information

Entry
Database: EMDB / ID: EMD-1858
TitleStructure of the ribosome-SecYE complex in the membrane environment
Map dataThis map represents an E.coli 70S ribosome carrying an elongation arrested nascent chain of 118 amino acid residues, with the first 102 residues representing the N-terminus of the membrane protein FtsQ with the signal anchor, a tRNA in the P-site and the E.coli SecYEG complex embedded in a E.coli lipid bilayer (Nanodisc).
Sample
  • Sample: An active E.coli SecYEG complex embedded in a lipid bilayer (Nanodisc), bound to a translating E.coli ribosome
  • Complex: 70S ribosome nascent chain complex
  • Ligand: Nd-SecYEG
Function / homology
Function and homology information


cell septum assembly / Defective ABCA1 causes TGD / Scavenging by Class B Receptors / HDL clearance / high-density lipoprotein particle receptor binding / spherical high-density lipoprotein particle / positive regulation of hydrolase activity / negative regulation of response to cytokine stimulus / regulation of intestinal cholesterol absorption / protein oxidation ...cell septum assembly / Defective ABCA1 causes TGD / Scavenging by Class B Receptors / HDL clearance / high-density lipoprotein particle receptor binding / spherical high-density lipoprotein particle / positive regulation of hydrolase activity / negative regulation of response to cytokine stimulus / regulation of intestinal cholesterol absorption / protein oxidation / vitamin transport / cholesterol import / high-density lipoprotein particle binding / protein transport by the Sec complex / ABC transporters in lipid homeostasis / intracellular protein transmembrane transport / blood vessel endothelial cell migration / negative regulation of heterotypic cell-cell adhesion / apolipoprotein receptor binding / apolipoprotein A-I receptor binding / negative regulation of cytokine production involved in immune response / negative regulation of cell adhesion molecule production / HDL assembly / 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 / phospholipid homeostasis / chylomicron / high-density lipoprotein particle remodeling / phospholipid efflux / chemorepellent activity / cholesterol transfer activity / reverse cholesterol transport / very-low-density lipoprotein particle / high-density lipoprotein particle assembly / low-density lipoprotein particle / positive regulation of CoA-transferase activity / lipoprotein biosynthetic process / cholesterol transport / high-density lipoprotein particle / FtsZ-dependent cytokinesis / regulation of Cdc42 protein signal transduction / triglyceride homeostasis / HDL remodeling / endothelial cell proliferation / negative regulation of interleukin-1 beta production / Scavenging by Class A Receptors / cholesterol efflux / negative chemotaxis / positive regulation of cholesterol efflux / positive regulation of Rho protein signal transduction / adrenal gland development / cholesterol binding / cell division site / stringent response / cholesterol biosynthetic process / plasma membrane => GO:0005886 / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / endocytic vesicle / RNA folding / protein secretion / negative regulation of tumor necrosis factor-mediated signaling pathway / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / protein targeting / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / Scavenging of heme from plasma / Retinoid metabolism and transport / four-way junction DNA binding / translational termination / positive regulation of substrate adhesion-dependent cell spreading / DnaA-L2 complex / positive regulation of phagocytosis / translation repressor activity / negative regulation of translational initiation / positive regulation of stress fiber assembly / endocytic vesicle lumen / negative regulation of DNA-templated DNA replication initiation / heat shock protein binding / regulation of mRNA stability / cholesterol metabolic process / mRNA regulatory element binding translation repressor activity / ribosome assembly / positive regulation of RNA splicing / assembly of large subunit precursor of preribosome
Similarity search - Function
Cell division protein FtsQ / Cell division protein FtsQ/DivIB, C-terminal / POTRA domain, FtsQ-type / Cell division protein FtsQ/DivIB, C-terminal / POTRA domain, FtsQ-type / SecE subunit of protein translocation complex, bacterial-like / SecE superfamily / Protein translocase subunit SecY / : / Apolipoprotein A/E ...Cell division protein FtsQ / Cell division protein FtsQ/DivIB, C-terminal / POTRA domain, FtsQ-type / Cell division protein FtsQ/DivIB, C-terminal / POTRA domain, FtsQ-type / SecE subunit of protein translocation complex, bacterial-like / SecE superfamily / Protein translocase subunit SecY / : / Apolipoprotein A/E / Apolipoprotein A1/A4/E domain / Protein secE/sec61-gamma signature. / Protein secY signature 1. / Protein secY signature 2. / SecE/Sec61-gamma subunits of protein translocation complex / Protein translocase complex, SecE/Sec61-gamma subunit / SecY/SEC61-alpha family / SecY domain superfamily / SecY conserved site / SecY / POTRA domain / POTRA domain profile. / Ribosomal protein L1, bacterial-type / Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L1 / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein L25, short-form / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Ribosomal protein L11, bacterial-type / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / : / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L16 signature 1. / : / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L17 signature. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11, RNA binding domain / Ribosomal protein L11/L12 / Ribosomal protein L36 signature. / Ribosomal protein L28/L24 superfamily / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L32p, bacterial type / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein S12, bacterial-type / : / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / : / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L28 / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L5, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein S3, bacterial-type / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein L20 signature.
Similarity search - Domain/homology
Protein translocase subunit SecY / Protein translocase subunit SecE / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL15 / Apolipoprotein A-I / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein uL1 / Large ribosomal subunit protein bL20 ...Protein translocase subunit SecY / Protein translocase subunit SecE / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL15 / Apolipoprotein A-I / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein uL1 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL36A / Large ribosomal subunit protein bL9 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL23 / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL5 / Small ribosomal subunit protein bS21 / Large ribosomal subunit protein bL25 / Protein translocase subunit SecE / Protein translocase subunit SecY / Cell division protein FtsQ
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.1 Å
AuthorsFrauenfeld J / Gumbart J / Sluis EO / Funes S / Gartmann M / Beatrix B / Mielke T / Berninghausen O / Becker T / Schulten K / Beckmann R
CitationJournal: 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
DepositionJan 17, 2011-
Header (metadata) releaseApr 21, 2011-
Map releaseApr 21, 2011-
UpdateDec 11, 2013-
Current statusDec 11, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.7
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.7
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-4v6m
  • Surface level: 0.8
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-1858_ima...

