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- EMDB-33192: Structure of the SecA/SecYE/proOmpA(4Y)-sfGFP complex with ADP.BeF3-. -

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Basic information

Entry
Database: EMDB / ID: EMD-33192
TitleStructure of the SecA/SecYE/proOmpA(4Y)-sfGFP complex with ADP.BeF3-.
Map data
Sample
  • Complex: Complex of the SecA/SecYE/proOmpA(4Y)-sfGFP with ADP.BeF3-
    • Complex: SecA
      • Protein or peptide: Protein translocase subunit SecA
    • Complex: SecY
      • Protein or peptide: Protein translocase subunit SecY
    • Complex: SecE
      • Protein or peptide: Protein translocase subunit SecE
    • Complex: sfGFP
      • Protein or peptide: Translocating polypeptide
  • Ligand: MAGNESIUM ION
  • Ligand: BERYLLIUM TRIFLUORIDE ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsSecA ATPase / membrane protein / TRANSLOCATE / TRANSLOCASE
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 / protein secretion / protein transmembrane transporter activity / protein targeting / membrane raft ...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 / protein secretion / protein transmembrane transporter activity / protein targeting / membrane raft / ATP binding / metal ion binding / 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 / 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
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria) / Geobacillus thermodenitrificans NG80-2 (bacteria) / Escherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.35 Å
AuthorsDong L / Li L
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870835 China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2023
Title: Structural basis of SecA-mediated protein translocation.
Authors: Linlin Dong / Song Yang / Jingxia Chen / Xiaofei Wu / Dongjie Sun / Chen Song / Long Li /
Abstract: Secretory proteins are cotranslationally or posttranslationally translocated across lipid membranes via a protein-conducting channel named SecY in prokaryotes and Sec61 in eukaryotes. The vast ...Secretory proteins are cotranslationally or posttranslationally translocated across lipid membranes via a protein-conducting channel named SecY in prokaryotes and Sec61 in eukaryotes. The vast majority of secretory proteins in bacteria are driven through the channel posttranslationally by SecA, a highly conserved ATPase. How a polypeptide chain is moved by SecA through the SecY channel is poorly understood. Here, we report electron cryomicroscopy structures of the active SecA-SecY translocon with a polypeptide substrate. The substrate is captured in different translocation states when clamped by SecA with different nucleotides. Upon binding of an ATP analog, SecA undergoes global conformational changes to push the polypeptide substrate toward the channel in a way similar to how the RecA-like helicases translocate their nucleic acid substrates. The movements of the polypeptide substrates in the SecA-SecY translocon share a similar structural basis to those in the ribosome-SecY complex during cotranslational translocation.
History
DepositionApr 7, 2022-
Header (metadata) releaseJan 11, 2023-
Map releaseJan 11, 2023-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33192.png

Downloads & links

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Map

FileDownload / File: emd_33192.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.)Y (Row.)X (Col.)
1.06 Å/pix.
x 320 pix.
= 337.6 Å		1.06 Å/pix.
x 320 pix.
= 337.6 Å		1.06 Å/pix.
x 320 pix.
= 337.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.055 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.46
Minimum - Maximum-3.9374402 - 5.3480625
Average (Standard dev.)0.001177984 (±0.07709866)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 337.59998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_33192_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_33192_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of the SecA/SecYE/proOmpA(4Y)-sfGFP with ADP.BeF3-

EntireName: Complex of the SecA/SecYE/proOmpA(4Y)-sfGFP with ADP.BeF3-
Components
  • Complex: Complex of the SecA/SecYE/proOmpA(4Y)-sfGFP with ADP.BeF3-
    • Complex: SecA
      • Protein or peptide: Protein translocase subunit SecA
    • Complex: SecY
      • Protein or peptide: Protein translocase subunit SecY
    • Complex: SecE
      • Protein or peptide: Protein translocase subunit SecE
    • Complex: sfGFP
      • Protein or peptide: Translocating polypeptide
  • Ligand: MAGNESIUM ION
  • Ligand: BERYLLIUM TRIFLUORIDE ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Complex of the SecA/SecYE/proOmpA(4Y)-sfGFP with ADP.BeF3-

SupramoleculeName: Complex of the SecA/SecYE/proOmpA(4Y)-sfGFP with ADP.BeF3-
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 180 KDa

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Supramolecule #2: SecA

SupramoleculeName: SecA / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Geobacillus thermodenitrificans NG80-2 (bacteria)

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Supramolecule #3: SecY

SupramoleculeName: SecY / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Geobacillus thermodenitrificans NG80-2 (bacteria)

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Supramolecule #4: SecE

SupramoleculeName: SecE / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Escherichia coli (E. coli)

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Supramolecule #5: sfGFP

SupramoleculeName: sfGFP / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #4

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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)
Strain: 168
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) / Strain: NG80-2
Molecular weightTheoretical: 47.628238 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 YAQQFENVGE DLFLRIVRLL 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) / Strain: NG80-2
Molecular weightTheoretical: 7.03032 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString:
MQRVTNFFKE VVRELKKVSW PNRKELVNYT AVVLATVAFF TVFFAVIDLG ISQLIRLVFE

UniProtKB: Protein translocase subunit SecE

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Macromolecule #4: Translocating polypeptide

MacromoleculeName: Translocating polypeptide / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 33.18109 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString: MAKKTAIAIA VALAGFATVA SYAQYEDGCS GELERQHTFA GGARSIASGY YYYSGDKLPE GVLQSGGSGS KGEELFTGVV PILVELDGD VNGHKFSVRG EGEGDATNGK LTLKFICTTG KLPVPWPTLV TTLTYGVQCF SRYPDHMKRH DFFKSAMPEG Y VQERTISF ...String:
MAKKTAIAIA VALAGFATVA SYAQYEDGCS GELERQHTFA GGARSIASGY YYYSGDKLPE GVLQSGGSGS KGEELFTGVV PILVELDGD VNGHKFSVRG EGEGDATNGK LTLKFICTTG KLPVPWPTLV TTLTYGVQCF SRYPDHMKRH DFFKSAMPEG Y VQERTISF KDDGTYKTRA EVKFEGDTLV NRIELKGIDF KEDGNILGHK LEYNFNSHNV YITADKQKNG IKANFKIRHN VE DGSVQLA DHYQQNTPIG DGPVLLPDNH YLSTQSVLSK DPNEKRDHMV LLEFVTAAGI THGSAG

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #6: BERYLLIUM TRIFLUORIDE ION

MacromoleculeName: BERYLLIUM TRIFLUORIDE ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: BEF
Molecular weightTheoretical: 66.007 Da
Chemical component information

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

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Macromolecule #7: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 7 / 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: 57.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

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

9731

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1198498
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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