[English] 日本語
Yorodumi
- PDB-3j46: Structure of the SecY protein translocation channel in action -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3j46
TitleStructure of the SecY protein translocation channel in action
Components
  • (23S ribosomal ...) x 4
  • (50S ribosomal protein ...) x 4
  • A-tRNA
  • NC100
  • P-tRNA
  • Preprotein translocase subunit SecE
  • Protein translocase subunit SecY
  • Protein-export membrane protein SecG
KeywordsRIBOSOME/PROTEIN TRANSPORT / 70S / preprotein translocase / SECYEG / protein translocation channel / nascent chain / RIBOSOME-PROTEIN TRANSPORT complex
Function / homology
Function and homology information


protein insertion into membrane from inner side / cell envelope Sec protein transport complex / protein transport by the Sec complex / intracellular protein transmembrane transport / protein-transporting ATPase activity / SRP-dependent cotranslational protein targeting to membrane, translocation / signal sequence binding / protein transmembrane transporter activity / protein secretion / negative regulation of translational initiation ...protein insertion into membrane from inner side / cell envelope Sec protein transport complex / protein transport by the Sec complex / intracellular protein transmembrane transport / protein-transporting ATPase activity / SRP-dependent cotranslational protein targeting to membrane, translocation / signal sequence binding / protein transmembrane transporter activity / protein secretion / negative regulation of translational initiation / intracellular protein transport / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / structural constituent of ribosome / translation / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Preprotein translocase SecG subunit / Preprotein translocase SecG subunit / SecE subunit of protein translocation complex, bacterial-like / SecE superfamily / Protein translocase subunit SecY / 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 ...Preprotein translocase SecG subunit / Preprotein translocase SecG subunit / SecE subunit of protein translocation complex, bacterial-like / SecE superfamily / Protein translocase subunit SecY / 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 / Ribosomal protein L1, bacterial-type / Ribosomal protein L1, conserved site / Ribosomal protein L1 / Ribosomal protein L1 signature. / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L24 / Ribosomal protein L23/L25, conserved site / Ribosomal protein L23 signature. / Ribosomal protein L29, conserved site / Ribosomal protein L29 signature. / Ribosomal protein L29/L35 / Ribosomal protein L29/L35 superfamily / Ribosomal L29 protein / Ribosomal protein L24/L26, conserved site / KOW (Kyprides, Ouzounis, Woese) motif. / Ribosomal protein L25/L23 / Ribosomal protein L23 / Ribosomal protein L26/L24, KOW domain / Ribosomal protein L24 signature. / Ribosomal protein L23/L15e core domain superfamily / Translation protein SH3-like domain superfamily / KOW / KOW motif / Ribosomal protein L2, domain 2 / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / Large ribosomal subunit protein uL1 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL23 / Protein translocase subunit SecE / Protein-export membrane protein SecG / Protein translocase subunit SecY / Large ribosomal subunit protein uL24
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 10.1 Å
AuthorsAkey, C.W. / Park, E. / Menetret, J.F. / Gumbart, J.C. / Ludtke, S.J. / Li, W. / Whynot, A. / Rapoport, T.A.
CitationJournal: Nature / Year: 2014
Title: Structure of the SecY channel during initiation of protein translocation.
Authors: Eunyong Park / Jean-François Ménétret / James C Gumbart / Steven J Ludtke / Weikai Li / Andrew Whynot / Tom A Rapoport / Christopher W Akey /
Abstract: Many secretory proteins are targeted by signal sequences to a protein-conducting channel, formed by prokaryotic SecY or eukaryotic Sec61 complexes, and are translocated across the membrane during ...Many secretory proteins are targeted by signal sequences to a protein-conducting channel, formed by prokaryotic SecY or eukaryotic Sec61 complexes, and are translocated across the membrane during their synthesis. Crystal structures of the inactive channel show that the SecY subunit of the heterotrimeric complex consists of two halves that form an hourglass-shaped pore with a constriction in the middle of the membrane and a lateral gate that faces the lipid phase. The closed channel has an empty cytoplasmic funnel and an extracellular funnel that is filled with a small helical domain, called the plug. During initiation of translocation, a ribosome-nascent chain complex binds to the SecY (or Sec61) complex, resulting in insertion of the nascent chain. However, the mechanism of channel opening during translocation is unclear. Here we have addressed this question by determining structures of inactive and active ribosome-channel complexes with cryo-electron microscopy. Non-translating ribosome-SecY channel complexes derived from Methanocaldococcus jannaschii or Escherichia coli show the channel in its closed state, and indicate that ribosome binding per se causes only minor changes. The structure of an active E. coli ribosome-channel complex demonstrates that the nascent chain opens the channel, causing mostly rigid body movements of the amino- and carboxy-terminal halves of SecY. In this early translocation intermediate, the polypeptide inserts as a loop into the SecY channel with the hydrophobic signal sequence intercalated into the open lateral gate. The nascent chain also forms a loop on the cytoplasmic surface of SecY rather than entering the channel directly.
History
DepositionJun 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2013Group: Database references
Revision 1.2Feb 5, 2014Group: Database references
Revision 1.3Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id
Revision 2.0Jul 3, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / entity / struct_conn
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-5693
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-5693
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
y: Protein translocase subunit SecY
E: Preprotein translocase subunit SecE
G: Protein-export membrane protein SecG
n: NC100
p: P-tRNA
a: A-tRNA
5: 50S ribosomal protein L1
T: 50S ribosomal protein L23P
U: 50S ribosomal protein L24P
Y: 50S ribosomal protein L29P
1: 23S ribosomal RNA
2: 23S ribosomal RNA
3: 23S ribosomal RNA
4: 23S ribosomal RNA


