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- EMDB-39086: Structure of the SecA-SecY complex with the substrate HmBRI-3TM -

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Basic information

Entry
Database: EMDB / ID: EMD-39086
TitleStructure of the SecA-SecY complex with the substrate HmBRI-3TM
Map data
Sample
  • Complex: SecA-SecY complex with the substrate HmBRI-3TM
    • 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: Bacteriorhodopsin-I
  • 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


protein-exporting ATPase activity / cell envelope Sec protein transport complex / protein-secreting ATPase / intracellular protein transmembrane transport / protein transport by the Sec complex / protein import / monoatomic ion channel activity / protein secretion / protein transmembrane transporter activity / photoreceptor activity ...protein-exporting ATPase activity / cell envelope Sec protein transport complex / protein-secreting ATPase / intracellular protein transmembrane transport / protein transport by the Sec complex / protein import / monoatomic ion channel activity / protein secretion / protein transmembrane transporter activity / photoreceptor 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
Protein translocase subunit SecE / Protein translocase subunit SecY / Protein translocase subunit SecA / Bacteriorhodopsin-I
Similarity search - Component
Biological speciesGeobacillus thermodenitrificans NG80-2 (bacteria) / Bacillus subtilis subsp. subtilis str. 168 (bacteria) / Lama glama (llama) / Haloarcula marismortui ATCC 43049 (Halophile)
Methodsingle 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, 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-
UpdateApr 16, 2025-
Current statusApr 16, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39086.png

Downloads & links

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Map

FileDownload / File: emd_39086.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
1.07 Å/pix.
x 320 pix.
= 342.4 Å		1.07 Å/pix.
x 320 pix.
= 342.4 Å		1.07 Å/pix.
x 320 pix.
= 342.4 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-2.4913375 - 4.728012
Average (Standard dev.)0.00017366277 (±0.065012924)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 342.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_39086_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_39086_half_map_2.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Sample components

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Entire : SecA-SecY complex with the substrate HmBRI-3TM

EntireName: SecA-SecY complex with the substrate HmBRI-3TM
Components
  • Complex: SecA-SecY complex with the substrate HmBRI-3TM
    • 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: Bacteriorhodopsin-I
  • Ligand: MAGNESIUM ION
  • Ligand: BERYLLIUM TRIFLUORIDE ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: SecA-SecY complex with the substrate HmBRI-3TM

SupramoleculeName: SecA-SecY complex with the substrate HmBRI-3TM / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
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: 88.673906 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString: MLGILNKMFD PTKRTLNRYE KIANDIDAIR GDYENLSDDA LKHKTIEFKE RLEKGATTDD LLVEAFAVVR EASRRVTGMF PFKVQLMGG VALHDGNIAE MKTGEGKTLT STLPVYLNAL TGKGVHVVTV NEYLASRDAE QMGKIFEFLG LTVGLNLNSM S KDEKREAY ...String:
MLGILNKMFD PTKRTLNRYE KIANDIDAIR GDYENLSDDA LKHKTIEFKE RLEKGATTDD LLVEAFAVVR EASRRVTGMF PFKVQLMGG VALHDGNIAE MKTGEGKTLT STLPVYLNAL TGKGVHVVTV NEYLASRDAE QMGKIFEFLG LTVGLNLNSM S KDEKREAY AADITYSTNN ELGFDYLRDN MVLYKEQMVQ RPLHFAVIDE VDSILIDEAR TPLIISGQAA KSTKLYVQAN AF VRTLKAE KDYTYDIKTK AVQLTEEGMT KAEKAFGIDN LFDVKHVALN HHINQALKAH VAMQKDVDYV VEDGQVVIVD SFT GRLMKG RRYSEGLHQA IEAKEGLEIQ NESMTLATIT FQNYFRMYEK LAGMTGTAKT EEEEFRNIYN MQVVTIPTNR PVVR DDRPD LIYRTMEGKF KAVAEDVAQR YMTGQPVLVG TVAVETSELI SKLLKNKGIP HQVLNAKNHE REAQIIEEAG QKGAV TIAT NMAGRGTDIK LGEGVKELGG LAVVGTERHE SRRIDNQLRG RSGRQGDPGI TQFYLSMEDE LMRRFGAERT MAMLDR FGM DDSTPIQSKM VSRAVESSQK RVEGNNFDSR KQLLQYDDVL RQQREVIYKQ RFEVIDSENL REIVENMIKS SLERAIA AY TPREELPEEW KLDGLVDLIN TTYLDEGALE KSDIFGKEPD EMLELIMDRI ITKYNEKEEQ FGKEQMREFE KVIVLRAV D SKWMDHIDAM DQLRQGIHLR AYAQTNPLRE YQMEGFAMFE HMIESIEDEV AKFVMKA

