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- EMDB-49147: Local refinement of crosslinked LetB MCE Rings 5, 6 and 7 (Map 1c) -

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Basic information

Entry
Database: EMDB / ID: EMD-49147
TitleLocal refinement of crosslinked LetB MCE Rings 5, 6 and 7 (Map 1c)
Map data
Sample
  • Complex: LetB MCE Rings 5, 6 and 7 crosslinked with glutaraldehyde
KeywordsLipid transporter / Outer membrane integrity / MCE system / Metal-binding protein / Intermembrane complex / LIPID TRANSPORT
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsSantarossa CC / Bhabha G / Ekiert DC
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM128777 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1K99GM157496-01 United States
Other privateThe Charles H. Revson Foundation
CitationJournal: bioRxiv / Year: 2025
Title: LetA defines a structurally distinct transporter family involved in lipid trafficking.
Authors: Cristina C Santarossa / Yupeng Li / Sara Yousef / Hale S Hasdemir / Carlos C Rodriguez / Max B Haase / Minkyung Baek / Nicolas Coudray / John G Pavek / Kimber N Focke / Annika L Silverberg / ...Authors: Cristina C Santarossa / Yupeng Li / Sara Yousef / Hale S Hasdemir / Carlos C Rodriguez / Max B Haase / Minkyung Baek / Nicolas Coudray / John G Pavek / Kimber N Focke / Annika L Silverberg / Carmelita Bautista / Johannes Yeh / Michael T Marty / David Baker / Emad Tajkhorshid / Damian C Ekiert / Gira Bhabha
Abstract: Membrane transport proteins translocate diverse cargos, ranging from small sugars to entire proteins, across cellular membranes. A few structurally distinct protein families have been described that ...Membrane transport proteins translocate diverse cargos, ranging from small sugars to entire proteins, across cellular membranes. A few structurally distinct protein families have been described that account for most of the known membrane transport processes. However, many membrane proteins with predicted transporter functions remain uncharacterized. We determined the structure of LetAB, a phospholipid transporter involved in outer membrane integrity, and found that LetA adopts a distinct architecture that is structurally and evolutionarily unrelated to known transporter families. LetA functions as a pump at one end of a ~225 Å long tunnel formed by its binding partner, MCE protein LetB, creating a pathway for lipid transport between the inner and outer membranes. Unexpectedly, the LetA transmembrane domains adopt a fold that is evolutionarily related to the eukaryotic tetraspanin family of membrane proteins, including TARPs and claudins. LetA has no detectable homology to known transport proteins, and defines a new class of membrane transporters. Through a combination of deep mutational scanning, molecular dynamics simulations, AlphaFold-predicted alternative states, and functional studies, we present a model for how the LetA-like family of membrane transporters may use energy from the proton-motive force to drive the transport of lipids across the bacterial cell envelope.
History
DepositionFeb 10, 2025-
Header (metadata) releaseJul 16, 2025-
Map releaseJul 16, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49147.png

Downloads & links

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Map

FileDownload / File: emd_49147.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 256 pix.
= 263.386 Å		1.03 Å/pix.
x 256 pix.
= 263.386 Å		1.03 Å/pix.
x 256 pix.
= 263.386 Å

Surface

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Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.02885 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.119
Minimum - Maximum-0.49909496 - 0.9806194
Average (Standard dev.)-0.00029308666 (±0.03291958)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 263.3856 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_49147_additional_1.map
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Half map: #1

Fileemd_49147_half_map_1.map
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Half map: #2

Fileemd_49147_half_map_2.map
Projections & Slices
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Sample components

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Entire : LetB MCE Rings 5, 6 and 7 crosslinked with glutaraldehyde

EntireName: LetB MCE Rings 5, 6 and 7 crosslinked with glutaraldehyde
Components
  • Complex: LetB MCE Rings 5, 6 and 7 crosslinked with glutaraldehyde

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Supramolecule #1: LetB MCE Rings 5, 6 and 7 crosslinked with glutaraldehyde

SupramoleculeName: LetB MCE Rings 5, 6 and 7 crosslinked with glutaraldehyde
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MG1655

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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

Concentration1 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMTris-HCltris(hydroxymethyl)aminomethane hydrochloride
150.0 mMNaClsodium chloride
0.5 mMDDMn-Dodecyl-B-D-maltoside
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 5 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Number grids imaged: 1 / Number real images: 12464 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 4.0 µm / Calibrated defocus min: 0.1 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3582925
Details: Particles were selected by template-based auto-picking in cryoSPARC
CTF correctionSoftware - Name: cryoSPARC (ver. v3.2.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.0.2) / Number images used: 72671
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC

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Atomic model buiding 1

Initial modelPDB ID:

6v0e


Chain - Source name: PDB / Chain - Initial model type: experimental model
Details: The initial model consisted of the complete biological assembly for PDB entry 6V0E
DetailsModel was fit as a rigid-body into the individual map using Chimera. Real space refinement was carried out in PHENIX. Models were then manually inspected and adjusted in Coot. Iterative rounds of model building and refinement were performed.
RefinementSpace: REAL / Protocol: FLEXIBLE FIT

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