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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
  • (NanobodySingle-domain antibody) 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


ATPase-coupled protein transmembrane transporter activity / cell envelope Sec protein transport complex / protein transport by the Sec complex / protein import / intracellular protein transmembrane transport / P-P-bond-hydrolysis-driven protein transmembrane transporter activity / protein secretion / protein targeting / bioluminescence / generation of precursor metabolites and energy ...ATPase-coupled protein transmembrane transporter activity / cell envelope Sec protein transport complex / protein transport by the Sec complex / protein import / intracellular protein transmembrane transport / P-P-bond-hydrolysis-driven protein transmembrane transporter activity / protein secretion / protein targeting / bioluminescence / generation of precursor metabolites and energy / protein-chromophore linkage / integral component of plasma membrane / integral component of membrane / ATP binding / plasma membrane / metal ion binding / cytosol
SecA, preprotein cross-linking domain / SecY conserved site / SecA Wing/Scaffold / Protein secE/sec61-gamma signature. / Green fluorescent protein-related / SecA motor DEAD / SecA conserved site / SecY domain superfamily / Protein translocase subunit SecY / P-loop containing nucleoside triphosphate hydrolase ...SecA, preprotein cross-linking domain / SecY conserved site / SecA Wing/Scaffold / Protein secE/sec61-gamma signature. / Green fluorescent protein-related / SecA motor DEAD / SecA conserved site / SecY domain superfamily / Protein translocase subunit SecY / P-loop containing nucleoside triphosphate hydrolase / SecA, Wing/Scaffold superfamily / Green fluorescent protein / SecA, preprotein cross-linking domain superfamily / SecE superfamily / SecY translocase / SecE/Sec61-gamma subunits of protein translocation complex / SecA preprotein cross-linking domain / Green fluorescent protein / SEC-C motif / SecA Wing and Scaffold domain / SecA DEAD-like domain / SecA DEAD-like, N-terminal / SecE subunit of protein translocation complex, bacterial-like / Protein secY signature 2. / SecA family signature. / SecA family profile. / SEC-C motif / Protein secY signature 1. / Protein translocase subunit SecA / Protein translocase complex, SecE/Sec61-gamma subunit / Green fluorescent protein, GFP / SecY/SEC61-alpha family
Protein translocase subunit SecE / Protein translocase subunit SecY / Protein translocase subunit SecA / Green fluorescent protein
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 supportChina , 1件
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2016YFA0500700China
CitationJournal: To Be Published
Title: Structure of a substrate engaged SecA-SecY protein translocation machine
Authors: Ma, C.Y. / Wu, X.F. / Sun, D.J. / Park, E.Y. / Rapoport, T.A. / Gao, N. / Long, L.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 21, 2018 / Release: Jun 12, 2019
RevisionDateData content typeProviderType
1.0Jun 12, 2019Structure modelrepositoryInitial release

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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
Water0
1


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/peptide 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/peptide 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/peptide 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/peptide , 4 types, 4 molecules VBGC

#4: Protein/peptide Nanobody / Single-domain antibody


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)
#5: Protein/peptide 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)
#6: Protein/peptide 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
#7: Protein/peptide Nanobody / Single-domain antibody


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 / Magnesium
#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 / Adenosine diphosphate / 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 / Phosphatidylglycerol / Comment: phospholipid *YM

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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, 2, 3, 4, 5, 6, 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 FIELDBright-field microscopy
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
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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