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- PDB-7n6b: Structure of MmpL3 reconstituted into lipid nanodisc in the TMM b... -

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Basic information

Entry
Database: PDB / ID: 7n6b
TitleStructure of MmpL3 reconstituted into lipid nanodisc in the TMM bound state
ComponentsMmpL3 transporter
KeywordsTRANSLOCASE / transporter
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
Chem-0HJ / Trehalose monomycolate exporter MmpL3
Similarity search - Component
Biological speciesMycolicibacterium smegmatis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.66 Å
AuthorsSu, C.C. / Yu, E.
Funding support United States, 1items
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
DepositionJun 8, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release
Revision 1.0Sep 1, 2021Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 1, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 1, 2021Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Sep 1, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 1, 2021Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2May 21, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details
Item: _em_admin.last_update / _em_software.name / _pdbx_entry_details.has_protein_modification
Revision 1.1May 21, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Assembly

Deposited unit
A: MmpL3 transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,6523
Polymers109,5091
Non-polymers2,1432
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area31670 Å2

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Components

#1: Protein MmpL3 transporter


Mass: 109509.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: mmpL3, MSMEI_0243 / Production host: Escherichia coli (E. coli) / References: UniProt: I7G2R2
#2: Chemical ChemComp-0HJ / 6-O-[(2S)-2-{(1S)-18-[(1R,2R)-2-hexylcyclopropyl]-1-hydroxyoctadecyl}tricosanoyl]-alpha-D-glucopyranosyl alpha-D-glucopyranoside


Mass: 1071.593 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C62H118O13 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: MmpL3 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5 / Details: 20 mM Tris, 100 mM NaCl
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 37 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19_4080: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.66 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 415447 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0046063
ELECTRON MICROSCOPYf_angle_d0.6698228
ELECTRON MICROSCOPYf_dihedral_angle_d7.409881
ELECTRON MICROSCOPYf_chiral_restr0.045987
ELECTRON MICROSCOPYf_plane_restr0.0051018

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