[English] 日本語
Yorodumi
- EMDB-39088: Structure of the SecA-SecY complex with the substrate FtsQ-LacY(+20C) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-39088
TitleStructure of the SecA-SecY complex with the substrate FtsQ-LacY(+20C)
Map data
Sample
  • Complex: SecA-SecY complex with the substrate FtsQ-LacY(+20C)
    • Protein or peptide: Protein translocase subunit SecA
    • Protein or peptide: Protein translocase subunit SecY
    • Protein or peptide: Protein translocase subunit SecE
    • Protein or peptide: Cell division protein FtsQ,Lactose permease
    • Protein or peptide: Nanobody
    • Protein or peptide: Green fluorescent protein
  • Ligand: MAGNESIUM ION
  • Ligand: BERYLLIUM TRIFLUORIDE ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsProtein translocation / SecY / Membrane protein insertion / Protein chaperone / PROTEIN TRANSPORT
Function / homology
Function and homology information


lactose:proton symporter activity / lactose transport / FtsQBL complex / carbohydrate:proton symporter activity / divisome complex / protein-exporting ATPase activity / cell envelope Sec protein transport complex / lactose binding / protein-secreting ATPase / protein transport by the Sec complex ...lactose:proton symporter activity / lactose transport / FtsQBL complex / carbohydrate:proton symporter activity / divisome complex / protein-exporting ATPase activity / cell envelope Sec protein transport complex / lactose binding / protein-secreting ATPase / protein transport by the Sec complex / intracellular protein transmembrane transport / protein import / division septum assembly / FtsZ-dependent cytokinesis / cell division site / carbohydrate transport / protein secretion / protein transmembrane transporter activity / protein targeting / bioluminescence / generation of precursor metabolites and energy / membrane raft / cell division / ATP binding / metal ion binding / identical protein binding / membrane / 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 / Cell division protein FtsQ / Protein translocase subunit SecA / Green fluorescent protein
Similarity search - Component
Biological speciesGeobacillus thermodenitrificans NG80-2 (bacteria) / Bacillus subtilis subsp. subtilis str. 168 (bacteria) / Escherichia coli K-12 (bacteria) / Lama glama (llama) / Aequorea victoria (jellyfish)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.84 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-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_39088.png

Downloads & links

-
Map

FileDownload / File: emd_39088.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.)
1.06 Å/pix.
x 240 pix.
= 253.68 Å		1.06 Å/pix.
x 240 pix.
= 253.68 Å		1.06 Å/pix.
x 240 pix.
= 253.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.057 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-1.1165198 - 1.7571259
Average (Standard dev.)0.004565325 (±0.06960298)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 253.68001 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_39088_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_39088_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : SecA-SecY complex with the substrate FtsQ-LacY(+20C)

EntireName: SecA-SecY complex with the substrate FtsQ-LacY(+20C)
Components
  • Complex: SecA-SecY complex with the substrate FtsQ-LacY(+20C)
    • Protein or peptide: Protein translocase subunit SecA
    • Protein or peptide: Protein translocase subunit SecY
    • Protein or peptide: Protein translocase subunit SecE
    • Protein or peptide: Cell division protein FtsQ,Lactose permease
    • Protein or peptide: Nanobody
    • Protein or peptide: Green fluorescent protein
  • Ligand: MAGNESIUM ION
  • Ligand: BERYLLIUM TRIFLUORIDE ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

+
Supramolecule #1: SecA-SecY complex with the substrate FtsQ-LacY(+20C)

SupramoleculeName: SecA-SecY complex with the substrate FtsQ-LacY(+20C) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Geobacillus thermodenitrificans NG80-2 (bacteria)

+
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

+
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

+
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

+
Macromolecule #4: Cell division protein FtsQ,Lactose permease

MacromoleculeName: Cell division protein FtsQ,Lactose permease / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K-12
Molecular weightTheoretical: 8.71896 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString:
MAKKTILFLL TVLTTVLVSG WVVLGAQYED GSSGVVILKT LHMFCVPFLL VGAFSNADTS ISGDGDSPHS YHSGDGDKLP EGV

UniProtKB: Cell division protein FtsQ, Lactose permease

+
Macromolecule #5: Nanobody

MacromoleculeName: Nanobody / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 12.542883 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString:
VALVESGGAL VQPGGSLRLS CAASGFPVNR YSMRWYRQAP GKEREWVAGM SSAGDRSSYE DSVKGRFTIS RDDARNTVYL QMNSLKPED TAVYYCNVNV GFEYWGQGTQ VTVSS

+
Macromolecule #6: Green fluorescent protein

MacromoleculeName: Green fluorescent protein / type: protein_or_peptide / ID: 6 / 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

+
Macromolecule #7: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #8: BERYLLIUM TRIFLUORIDE ION

MacromoleculeName: BERYLLIUM TRIFLUORIDE ION / type: ligand / ID: 8 / Number of copies: 1 / Formula: BEF
Molecular weightTheoretical: 66.007 Da
Chemical component information

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

+
Macromolecule #9: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 9 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 57.6 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

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

9731

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.84 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 186802
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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