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- EMDB-49148: Intermembrane lipid transport complex LetAB from Escherichia coli... -

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Basic information

Entry
Database: EMDB / ID: EMD-49148
TitleIntermembrane lipid transport complex LetAB from Escherichia coli (Crosslinked, Composite Map 1)
Map data
Sample
  • Complex: LetAB complex crosslinked with glutaraldehyde
    • Protein or peptide: Intermembrane transport protein YebS
    • Protein or peptide: Intermembrane transport protein YebT
  • Ligand: ZINC ION
KeywordsLipid transporter / Outer membrane integrity / MCE system / Metal-binding protein / Intermembrane complex / LIPID TRANSPORT
Function / homology
Function and homology information


intermembrane lipid transfer / membrane organization / intracellular transport / outer membrane-bounded periplasmic space / response to heat / identical protein binding / plasma membrane
Similarity search - Function
Intermembrane transport protein PqiA-like, Enterobacteria-type / Intermembrane transport protein PqiA-like / Paraquat-inducible protein A / : / Mce/MlaD / MlaD protein / Multiheme cytochrome c family profile.
Similarity search - Domain/homology
Lipophilic envelope-spanning tunnel protein A / Lipophilic envelope-spanning tunnel protein B
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 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_49148.png

Downloads & links

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Map

FileDownload / File: emd_49148.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.03 Å/pix.
x 360 pix.
= 370.386 Å		1.03 Å/pix.
x 360 pix.
= 370.386 Å		1.03 Å/pix.
x 360 pix.
= 370.386 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.02885 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.25
Minimum - Maximum-10.027485 - 23.27833
Average (Standard dev.)0.015748618 (±0.6178917)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 370.386 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : LetAB complex crosslinked with glutaraldehyde

EntireName: LetAB complex crosslinked with glutaraldehyde
Components
  • Complex: LetAB complex crosslinked with glutaraldehyde
    • Protein or peptide: Intermembrane transport protein YebS
    • Protein or peptide: Intermembrane transport protein YebT
  • Ligand: ZINC ION

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Supramolecule #1: LetAB complex crosslinked with glutaraldehyde

SupramoleculeName: LetAB complex crosslinked with glutaraldehyde / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MG1655
Molecular weightTheoretical: 618 KDa

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Macromolecule #1: Intermembrane transport protein YebS

MacromoleculeName: Intermembrane transport protein YebS / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: str. K-12 substr. MG1655
Molecular weightTheoretical: 50.667746 KDa
Recombinant expressionOrganism: Escherichia coli B (bacteria)
SequenceString: MHHHHHHQHQ HENLYFQGMA LNTPQITPTK KITVRAIGEE LPRGDYQRCP QCDMLFSLPE INSHQSAYCP RCQAKIRDGR DWSLTRLAA MAFTMLLLMP FAWGEPLLHI WLLGIRIDAN VMQGIWQMTK QGDAITGSMV FFCVIGAPLI LVTSIAYLWF G NRLGMNLR ...String:
MHHHHHHQHQ HENLYFQGMA LNTPQITPTK KITVRAIGEE LPRGDYQRCP QCDMLFSLPE INSHQSAYCP RCQAKIRDGR DWSLTRLAA MAFTMLLLMP FAWGEPLLHI WLLGIRIDAN VMQGIWQMTK QGDAITGSMV FFCVIGAPLI LVTSIAYLWF G NRLGMNLR PVLLMLERLK EWVMLDIYLV GIGVASIKVQ DYAHIQAGVG LFSFVALVIL TTVTLSHLNV EELWERFYPQ RP ATRRDEK LRVCLGCHFT GYPDQRGRCP RCHIPLRLRR RHSLQKCWAA LLASIVLLLP ANLLPISIIY LNGGRQEDTI LSG IMSLAS SNIAVAGIVF IASILVPFTK VIVMFTLLLS IHFKCQQGLR TRILLLRMVT WIGRWSMLDL FVISLTMSLI NRDQ ILAFT MGPAAFYFGA AVILTILAVE WLDSRLLWDA HESGNARFDD

UniProtKB: Lipophilic envelope-spanning tunnel protein A

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Macromolecule #2: Intermembrane transport protein YebT

MacromoleculeName: Intermembrane transport protein YebT / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: str. K-12 substr. MG1655
Molecular weightTheoretical: 95.072211 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSQETPASTT EAQIKNKRRI SPFWLLPFIA LMIASWLIWD SYQDRGNTVT IDFMSADGIV PGRTPVRYQG VEVGTVQDIS LSDDLRKIE VKVSIKSDMK DALREETQFW LVTPKASLAG VSGLDALVGG NYIGMMPGKG KEQDHFVALD TQPKYRLDNG D LMIHLQAP ...String:
MSQETPASTT EAQIKNKRRI SPFWLLPFIA LMIASWLIWD SYQDRGNTVT IDFMSADGIV PGRTPVRYQG VEVGTVQDIS LSDDLRKIE VKVSIKSDMK DALREETQFW LVTPKASLAG VSGLDALVGG NYIGMMPGKG KEQDHFVALD TQPKYRLDNG D LMIHLQAP DLGSLNSGSL VYFRKIPVGK VYDYAINPNK QGVVIDVLIE RRFTDLVKKG SRFWNVSGVD ANVSISGAKV KL ESLAALV NGAIAFDSPE ESKPAEAEDT FGLYEDLAHS QRGVIIKLEL PSGAGLTADS TPLMYQGLEV GQLTKLDLNP GGK VTGEMT VDPSVVTLLR ENTRIELRNP KLSLSDANLS ALLTGKTFEL VPGDGEPRKE FVVVPGEKAL LHEPDVLTLT LTAP ESYGI DAGQPLILHG VQVGQVIDRK LTSKGVTFTV AIEPQHRELV KGDSKFVVNS RVDVKVGLDG VEFLGASASE WINGG IRIL PGDKGEMKAS YPLYANLEKA LENSLSDLPT TTVSLSAETL PDVQAGSVVL YRKFEVGEVI TVRPRANAFD IDLHIK PEY RNLLTSNSVF WAEGGAKVQL NGSGLTVQAS PLSRALKGAI SFDNLSGASA SQRKGDKRIL YASETAARAV GGQITLH AF DAGKLAVGMP IRYLGIDIGQ IQTLDLITAR NEVQAKAVLY PEYVQTFARG GTRFSVVTPQ ISAAGVEHLD TILQPYIN V EPGRGNPRRD FELQEATITD SRYLDGLSII VEAPEAGSLG IGTPVLFRGL EVGTVTGMTL GTLSDRVMIA MRISKRYQH LVRNNSVFWL ASGYSLDFGL TGGVVKTGTF NQFIRGGIAF ATPPGTPLAP KAQEGKHFLL QESEPKEWRE WGTALPK

UniProtKB: Lipophilic envelope-spanning tunnel protein B

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Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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 correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 158666
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

Initial model
PDB IDChainDetails

6v0j

source_name: PDB, initial_model_type: experimental modelThe initial model consisted of the complete biological assembly for PDB entry 6V0J

6v0f

source_name: PDB, initial_model_type: experimental modelThe initial model consisted of the complete biological assembly for PDB entry 6V0F

6v0e

source_name: PDB, initial_model_type: experimental modelThe initial model consisted of the complete biological assembly for PDB entry 6V0E

leta

source_name: RoseTTAFold, initial_model_type: in silico modelThe initial model consisted of the complete biological assembly for RoseTTAFold LetA
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
Output model

PDB-9n8w:
Intermembrane lipid transport complex LetAB from Escherichia coli (Crosslinked, Composite model corresponding to Map 1)

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