Downloads & links

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Map

FileDownload / File: emd_1858.map.gz / Format: CCP4 / Size: 122.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis map represents an E.coli 70S ribosome carrying an elongation arrested nascent chain of 118 amino acid residues, with the first 102 residues representing the N-terminus of the membrane protein FtsQ with the signal anchor, a tRNA in the P-site and the E.coli SecYEG complex embedded in a E.coli lipid bilayer (Nanodisc).
Voxel sizeX=Y=Z: 1.2375 Å
Density
Contour LevelBy AUTHOR: 0.5 / Movie #1: 0.7
Minimum - Maximum-3.53351 - 6.82334
Average (Standard dev.)0.0507365 (±0.456442)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-160-160-159
Dimensions320320320
Spacing320320320
CellA=B=C: 396 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.23751.23751.2375
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z396.000396.000396.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-160-160-159
NX/NY/NZ320320320
MAP C/R/S213
start NC/NR/NS-160-160-159
NC/NR/NS320320320
D min/max/mean-3.5346.8230.051

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Supplemental data

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Sample components

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Entire : An active E.coli SecYEG complex embedded in a lipid bilayer (Nano...

EntireName: An active E.coli SecYEG complex embedded in a lipid bilayer (Nanodisc), bound to a translating E.coli ribosome
Components
  • Sample: An active E.coli SecYEG complex embedded in a lipid bilayer (Nanodisc), bound to a translating E.coli ribosome
  • Complex: 70S ribosome nascent chain complex
  • Ligand: Nd-SecYEG

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Supramolecule #1000: An active E.coli SecYEG complex embedded in a lipid bilayer (Nano...

SupramoleculeName: An active E.coli SecYEG complex embedded in a lipid bilayer (Nanodisc), bound to a translating E.coli ribosome
type: sample / ID: 1000
Details: The heterotrimeric SecYEG complex was embedded in a lipid bilayer (nascent HDL, Nanodisc)
Oligomeric state: 70S ribosome bound to one copy of the E.coli SecYEG complex in a lipid bilayer
Number unique components: 2
Molecular weightTheoretical: 2.7 MDa

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Supramolecule #1: 70S ribosome nascent chain complex

SupramoleculeName: 70S ribosome nascent chain complex / type: complex / ID: 1 / Name.synonym: 70S RNC / Recombinant expression: No / Ribosome-details: ribosome-prokaryote: ALL
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 2.7 MDa

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Macromolecule #1: Nd-SecYEG

MacromoleculeName: Nd-SecYEG / type: ligand / ID: 1 / Name.synonym: SecYEG embedded in a Nanodisc / Number of copies: 1 / Oligomeric state: Heterotrimeric / Recombinant expression: Yes
Source (natural)Organism: Escherichia coli (E. coli) / Location in cell: Plasma membrane
Recombinant expressionOrganism: Escherichia coli (E. coli)

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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), 100 mM KOAc, 10 mM Mg(OAc)2, 1 mM DTT, 250 microg/ml chloramphenicol
VitrificationCryogen name: ETHANE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: PRIMESCAN / Digitization - Sampling interval: 4.76 µm / Average electron dose: 22 e/Å2 / Details: Scanned at 5334 dpi
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 38000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.26 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 39000
Sample stageSpecimen holder: FEI Polara cartridge system / Specimen holder model: OTHER
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Defocus group volumes
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 7.1 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER / Number images used: 85664

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