Theoretical massNumber of molelcules
Total (without water)256,08114
Polymers256,08114
Non-polymers00
Water0
1


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

-
Components

-
Protein , 4 types, 4 molecules yEGn

#1: Protein Protein translocase subunit SecY


Mass: 47659.371 Da / Num. of mol.: 1 / Mutation: S68C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pBAD(MazF)-NC100 / Production host: Escherichia coli (E. coli) / Strain (production host): EP72 / References: UniProt: P0AGA2
#2: Protein Preprotein translocase subunit SecE


Mass: 6123.306 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pBAD(MazF)-NC100 / Production host: Escherichia coli (E. coli) / Strain (production host): EP72 / References: UniProt: P0AG96
#3: Protein Protein-export membrane protein SecG


Mass: 6566.800 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pBAD(MazF)-NC100 / Production host: Escherichia coli (E. coli) / Strain (production host): EP72 / References: UniProt: P0AG99
#4: Protein NC100


Mass: 10780.095 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pBAD(MazF)-NC100 / Production host: Escherichia coli (E. coli) / Strain (production host): EP72

-
RNA chain , 2 types, 2 molecules pa

#5: RNA chain P-tRNA


Mass: 24478.502 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#6: RNA chain A-tRNA


Mass: 24599.748 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)

-
50S ribosomal protein ... , 4 types, 4 molecules 5TUY

#7: Protein 50S ribosomal protein L1 /


Mass: 24765.660 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7L0
#8: Protein 50S ribosomal protein L23P / Ribosome


Mass: 11222.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0ADZ0
#9: Protein 50S ribosomal protein L24P / Ribosome


Mass: 11208.054 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P60624
#10: Protein 50S ribosomal protein L29P / Ribosome


Mass: 7286.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7M6

-
23S ribosomal ... , 4 types, 4 molecules 1234

#11: RNA chain 23S ribosomal RNA /


Mass: 20350.104 Da / Num. of mol.: 1 / Fragment: helix 6 - helix 7 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#12: RNA chain 23S ribosomal RNA /


Mass: 11661.961 Da / Num. of mol.: 1 / Fragment: helix 50 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#13: RNA chain 23S ribosomal RNA /


Mass: 14261.592 Da / Num. of mol.: 1 / Fragment: helix 59 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#14: RNA chain 23S ribosomal RNA /


Mass: 35116.715 Da / Num. of mol.: 1 / Fragment: helix 76 - helix 78 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY / Number of used crystals: 1
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

Component
IDNameTypeParent-ID
1active ribosome-nascent chain-SecYEG complexCOMPLEX0
270S ribosomeRibosomeRIBOSOME1
3SecYEG channel1
4NC100- nascent chain1
Molecular weightValue: 2.5 MDa / Experimental value: NO
Buffer solutionName: 50 mM Tris-acetate, 10 mM Mg(OAc)2, 80 mM KOAc, 0.06% DDM
pH: 7.2
Details: 50 mM Tris-acetate, 10 mM Mg(OAc)2, 80 mM KOAc, 0.06% DDM
SpecimenConc.: 8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 400 mesh Quantifoil holey grids with 2/1 or 1.2/1.2
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Temp: 77 K / Humidity: 95 %
Details: Blot 1-2 seconds before plunging into liquid ethane (FEI VITROBOT MARK III).

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20 / Date: Feb 10, 2012
Details: Low dose imaging: automated single particle data collection program from TVIPS was used.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 160 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 42000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2 mm
Specimen holderSpecimen holder model: OTHER / Specimen holder type: CT3500 / Temperature: 94 K
Image recordingElectron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM / Details: Tietz 4096 x 4096 CCD
Image scansNum. digital images: 4900
Radiation wavelengthRelative weight: 1

-
Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.11data extraction
EM software
IDNameVersionCategory
1MDFFmodel fitting
2UCSF Chimeramodel fitting
3EMAN23D reconstruction
CTF correctionDetails: per micrograph
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: projection matching / Resolution: 10.1 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 53000 / Nominal pixel size: 2.12 Å / Actual pixel size: 2.12 Å
Details: The structure was solved twice: first with a model starting from a 25-Angstrom filtered E. coli ribosome map generated in house, and then a second time using a filtered ribosome model (EMD- ...Details: The structure was solved twice: first with a model starting from a 25-Angstrom filtered E. coli ribosome map generated in house, and then a second time using a filtered ribosome model (EMD-5036). In each case, after convergence, maps from two EMAN2 refinements with different parameters were averaged after alignment in Chimera. Four maps in total were averaged to reduce the noise. Resolution method was FSC at 0.5 cut-off for a comparison between the full experimental 3D density map and a calculated map of the docked E. coli ribosome model (this map was calculated to 7 Angstrom resolution with EMAN).
Num. of class averages: 5300 / Symmetry type: POINT
Atomic model building
IDProtocolSpaceDetails
1FLEXIBLE FITREALREFINEMENT PROTOCOL--FLEXIBLE
2FLEXIBLE FITREALREFINEMENT PROTOCOL--FLEXIBLE
3FLEXIBLE FITREALREFINEMENT PROTOCOL--FLEXIBLE DETAILS--A- and P-site tRNAs from T. thermophilus ribosome structure. mRNA from this structure also used for some modeling steps.
Atomic model building
IDPDB-IDPdb chain-ID 3D fitting-ID
12I2P

2i2p
PDB Unreleased entry

1
23J01

3j01
PDB Unreleased entry

2
33I8G

3i8g
PDB Unreleased entry

B3
43I8G

3i8g
PDB Unreleased entry

C3
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms8833 8645 0 0 17478

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more