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: 47.512051 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString: MFRTISNFMR VSDIRNKIIF TLLMLIVFRI GTFIPVPSVN TDVLKLQDQL NAFGVLNIFC GGALQNFSIF AMGVMPYITA SIIVQLLQM DVVPKFAEWS KQGEMGRRKL AQFTRYFTIV LGFIQALGMS YGFNNLAGGM LIQNPGIGTY LLIAVVLTAG T AFLMWLGE ...String:
MFRTISNFMR VSDIRNKIIF TLLMLIVFRI GTFIPVPSVN TDVLKLQDQL NAFGVLNIFC GGALQNFSIF AMGVMPYITA SIIVQLLQM DVVPKFAEWS KQGEMGRRKL AQFTRYFTIV LGFIQALGMS YGFNNLAGGM LIQNPGIGTY LLIAVVLTAG T AFLMWLGE QITAKGVGNG ISIIIFAGIV SGIPTILNQI YAQTFENVGE DLTLNIVRLL LVALAVVAVI VGVIYIQQAF RK IPIQYAK RLEGRNPVGG HSTHLPLKVN PAGVIPVIFA VSFLIAPPTI ASFFGTNDVT LWIRRTFDYT HPVGMTIYVV LII AFTYFY AFVQVNPEQM ADNLKKQGGY IPGIRPGKNT QEYVTRILYR LTLVGSLFLA FIAVLPVFFV NFANLPPSAQ IGGT SLLIV VGVALETMKQ LESQLVKRHY RGFIK

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: 8.2496 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString:
MQRVTNFFKE VVRELKKVSW PNRKELVNYT AVVLATVAFF TVFFAVIDLG ISQLIRLVFE GGHHHHHHHH

UniProtKB: Protein translocase subunit SecE

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Macromolecule #4: Nanobody

MacromoleculeName: Nanobody / type: protein_or_peptide / ID: 4 / Details: The NCBI accession for the Nanobody is 6ITC_V. / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 13.006622 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString:
QVQLVETGGG LVQPGGSLRL SCGASGSIFN MYAMGWYRQA PGKRREVVAR IATDDSTMYP DSVKGRFTIS RDNAKNTVYL QMNSLKPED TAVYYCYYQR TVMSQPYWGQ GTQVTVSS

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Macromolecule #5: Bacteriorhodopsin-I

MacromoleculeName: Bacteriorhodopsin-I / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Haloarcula marismortui ATCC 43049 (Halophile) / Strain: ATCC 43049
Molecular weightTheoretical: 11.203066 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString:
MPAPGSEGIW LWLGTAGMFL GMLYFIARGW GETDGRRQKF YIATILITAI AFVNYLAMAL GFGLTFIEFG GEQHCIYWAR YTDWLFTTP LLLYDLGLLA

UniProtKB: Bacteriorhodopsin-I

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Macromolecule #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #7: BERYLLIUM TRIFLUORIDE ION

MacromoleculeName: BERYLLIUM TRIFLUORIDE ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: BEF
Molecular weightTheoretical: 66.007 Da
Chemical component information

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

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Macromolecule #8: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 8 / 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 K3 (6k 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.41 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 380199
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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