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- EMDB-22724: CryoEM structure of a trehalose monomycolate transporter in lipid... -

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Basic information

Entry
Database: EMDB / ID: EMD-22724
TitleCryoEM structure of a trehalose monomycolate transporter in lipid nanodiscs
Map data
Sample
  • Complex: RDN family transporter
    • Protein or peptide: Drug exporters of the RND superfamily-like protein
Keywordstrehalose monomycolate transporter / TRANSLOCASE
Function / homology
Function and homology information


phosphatidylethanolamine transfer activity / phosphatidylglycerol binding / trehalose transmembrane transporter activity / trehalose transport / mycolate cell wall layer assembly / cell wall biogenesis / diacylglycerol binding / cell pole / cell tip / mycolic acid biosynthetic process ...phosphatidylethanolamine transfer activity / phosphatidylglycerol binding / trehalose transmembrane transporter activity / trehalose transport / mycolate cell wall layer assembly / cell wall biogenesis / diacylglycerol binding / cell pole / cell tip / mycolic acid biosynthetic process / cell septum / phospholipid transport / cardiolipin binding / phosphatidylethanolamine binding / phosphatidylinositol binding / regulation of membrane potential / cell wall organization / response to xenobiotic stimulus / response to antibiotic / plasma membrane
Similarity search - Function
: / Membrane transport protein MMPL domain / MMPL family
Similarity search - Domain/homology
Trehalose monomycolate exporter MmpL3
Similarity search - Component
Biological speciesMycolicibacterium smegmatis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.65 Å
AuthorsSu C-C
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: PLoS Biol / Year: 2021
Title: Structures of the mycobacterial membrane protein MmpL3 reveal its mechanism of lipid transport.
Authors: Chih-Chia Su / Philip A Klenotic / Meng Cui / Meinan Lyu / Christopher E Morgan / Edward W Yu /
Abstract: The mycobacterial membrane protein large 3 (MmpL3) transporter is essential and required for shuttling the lipid trehalose monomycolate (TMM), a precursor of mycolic acid (MA)-containing trehalose ...The mycobacterial membrane protein large 3 (MmpL3) transporter is essential and required for shuttling the lipid trehalose monomycolate (TMM), a precursor of mycolic acid (MA)-containing trehalose dimycolate (TDM) and mycolyl arabinogalactan peptidoglycan (mAGP), in Mycobacterium species, including Mycobacterium tuberculosis and Mycobacterium smegmatis. However, the mechanism that MmpL3 uses to facilitate the transport of fatty acids and lipidic elements to the mycobacterial cell wall remains elusive. Here, we report 7 structures of the M. smegmatis MmpL3 transporter in its unbound state and in complex with trehalose 6-decanoate (T6D) or TMM using single-particle cryo-electron microscopy (cryo-EM) and X-ray crystallography. Combined with calculated results from molecular dynamics (MD) and target MD simulations, we reveal a lipid transport mechanism that involves a coupled movement of the periplasmic domain and transmembrane helices of the MmpL3 transporter that facilitates the shuttling of lipids to the mycobacterial cell wall.
History
DepositionSep 26, 2020-
Header (metadata) releaseSep 22, 2021-
Map releaseSep 22, 2021-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.2
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  • Surface view colored by height
  • Surface level: 0.2
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  • Surface view with fitted model
  • Atomic models: PDB-7k8a
  • Surface level: 0.2
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7k8a
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22724.png

Downloads & links

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Map

FileDownload / File: emd_22724.map.gz / Format: CCP4 / Size: 4.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.06 Å/pix.
x 98 pix.
= 103.88 Å		1.06 Å/pix.
x 108 pix.
= 114.48 Å		1.06 Å/pix.
x 104 pix.
= 110.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2 / Movie #1: 0.2
Minimum - Maximum-3.358537 - 12.710715
Average (Standard dev.)0.000000000001642 (±0.18060209)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin9989101
Dimensions10810498
Spacing98108104
CellA: 103.88 Å / B: 114.479996 Å / C: 110.23999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z98108104
origin x/y/z0.0000.0000.000
length x/y/z103.880114.480110.240
α/β/γ90.00090.00090.000
start NX/NY/NZ1019989
NX/NY/NZ98108104
MAP C/R/S321
start NC/NR/NS8999101
NC/NR/NS10410898
D min/max/mean-3.35912.7110.000

