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- EMDB-39087: Structure of the SecA-SecY complex with the substrate FtsQ-LacY(+7C) -

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Entry
Database: EMDB / ID: EMD-39087
TitleStructure of the SecA-SecY complex with the substrate FtsQ-LacY(+7C)
Map data
Sample
  • Complex: SecA-SecY complex with the substrate FtsQ-LacY(+7C)
    • Protein or peptide: Protein translocase subunit SecA
    • Protein or peptide: Protein translocase subunit SecY
    • Protein or peptide: Protein translocase subunit SecE
    • Protein or peptide: Nanobody
    • Protein or peptide: Cell division protein FtsQ,Lactose permease
    • Protein or peptide: Green fluorescent protein
    • Protein or peptide: Nanobody
  • Ligand: MAGNESIUM ION
  • Ligand: BERYLLIUM TRIFLUORIDE ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsProtein translocation / Membrane protein insertion / Protein chaperone / PROTEIN TRANSPORT
Function / homology
Function and homology information


lactose:proton symporter activity / lactose transport / cell septum assembly / carbohydrate:proton symporter activity / protein-exporting ATPase activity / lactose binding / cell envelope Sec protein transport complex / protein-secreting ATPase / intracellular protein transmembrane transport / protein transport by the Sec complex ...lactose:proton symporter activity / lactose transport / cell septum assembly / carbohydrate:proton symporter activity / protein-exporting ATPase activity / lactose binding / cell envelope Sec protein transport complex / protein-secreting ATPase / intracellular protein transmembrane transport / protein transport by the Sec complex / SRP-dependent cotranslational protein targeting to membrane, translocation / protein import / signal sequence binding / FtsZ-dependent cytokinesis / cell division site / carbohydrate transport / protein transmembrane transporter activity / protein secretion / protein targeting / bioluminescence / generation of precursor metabolites and energy / membrane raft / ATP binding / membrane / metal ion binding / plasma membrane / cytoplasm
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 / 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 / POTRA domain / POTRA domain profile. / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Protein translocase subunit SecE / Protein translocase subunit SecY / Lactose permease / Protein translocase subunit SecA / Green fluorescent protein / Cell division protein FtsQ
Similarity search - Component
Biological speciesGeobacillus thermodenitrificans NG80-2 (bacteria) / Bacillus subtilis subsp. subtilis str. 168 (bacteria) / Lama glama (llama) / Escherichia coli K-12 (bacteria) / Aequorea victoria (jellyfish)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.97 Å
AuthorsOu X / Ma C / Sun D / Xu J / Wu X / Gao N / Li L
Funding support China, 3 items
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, 2024-
Header (metadata) releaseFeb 26, 2025-
Map releaseFeb 26, 2025-
UpdateMar 5, 2025-
Current statusMar 5, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39087.png

Downloads & links

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Map

FileDownload / File: emd_39087.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 240 pix.
= 252.48 Å		1.05 Å/pix.
x 240 pix.
= 252.48 Å		1.05 Å/pix.
x 240 pix.
= 252.48 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.052 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025
Minimum - Maximum-0.071063675 - 0.17555195
Average (Standard dev.)0.00037922527 (±0.003924762)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 252.48001 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_39087_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_39087_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : SecA-SecY complex with the substrate FtsQ-LacY(+7C)

EntireName: SecA-SecY complex with the substrate FtsQ-LacY(+7C)
Components
  • Complex: SecA-SecY complex with the substrate FtsQ-LacY(+7C)
    • Protein or peptide: Protein translocase subunit SecA
    • Protein or peptide: Protein translocase subunit SecY
    • Protein or peptide: Protein translocase subunit SecE
    • Protein or peptide: Nanobody
    • Protein or peptide: Cell division protein FtsQ,Lactose permease
    • Protein or peptide: Green fluorescent protein
    • Protein or peptide: Nanobody
  • Ligand: MAGNESIUM ION
  • Ligand: BERYLLIUM TRIFLUORIDE ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: SecA-SecY complex with the substrate FtsQ-LacY(+7C)

