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- EMDB-3035: The structure of YnaI implies structural and mechanistic conserva... -

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Basic information

Entry
Database: EMDB / ID: EMD-3035
TitleThe structure of YnaI implies structural and mechanistic conservation in the MscS-family of mechanosensitive channels
Map dataReconstruction of YnaI
Sample
  • Sample: Low conductance mechanosensitive channel YnaI
  • Protein or peptide: YnaI
KeywordsYnaI / mechanosensitive channels / lipid-protein interaction / osmotic stress
Function / homology
Function and homology information


mechanosensitive monoatomic ion channel activity / cellular response to osmotic stress / transmembrane transport / identical protein binding / plasma membrane
Similarity search - Function
Mechanosensitive ion channel protein YnaI-like / : / : / Mechanosensitive ion channel MscS, C-terminal / Mechanosensitive ion channel, transmembrane helices 2/3 / Mechanosensitive ion channel MscS, conserved site / Mechanosensitive ion channel MscS, conserved site / Uncharacterized protein family UPF0003 signature. / Mechanosensitive ion channel MscS, C-terminal / Mechanosensitive ion channel MscS, C-terminal ...Mechanosensitive ion channel protein YnaI-like / : / : / Mechanosensitive ion channel MscS, C-terminal / Mechanosensitive ion channel, transmembrane helices 2/3 / Mechanosensitive ion channel MscS, conserved site / Mechanosensitive ion channel MscS, conserved site / Uncharacterized protein family UPF0003 signature. / Mechanosensitive ion channel MscS, C-terminal / Mechanosensitive ion channel MscS, C-terminal / Mechanosensitive ion channel MscS, transmembrane-2 / Mechanosensitive ion channel MscS, transmembrane-2 / Mechanosensitive ion channel MscS / Mechanosensitive ion channel MscS / Mechanosensitive ion channel, beta-domain / Mechanosensitive ion channel MscS, beta-domain superfamily / LSM domain superfamily / LSM domain superfamily
Similarity search - Domain/homology
Low conductance mechanosensitive channel YnaI
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 12.6 Å
AuthorsBottcher B / Prazak V / Rasmussen A / Black SS / Rasmussen T
CitationJournal: Structure / Year: 2015
Title: The Structure of YnaI Implies Structural and Mechanistic Conservation in the MscS Family of Mechanosensitive Channels.
Authors: Bettina Böttcher / Vojtech Prazak / Akiko Rasmussen / Susan S Black / Tim Rasmussen /
Abstract: Mechanosensitive channels protect bacteria against lysis caused by a sudden drop in osmolarity in their surroundings. Besides the channel of large conductance (MscL) and small conductance (MscS), ...Mechanosensitive channels protect bacteria against lysis caused by a sudden drop in osmolarity in their surroundings. Besides the channel of large conductance (MscL) and small conductance (MscS), Escherichia coli has five additional paralogs of MscS that are functional and widespread in the bacterial kingdom. Here, we present the structure of YnaI by cryo-electron microscopy to a resolution of 13 Å. While the cytosolic vestibule is structurally similar to that in MscS, additional density is seen in the transmembrane (TM) region consistent with the presence of two additional TM helices predicted for YnaI. The location of this density suggests that the extra TM helices are tilted, which could induce local membrane curvature extending the tension-sensing paddles seen in MscS. Off-center lipid-accessible cavities are seen that resemble gaps between the sensor paddles in MscS. The conservation of the tapered shape and the cavities in YnaI suggest a mechanism similar to that of MscS.
History
DepositionJun 1, 2015-
Header (metadata) releaseJul 15, 2015-
Map releaseAug 26, 2015-
UpdateSep 9, 2015-
Current statusSep 9, 2015Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.045
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.045
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3035.png

Downloads & links

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Map

FileDownload / File: emd_3035.map.gz / Format: CCP4 / Size: 15.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of YnaI
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.73 Å/pix.
x 160 pix.
= 276.48 Å		1.73 Å/pix.
x 160 pix.
= 276.48 Å		1.73 Å/pix.
x 160 pix.
= 276.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.728 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.045 / Movie #1: 0.045
Minimum - Maximum-0.03759287 - 0.12191901
Average (Standard dev.)0.00122589 (±0.01530758)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 276.48 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.7281.7281.728
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z276.480276.480276.480
α/β/γ90.00090.00090.000
start NX/NY/NZ-800-4
NX/NY/NZ1611358
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.0380.1220.001

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Supplemental data

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Sample components

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Entire : Low conductance mechanosensitive channel YnaI

EntireName: Low conductance mechanosensitive channel YnaI
Components
  • Sample: Low conductance mechanosensitive channel YnaI
  • Protein or peptide: YnaI

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Supramolecule #1000: Low conductance mechanosensitive channel YnaI

SupramoleculeName: Low conductance mechanosensitive channel YnaI / type: sample / ID: 1000 / Oligomeric state: 7 / Number unique components: 1
Molecular weightTheoretical: 271 KDa

