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- EMDB-9731: Structure of a substrate engaged SecA-SecY protein translocation ... -

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Basic information

Entry
Database: EMDB / ID: EMD-9731
TitleStructure of a substrate engaged SecA-SecY protein translocation machine
Map data
SampleSecA-SecY complex:
(Protein translocase subunit ...) x 3 / (NanobodySingle-domain antibody) x 2 / Translocating peptide / Green fluorescent protein / (ligand) x 4
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) / Bacillus subtilis (strain 168) (bacteria) / Geobacillus thermodenitrificans (strain NG80-2) (bacteria) / Lama glama (llama) / Escherichia coli (E. coli) / Aequorea victoria (jellyfish)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.45 Å
AuthorsMa CY / Wu XF / Sun DJ / Park EY / Rapoport TA / Gao N / Long L
CitationJournal: To Be Published
Title: Structure of a substrate engaged SecA-SecY protein translocation machine
Authors: Ma CY / Wu XF / Sun DJ / Park EY / Rapoport TA / Gao N / Long L
Validation ReportPDB-ID: 6itc

SummaryFull reportAbout validation report
DateDeposition: Nov 21, 2018 / Header (metadata) release: Jun 12, 2019 / Map release: Jun 12, 2019 / Update: Jun 12, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0242
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0242
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6itc
  • Surface level: 0.0242
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_9731.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.)
1.05 Å/pix.
x 240 pix.
= 252. Å
1.05 Å/pix.
x 240 pix.
= 252. Å
1.05 Å/pix.
x 240 pix.
= 252. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density
Contour LevelBy AUTHOR: 0.0242 / Movie #1: 0.0242
Minimum - Maximum-0.09917147 - 0.14502499
Average (Standard dev.)0.0003700985 (±0.0036889222)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 251.99998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z252.000252.000252.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ192192192
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.0990.1450.000

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Supplemental data

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Sample components

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Entire SecA-SecY complex

EntireName: SecA-SecY complex / Number of components: 12

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Component #1: protein, SecA-SecY complex

ProteinName: SecA-SecY complex / Recombinant expression: No
SourceSpecies: Bacillus subtilis (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #2: protein, Protein translocase subunit SecA

ProteinName: Protein translocase subunit SecA / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 88.91618 kDa
SourceSpecies: Bacillus subtilis (strain 168) (bacteria) / Strain: 168
Source (engineered)Expression System: Escherichia coli #1/H766 (bacteria)

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Component #3: protein, Protein translocase subunit SecY

ProteinName: Protein translocase subunit SecY / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 46.768301 kDa
SourceSpecies: Geobacillus thermodenitrificans (strain NG80-2) (bacteria)
Strain: NG80-2
Source (engineered)Expression System: Escherichia coli K-12 (bacteria)

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Component #4: protein, Protein translocase subunit SecE

ProteinName: Protein translocase subunit SecE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.2496 kDa
SourceSpecies: Geobacillus thermodenitrificans (strain NG80-2) (bacteria)
Strain: NG80-2
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #5: protein, Nanobody

ProteinName: NanobodySingle-domain antibody / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.919544 kDa
SourceSpecies: Lama glama (llama)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #6: protein, Translocating peptide

ProteinName: Translocating peptide / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.024562 kDa
SourceSpecies: Escherichia coli (E. coli)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #7: protein, Green fluorescent protein

ProteinName: Green fluorescent protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.813113 kDa
SourceSpecies: Aequorea victoria (jellyfish)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #8: protein, Nanobody

ProteinName: NanobodySingle-domain antibody / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.368727 kDa
SourceSpecies: Lama glama (llama)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #9: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Component #10: ligand, BERYLLIUM TRIFLUORIDE ION

LigandName: BERYLLIUM TRIFLUORIDE ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.600705 MDa

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Component #11: ligand, ADENOSINE-5'-DIPHOSPHATE

LigandName: ADENOSINE-5'-DIPHOSPHATE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.427201 kDa

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Component #12: ligand, (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHOR...

LigandName: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.749007 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 5 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 130153
3D reconstructionResolution: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Refinement protocol: flexible
Output model

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