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- PDB-6itc: Structure of a substrate engaged SecA-SecY protein translocation ... -

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Entry
Database: PDB / ID: 6itc
TitleStructure of a substrate engaged SecA-SecY protein translocation machine
Components
  • (Nanobody) x 2
  • (Protein translocase subunit ...) x 3
  • Green fluorescent protein
  • Translocating peptide
KeywordsPROTEIN TRANSPORT / SecA / SecY / Translocation / Cryo-EM
Function / homology
Function and homology information


outer membrane protein complex / protein-exporting ATPase activity / cell envelope Sec protein transport complex / protein-secreting ATPase / monoatomic ion transmembrane transporter activity / protein transport by the Sec complex / intracellular protein transmembrane transport / detection of virus / outer membrane / protein import ...outer membrane protein complex / protein-exporting ATPase activity / cell envelope Sec protein transport complex / protein-secreting ATPase / monoatomic ion transmembrane transporter activity / protein transport by the Sec complex / intracellular protein transmembrane transport / detection of virus / outer membrane / protein import / porin activity / pore complex / protein secretion / protein transmembrane transporter activity / protein targeting / monoatomic ion transport / bioluminescence / generation of precursor metabolites and energy / cell outer membrane / outer membrane-bounded periplasmic space / membrane raft / DNA damage response / symbiont entry into host cell / ATP binding / metal ion binding / identical protein binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
Pre-protein croslinking domain of SecA / SecA, preprotein cross-linking domain / Outer membrane protein OmpA-like, transmembrane domain / Outer membrane protein, OmpA / OmpA-like transmembrane domain / Helical scaffold and wing domains of SecA / Helical scaffold and wing domains of SecA / SecE subunit of protein translocation complex, bacterial-like / SecE superfamily / SEC-C motif ...Pre-protein croslinking domain of SecA / SecA, preprotein cross-linking domain / Outer membrane protein OmpA-like, transmembrane domain / Outer membrane protein, OmpA / OmpA-like transmembrane domain / Helical scaffold and wing domains of SecA / Helical scaffold and wing domains of SecA / SecE subunit of protein translocation complex, bacterial-like / SecE superfamily / SEC-C motif / SEC-C motif / Outer membrane protein, OmpA-like, conserved site / OmpA-like domain. / 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 / Outer membrane protein, bacterial / : / OmpA-like domain profile. / OmpA-like domain superfamily / OmpA family / OmpA-like domain / 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 / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / 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 nucleotide triphosphate hydrolases / Alpha-Beta Complex / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / Chem-PGV / Protein translocase subunit SecE / Protein translocase subunit SecY / Outer membrane protein A / Protein translocase subunit SecA / Green fluorescent protein
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
Geobacillus thermodenitrificans (bacteria)
Lama glama (llama)
Escherichia coli (E. coli)
Aequorea victoria (jellyfish)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.45 Å
AuthorsMa, C.Y. / Wu, X.F. / Sun, D.J. / Park, E.Y. / Rapoport, T.A. / Gao, N. / Long, L.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2016YFA0500700 China
CitationJournal: Nat Commun / Year: 2019
Title: Structure of the substrate-engaged SecA-SecY protein translocation machine.
Authors: Chengying Ma / Xiaofei Wu / Dongjie Sun / Eunyong Park / Marco A Catipovic / Tom A Rapoport / Ning Gao / Long Li /
Abstract: The Sec61/SecY channel allows the translocation of many proteins across the eukaryotic endoplasmic reticulum membrane or the prokaryotic plasma membrane. In bacteria, most secretory proteins are ...The Sec61/SecY channel allows the translocation of many proteins across the eukaryotic endoplasmic reticulum membrane or the prokaryotic plasma membrane. In bacteria, most secretory proteins are transported post-translationally through the SecY channel by the SecA ATPase. How a polypeptide is moved through the SecA-SecY complex is poorly understood, as structural information is lacking. Here, we report an electron cryo-microscopy (cryo-EM) structure of a translocating SecA-SecY complex in a lipid environment. The translocating polypeptide chain can be traced through both SecA and SecY. In the captured transition state of ATP hydrolysis, SecA's two-helix finger is close to the polypeptide, while SecA's clamp interacts with the polypeptide in a sequence-independent manner by inducing a short β-strand. Taking into account previous biochemical and biophysical data, our structure is consistent with a model in which the two-helix finger and clamp cooperate during the ATPase cycle to move a polypeptide through the channel.
History
DepositionNov 21, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.0Jun 12, 2019Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 12, 2019Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 12, 2019Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Jun 12, 2019Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 12, 2019Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Jun 12, 2019Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 12, 2019Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Jun 12, 2019Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 12, 2019Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Category: citation / citation_author
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Revision 1.2Nov 6, 2019Group: Data collection / Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_main_chain_plane / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Jun 25, 2025Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
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Revision 1.1Jun 25, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

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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: Translocating peptide
G: Green fluorescent protein
C: Nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,07612
Polymers202,0607
Non-polymers2,0165
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area20690 Å2
ΔGint-133 kcal/mol
Surface area75080 Å2

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Components

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

#1: Protein Protein translocase subunit SecA


Mass: 88916.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: secA, div+, BSU35300 / Production host: Escherichia coli #1/H766 (bacteria) / Strain (production host): #1/H766 / References: UniProt: P28366
#2: Protein Protein translocase subunit SecY


Mass: 46768.301 Da / Num. of mol.: 1 / Mutation: G60C,Q202T,L210G,F211G,R213N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus thermodenitrificans (strain NG80-2) (bacteria)
Strain: NG80-2 / Gene: secY, GTNG_0125 / 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 (strain NG80-2) (bacteria)
Strain: NG80-2 / Gene: secE, GTNG_0091 / Production host: Escherichia coli (E. coli) / References: UniProt: A4IJH4

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Protein , 2 types, 2 molecules BG

#5: Protein Translocating peptide


Mass: 6024.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A910*PLUS
#6: Protein Green fluorescent protein


Mass: 26813.113 Da / Num. of mol.: 1 / Mutation: Q80R,F99S,M153T,V163A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Production host: Escherichia coli (E. coli) / References: UniProt: P42212

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Antibody , 2 types, 2 molecules VC

#4: Antibody Nanobody


Mass: 12919.544 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#7: Antibody Nanobody


Mass: 12368.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)

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Non-polymers , 4 types, 5 molecules

#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#9: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3
#10: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#11: Chemical ChemComp-PGV / (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE / PHOSPHATIDYLGLYCEROL / 2-VACCENOYL-1-PALMITOYL-SN-GLYCEROL-3-PHOSPHOGLYCEROL


Mass: 749.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H77O10P / Comment: phospholipid*YM

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Details

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 / Type: COMPLEX / Entity ID: #1-#7 / Source: RECOMBINANT
Source (natural)Organism: Bacillus subtilis (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
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
Image recordingElectron dose: 5 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.13_2998: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 130153 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT

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