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- PDB-8y9z: Structure of the SecA-SecY complex with the substrate HmBRI-3TM -

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Basic information

Entry
Database: PDB / ID: 8y9z
TitleStructure of the SecA-SecY complex with the substrate HmBRI-3TM
Components
  • (Protein translocase subunit ...) x 3
  • Bacteriorhodopsin-I
  • Nanobody
KeywordsPROTEIN TRANSPORT / Protein translocation / Membrane protein insertion / Protein chaperone
Function / homology
Function and homology information


protein-exporting ATPase activity / cell envelope Sec protein transport complex / protein-secreting ATPase / protein transport by the Sec complex / intracellular protein transmembrane transport / protein import / monoatomic ion channel activity / protein secretion / photoreceptor activity / protein transmembrane transporter activity ...protein-exporting ATPase activity / cell envelope Sec protein transport complex / protein-secreting ATPase / protein transport by the Sec complex / intracellular protein transmembrane transport / protein import / monoatomic ion channel activity / protein secretion / photoreceptor activity / protein transmembrane transporter activity / phototransduction / protein targeting / proton transmembrane transport / membrane raft / ATP binding / metal ion binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
SecE subunit of protein translocation complex, bacterial-like / SecE superfamily / SEC-C motif / SEC-C motif / Protein translocase subunit SecA / SecA DEAD-like, N-terminal / SecA Wing/Scaffold / SecA, preprotein cross-linking domain / SecA motor DEAD / SecA conserved site ...SecE subunit of protein translocation complex, bacterial-like / SecE superfamily / SEC-C motif / SEC-C motif / Protein translocase subunit SecA / SecA DEAD-like, N-terminal / SecA Wing/Scaffold / SecA, preprotein cross-linking domain / SecA motor DEAD / SecA conserved site / SecA, Wing/Scaffold superfamily / SecA, preprotein cross-linking domain superfamily / SecA, C-terminal helicase domain / SecA preprotein cross-linking domain / SecA Wing and Scaffold domain / SecA DEAD-like domain / SecA P-loop domain / SecA family signature. / SecA family profile. / SecA DEAD-like domain / SecA preprotein cross-linking domain / 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 / Bacterial rhodopsins retinal binding site. / Bacterial rhodopsins signature 1. / Rhodopsin, retinal binding site / Bacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / Protein translocase subunit SecE / Protein translocase subunit SecY / Protein translocase subunit SecA / Bacteriorhodopsin-I
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
Geobacillus thermodenitrificans NG80-2 (bacteria)
Lama glama (llama)
Haloarcula marismortui ATCC 43049 (Halophile)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.41 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
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein translocase subunit SecA
Y: Protein translocase subunit SecY
E: Protein translocase subunit SecE
V: Nanobody
B: Bacteriorhodopsin-I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,1638
Polymers168,6455
Non-polymers5183
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

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Protein translocase subunit ... , 3 types, 3 molecules AYE

#1: Protein Protein translocase subunit SecA


Mass: 88673.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: secA / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: P28366, protein-secreting ATPase
#2: 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
#3: 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

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Antibody / Protein , 2 types, 2 molecules VB

#4: Antibody Nanobody


Mass: 13006.622 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The NCBI accession for the Nanobody is 6ITC_V. / Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12
#5: Protein Bacteriorhodopsin-I / HmBRI


Mass: 11203.066 Da / Num. of mol.: 1 / Mutation: P75C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haloarcula marismortui ATCC 43049 (Halophile)
Strain: ATCC 43049 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: Q5UXY6

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Non-polymers , 3 types, 3 molecules

#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM

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Details

Has ligand of interestY
Has protein modificationY

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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 HmBRI-3TM / Type: COMPLEX / Entity ID: #1-#5 / 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: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.41 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 380199 / Symmetry type: POINT

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