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Macromolecule #1: YnaI

MacromoleculeName: YnaI / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Oligomeric state: heptamer / Recombinant expression: No
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MJF641 / Location in cell: Pasma membrane
Molecular weightTheoretical: 38.76 KDa
SequenceUniProtKB: Low conductance mechanosensitive channel YnaI / GO: transmembrane transport
InterPro: Mechanosensitive ion channel MscS, Mechanosensitive ion channel MscS, transmembrane-2, LSM domain superfamily, Mechanosensitive ion channel MscS, C-terminal, Mechanosensitive ion channel MscS, conserved site

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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

Concentration2.2 mg/mL
BufferpH: 7.2
GridDetails: 1.2/1.3 Quantifoil 400 mesh copper Rh/grids, glow discharge for 1 min in air
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: HOMEMADE PLUNGER
Method: blot for 15 s with 2 layers of filter paper Whatman No 1 before plunging into Ethane cooled by N2; heater is used for preventing freezing of ethane; plunger has an environmental chamber, ...Method: blot for 15 s with 2 layers of filter paper Whatman No 1 before plunging into Ethane cooled by N2; heater is used for preventing freezing of ethane; plunger has an environmental chamber, which is humidified with 2 water soaked sponges (Bellare Design); Bellare design of

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Electron microscopy #1

Microscopy ID1
MicroscopeFEI TECNAI F20
TemperatureAverage: 95 K
Alignment procedureLegacy - Astigmatism: at 200,000 magnification on carbon; computationally during image processing
DateMar 15, 2013
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Digitization - Sampling interval: 15.6 µm / Number real images: 3308 / Average electron dose: 25 e/Å2 / Bits/pixel: 12
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 5.7 µm / Nominal defocus min: 1.39 µm / Nominal magnification: 62000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Electron microscopy #2

Microscopy ID2
MicroscopeFEI TECNAI F20
TemperatureAverage: 95 K
Alignment procedureLegacy - Astigmatism: at 200,000 magnification on carbon; computationally during image processing
DateMar 15, 2013
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Digitization - Sampling interval: 15.6 µm / Number real images: 3308 / Average electron dose: 25 e/Å2 / Bits/pixel: 12
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 5.7 µm / Nominal defocus min: 1.39 µm / Nominal magnification: 62000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Electron microscopy #3

Microscopy ID3
MicroscopeFEI TECNAI F20
TemperatureAverage: 95 K
Alignment procedureLegacy - Astigmatism: at 200,000 magnification on carbon; computationally during image processing
DateApr 7, 2013
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Digitization - Sampling interval: 15.6 µm / Number real images: 3308 / Average electron dose: 25 e/Å2 / Bits/pixel: 12
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 5.7 µm / Nominal defocus min: 1.39 µm / Nominal magnification: 62000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Electron microscopy #4

Microscopy ID4
MicroscopeFEI TECNAI F20
TemperatureAverage: 95 K
Alignment procedureLegacy - Astigmatism: at 200,000 magnification on carbon; computationally during image processing
DateApr 15, 2013
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Digitization - Sampling interval: 15.6 µm / Number real images: 3308 / Average electron dose: 25 e/Å2 / Bits/pixel: 12
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 5.7 µm / Nominal defocus min: 1.39 µm / Nominal magnification: 62000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Electron microscopy #5

Microscopy ID5
MicroscopeFEI TECNAI F20
TemperatureAverage: 95 K
Alignment procedureLegacy - Astigmatism: at 200,000 magnification on carbon; computationally during image processing
DateApr 17, 2013
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Digitization - Sampling interval: 15.6 µm / Number real images: 3308 / Average electron dose: 25 e/Å2 / Bits/pixel: 12
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 5.7 µm / Nominal defocus min: 1.39 µm / Nominal magnification: 62000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Electron microscopy #6

Microscopy ID6
MicroscopeFEI TECNAI F20
TemperatureAverage: 95 K
Alignment procedureLegacy - Astigmatism: at 200,000 magnification on carbon; computationally during image processing
DateApr 19, 2013
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Digitization - Sampling interval: 15.6 µm / Number real images: 3308 / Average electron dose: 25 e/Å2 / Bits/pixel: 12
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 5.7 µm / Nominal defocus min: 1.39 µm / Nominal magnification: 62000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Detailsparticle image were selected manually with e2-boxer, initial reference map was determined with Imagic, particle orientations were refined with Relion 1.3
CTF correctionDetails: each particle
Final reconstructionApplied symmetry - Point group: C7 (7 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 12.6 Å / Resolution method: OTHER / Software - Name: Imagic, Relion
Details: resolution was determined from independently processed halves
Number images used: 7202
Final angle assignmentDetails: euler angles were determined with relion using auto_refine
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

2oau


Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B / Chain - #2 - Chain ID: C / Chain - #3 - Chain ID: D / Chain - #4 - Chain ID: E / Chain - #5 - Chain ID: F / Chain - #6 - Chain ID: G
SoftwareName: Chimera
DetailsThe structure of the related MscS (2oAU) was fitted manually as rigid body, the fit was optimized by the fit in map option of chimera using residues 129-281 of MscS (cytosolic part)
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: overlap

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