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Supplemental data

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Sample components

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Entire : RDN family transporter

EntireName: RDN family transporter
Components
  • Complex: RDN family transporter
    • Protein or peptide: Drug exporters of the RND superfamily-like protein

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Supramolecule #1: RDN family transporter

SupramoleculeName: RDN family transporter / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria) / Strain: MC2 155

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Macromolecule #1: Drug exporters of the RND superfamily-like protein

MacromoleculeName: Drug exporters of the RND superfamily-like protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 110.338109 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MFAWWGRTVY QFRYIVIGVM VALCLGGGVY GISLGNHVTQ SGFYDEGSQS VAASLIGDEV YGRDRTSHVV AILTPPDDKK VTDKAWQKK VTEELDQVVK DHEDQIVGWV GWLKAPDTTD PTVSAMKTQD LRHTFISIPL QGDDDDEILK NYQVVEPELQ Q VNGGDIRL ...String:
MFAWWGRTVY QFRYIVIGVM VALCLGGGVY GISLGNHVTQ SGFYDEGSQS VAASLIGDEV YGRDRTSHVV AILTPPDDKK VTDKAWQKK VTEELDQVVK DHEDQIVGWV GWLKAPDTTD PTVSAMKTQD LRHTFISIPL QGDDDDEILK NYQVVEPELQ Q VNGGDIRL AGLNPLASEL TGTIGEDQKR AEVAAIPLVA VVLFFVFGTV IAAALPAIIG GLAIAGALGI MRLVAEFTPV HF FAQPVVT LIGLGIAIDY GLFIVSRFRE EIAEGYDTEA AVRRTVMTSG RTVVFSAVII VASSVPLLLF PQGFLKSITY AII ASVMLA AILSITVLAA ALAILGPRVD ALGVTTLLKI PFLANWQFSR RIIDWFAEKT QKTKTREEVE RGFWGRLVNV VMKR PIAFA APILVVMVLL IIPLGQLSLG GISEKYLPPD NAVRQSQEQF DKLFPGFRTE PLTLVMKRED GEPITDAQIA DMRAK ALTV SGFTDPDNDP EKMWKERPAN DSGSKDPSVR VIQNGLENRN DAAKKIDELR ALQPPHGIEV FVGGTPALEQ DSIHSL FDK LPLMALILIV TTTVLMFLAF GSVVLPIKAA LMSALTLGST MGILTWMFVD GHGSGLMNYT PQPLMAPMIG LIIAVIW GL STDYEVFLVS RMVEARERGM STAEAIRIGT ATTGRLITGA ALILAVVAGA FVFSDLVMMK YLAFGLLIAL LLDATIIR M FLVPAVMKLL GDDCWWAPRW MKRVQEKLGL GETELPDERK RPTVRESETD QRALVGVGAP PPPPRPHDPT HPAPEPVRP MPPMRSNAPS AAGTARISTP PQPPQPPQAP AQQAGDEPAT TRFAMARNAV RNAVNSAVHG GAGSAAAPTE RAPRPGGPAQ PPAPPQREE REIESWLGAL RGPAPAKNVP QPPAQPQRPS TDTTRAMPPQ GRPPAGPADR GNENAPTTAF SAQRPPNGGA P ADATTAIP TPPQREQEPS TEKLNTREDA PEDPETKRRG GGMSAQDLLR REGRLHHHHH H

UniProtKB: Trehalose monomycolate exporter MmpL3

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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

Concentration0.2 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
0.02 MTris
0.1 Msodium chlorideNaCl
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.65 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 75398
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: ANGULAR RECONSTITUTION

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