SupramoleculeName: SecA-SecY complex with the substrate FtsQ-LacY(+7C) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5, #7, #6
Source (natural)Organism: Geobacillus thermodenitrificans NG80-2 (bacteria)

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Macromolecule #1: Protein translocase subunit SecA

MacromoleculeName: Protein translocase subunit SecA / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: protein-secreting ATPase
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 87.182039 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString: RTLNRYEKIA NDIDAIRGDY ENLSDDALKH KTIEFKERLE KGATTDDLLV EAFAVVREAS RRVTGMFPFK VQLMGGVALH DGNIAEMKT GEGKTLTSTL PVYLNALTGK GVHVVTVNEY LASRDAEQMG KIFEFLGLTV GLNLNSMSKD EKREAYAADI T YSTNNELG ...String:
RTLNRYEKIA NDIDAIRGDY ENLSDDALKH KTIEFKERLE KGATTDDLLV EAFAVVREAS RRVTGMFPFK VQLMGGVALH DGNIAEMKT GEGKTLTSTL PVYLNALTGK GVHVVTVNEY LASRDAEQMG KIFEFLGLTV GLNLNSMSKD EKREAYAADI T YSTNNELG FDYLRDNMVL YKEQMVQRPL HFAVIDEVDS ILIDEARTPL IISGQAAKST KLYVQANAFV RTLKAEKDYT YD IKTKAVQ LTEEGMTKAE KAFGIDNLFD VKHVALNHHI NQALKAHVAM QKDVDYVVED GQVVIVDSFT GRLMKGRRYS EGL HQAIEA KEGLEIQNES MTLATITFQN YFRMYEKLAG MTGTAKTEEE EFRNIYNMQV VTIPTNRPVV RDDRPDLIYR TMEG KFKAV AEDVAQRYMT GQPVLVGTVA VETSELISKL LKNKGIPHQV LNAKNHEREA QIIEEAGQKG AVTIATNMAG RGTDI KLGE GVKELGGLAV VGTERHESRR IDNQLRGRSG RQGDPGITQF YLSMEDELMR RFGAERTMAM LDRFGMDDST PIQSKM VSR AVESSQKRVE GNNFDSRKQL LQYDDVLRQQ REVIYKQRFE VIDSENLREI VENMIKSSLE RAIAAYTPRE ELPEEWK LD GLVDLINTTY LDEGALEKSD IFGKEPDEML ELIMDRIITK YNEKEEQFGK EQMREFEKVI VLRAVDSKWM DHIDAMDQ L RQGIHLRAYA QTNPLREYQM EGFAMFEHMI ESIEDEVAKF VMKA

UniProtKB: Protein translocase subunit SecA

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Macromolecule #2: Protein translocase subunit SecY

MacromoleculeName: Protein translocase subunit SecY / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Geobacillus thermodenitrificans NG80-2 (bacteria)
Molecular weightTheoretical: 47.380855 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString: FRTISNFMRV SDIRNKIIFT LLMLIVFRIG TFIPVPSVNT DVLKLQDQLN AFGVLNIFCG GALQNFSIFA MGVMPYITAS IIVQLLQMD VVPKFAEWSK QGEMGRRKLA QFTRYFTIVL GFIQALGMSY GFNNLAGGML IQNPGIGTYL LIAVVLTAGT A FLMWLGEQ ...String:
FRTISNFMRV SDIRNKIIFT LLMLIVFRIG TFIPVPSVNT DVLKLQDQLN AFGVLNIFCG GALQNFSIFA MGVMPYITAS IIVQLLQMD VVPKFAEWSK QGEMGRRKLA QFTRYFTIVL GFIQALGMSY GFNNLAGGML IQNPGIGTYL LIAVVLTAGT A FLMWLGEQ ITAKGVGNGI SIIIFAGIVS GIPTILNQIY AQTFENVGED LTLNIVRLLL VALAVVAVIV GVIYIQQAFR KI PIQYAKR LEGRNPVGGH STHLPLKVNP AGVIPVIFAV SFLIAPPTIA SFFGTNDVTL WIRRTFDYTH PVGMTIYVVL IIA FTYFYA FVQVNPEQMA DNLKKQGGYI PGIRPGKNTQ EYVTRILYRL TLVGSLFLAF IAVLPVFFVN FANLPPSAQI GGTS LLIVV GVALETMKQL ESQLVKRHYR GFIK

