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- PDB-8ya3: Structure of the SecA-SecY complex with the substrate FtsQ-LacY(+... -

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Basic information

Entry
Database: PDB / ID: 8ya3
TitleStructure of the SecA-SecY complex with the substrate FtsQ-LacY(+7C) treated with DTT
Components
  • Cell division protein FtsQ,Lactose permease
  • Protein translocase subunit SecE
  • Protein translocase subunit SecY
KeywordsPROTEIN TRANSPORT / Protein translocation / Membrane protein insertion / Protein chaperone
Function / homology
Function and homology information


lactose:proton symporter activity / lactose transport / FtsQBL complex / carbohydrate:proton symporter activity / divisome complex / lactose binding / intracellular protein transmembrane transport / protein transport by the Sec complex / division septum assembly / FtsZ-dependent cytokinesis ...lactose:proton symporter activity / lactose transport / FtsQBL complex / carbohydrate:proton symporter activity / divisome complex / lactose binding / intracellular protein transmembrane transport / protein transport by the Sec complex / division septum assembly / FtsZ-dependent cytokinesis / cell division site / carbohydrate transport / protein secretion / protein transmembrane transporter activity / protein targeting / cell division / identical protein binding / membrane / plasma membrane
Similarity search - Function
LacY/RafB permease family / LacY/RafB permease family, conserved site / LacY proton/sugar symporter / LacY family proton/sugar symporters signature 1. / LacY family proton/sugar symporters signature 2. / Cell division protein FtsQ / Cell division protein FtsQ, C-terminal / Cell division protein FtsQ/DivIB, C-terminal / POTRA domain, FtsQ-type / Cell division protein FtsQ/DivIB, C-terminal ...LacY/RafB permease family / LacY/RafB permease family, conserved site / LacY proton/sugar symporter / LacY family proton/sugar symporters signature 1. / LacY family proton/sugar symporters signature 2. / Cell division protein FtsQ / Cell division protein FtsQ, C-terminal / 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 / 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. / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily
Similarity search - Domain/homology
Protein translocase subunit SecE / Protein translocase subunit SecY / Lactose permease / Cell division protein FtsQ
Similarity search - Component
Biological speciesGeobacillus thermodenitrificans NG80-2 (bacteria)
Escherichia coli K-12 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.27 Å
AuthorsOu, X. / Ma, C. / Sun, D. / Xu, J. / Wu, X. / Gao, N. / Li, L.
Funding support China, 3items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2019YFA0508900,2016YFA0500401 China
National Natural Science Foundation of China (NSFC)31725007,31630087,31800625,21873006,31870835 China
Other government2018M631249,2019M650327
CitationJournal: Cell / Year: 2025
Title: SecY translocon chaperones protein folding during membrane protein insertion.
Authors: Xiaomin Ou / Chengying Ma / Dongjie Sun / Jinkun Xu / Yang Wang / Xiaofei Wu / Dali Wang / Song Yang / Ning Gao / Chen Song / Long Li /
Abstract: The Sec translocon is vital for guiding membrane protein insertion into lipid bilayers. The insertion and folding processes of membrane proteins are poorly understood. Here, we report cryo-electron ...The Sec translocon is vital for guiding membrane protein insertion into lipid bilayers. The insertion and folding processes of membrane proteins are poorly understood. Here, we report cryo-electron microscopy structures of multi-spanning membrane proteins inserting through the SecY channel, the Sec translocon in prokaryotes. The high-resolution structures illustrate how bulky amino acids pass the narrow channel restriction. Comparison of different translocation states reveals that the cytoplasmic and extracellular cavities of the channel create distinct environments for promoting the unfolding and folding of transmembrane segments (TMs), respectively. Released substrate TMs are either flexible or stabilized by an unexpected hydrophilic groove between TM3 and TM4 of SecY. Disruption of the groove causes global defects in the folding of the membrane proteome. These findings demonstrate that beyond its role as a passive protein-conducting channel, the SecY translocon actively serves as a chaperone, employing multiple mechanisms to promote membrane protein insertion and folding.
History
DepositionFeb 7, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 26, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
Y: Protein translocase subunit SecY
E: Protein translocase subunit SecE
B: Cell division protein FtsQ,Lactose permease


Theoretical massNumber of molelcules
Total (without water)64,0343
Polymers64,0343
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Protein translocase subunit SecY


Mass: 47512.051 Da / Num. of mol.: 1 / Mutation: G60C, Q202T, F211T, R213N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus thermodenitrificans NG80-2 (bacteria)
Gene: secY / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: A4IJK8
#2: Protein Protein translocase subunit SecE


Mass: 8249.600 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus thermodenitrificans NG80-2 (bacteria)
Gene: secE / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: A4IJH4
#3: Protein Cell division protein FtsQ,Lactose permease / Lactose-proton symport


Mass: 8272.546 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: ftsQ, b0093, JW0091, lacY, b0343, JW0334 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: P06136, UniProt: P02920
Has protein modificationN

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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: SecA-SecY complex with the substrate FtsQ-LacY(+7C) treated with DTT
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Geobacillus thermodenitrificans NG80-2 (bacteria)
Source (recombinant)Organism: Escherichia coli K-12 (bacteria)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 64 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 123581 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00913143
ELECTRON MICROSCOPYf_angle_d0.92817742
ELECTRON MICROSCOPYf_dihedral_angle_d16.791787
ELECTRON MICROSCOPYf_chiral_restr0.0572007
ELECTRON MICROSCOPYf_plane_restr0.0072264

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