UniProtKB: Protein translocase subunit SecY

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Macromolecule #3: Protein translocase subunit SecE

MacromoleculeName: Protein translocase subunit SecE / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Geobacillus thermodenitrificans NG80-2 (bacteria)
Molecular weightTheoretical: 6.770011 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString:
QRVTNFFKEV VRELKKVSWP NRKELVNYTA VVLATVAFFT VFFAVIDLGI SQLIRLVF

UniProtKB: Protein translocase subunit SecE

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Macromolecule #4: Nanobody

MacromoleculeName: Nanobody / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 12.919544 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString:
QVQLVETGGG LVQPGGSLRL SCGASGSIFN MYAMGWYRQA PGKRREVVAR IATDDSTMYP DSVKGRFTIS RDNAKNTVYL QMNSLKPED TAVYYCYYQR TVMSQPYWGQ GTQVTVS

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Macromolecule #5: Cell division protein FtsQ,Lactose permease

MacromoleculeName: Cell division protein FtsQ,Lactose permease / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K-12
Molecular weightTheoretical: 7.660771 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString:
AKKTILFLLT VLTTVLVSGW VVLGAQYEDG CSGVVILKTL HMFEVPFLLV GAFSNADTSI SGDGDSPHSY HS

UniProtKB: Cell division protein FtsQ, Lactose permease

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Macromolecule #6: Nanobody

MacromoleculeName: Nanobody / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 12.455806 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString:
VALVESGGAL VQPGGSLRLS CAASGFPVNR YSMRWYRQAP GKEREWVAGM SSAGDRSSYE DSVKGRFTIS RDDARNTVYL QMNSLKPED TAVYYCNVNV GFEYWGQGTQ VTVS

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Macromolecule #7: Green fluorescent protein

MacromoleculeName: Green fluorescent protein / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Aequorea victoria (jellyfish)
Molecular weightTheoretical: 25.517627 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString: KGEELFTGVV PILVELDGDV NGHKFSVSGE GEGDATYGKL TLKFICTTGK LPVPWPTLVT TF(GYS)VQCFSRY PDHMKR HDF FKSAMPEGYV QERTISFKDD GNYKTRAEVK FEGDTLVNRI ELKGIDFKED GNILGHKLEY NYNSHNVYIT ADKQKNG IK ANFKIRHNIE ...String:
KGEELFTGVV PILVELDGDV NGHKFSVSGE GEGDATYGKL TLKFICTTGK LPVPWPTLVT TF(GYS)VQCFSRY PDHMKR HDF FKSAMPEGYV QERTISFKDD GNYKTRAEVK FEGDTLVNRI ELKGIDFKED GNILGHKLEY NYNSHNVYIT ADKQKNG IK ANFKIRHNIE DGSVQLADHY QQNTPIGDGP VLLPDNHYLS TQSALSKDPN EKRDHMVLLE FVTAAGI

UniProtKB: Green fluorescent protein

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Macromolecule #8: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 8 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #9: BERYLLIUM TRIFLUORIDE ION

MacromoleculeName: BERYLLIUM TRIFLUORIDE ION / type: ligand / ID: 9 / Number of copies: 1 / Formula: BEF
Molecular weightTheoretical: 66.007 Da
Chemical component information

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

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Macromolecule #10: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 10 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

9731

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 443770
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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