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- EMDB-44167: Mycolicibacterium smegmatis MmpL4 structure -

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Basic information

Entry
Database: EMDB / ID: EMD-44167
TitleMycolicibacterium smegmatis MmpL4 structure
Map dataMycolicibacterium smegmatis MmpL4 structure
Sample
  • Complex: MmpL4
    • Protein or peptide: MmpL4 protein
KeywordsSiderophore / MmpL4 / TRANSPORT PROTEIN
Function / homologyMembrane transport protein MmpL family / : / Membrane transport protein MMPL domain / MMPL family / plasma membrane / MmpL4 protein
Function and homology information
Biological speciesMycolicibacterium smegmatis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.95 Å
AuthorsMaharjan R / Klenotic PA / Zhang Z / Yu EW
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI145069 United States
CitationJournal: PLoS Biol / Year: 2024
Title: Structures of the mycobacterial MmpL4 and MmpL5 transporters provide insights into their role in siderophore export and iron acquisition.
Authors: Rakesh Maharjan / Zhemin Zhang / Philip A Klenotic / William D Gregor / Marios L Tringides / Meng Cui / Georgiana E Purdy / Edward W Yu /
Abstract: The Mycobacterium tuberculosis (Mtb) pathogen, the causative agent of the airborne infection tuberculosis (TB), harbors a number of mycobacterial membrane protein large (MmpL) transporters. These ...The Mycobacterium tuberculosis (Mtb) pathogen, the causative agent of the airborne infection tuberculosis (TB), harbors a number of mycobacterial membrane protein large (MmpL) transporters. These membrane proteins can be separated into 2 distinct subclasses, where they perform important functional roles, and thus, are considered potential drug targets to combat TB. Previously, we reported both X-ray and cryo-EM structures of the MmpL3 transporter, providing high-resolution structural information for this subclass of the MmpL proteins. Currently, there is no structural information available for the subclass associated with MmpL4 and MmpL5, transporters that play a critical role in iron homeostasis of the bacterium. Here, we report cryo-EM structures of the M. smegmatis MmpL4 and MmpL5 transporters to resolutions of 2.95 Å and 3.00 Å, respectively. These structures allow us to propose a plausible pathway for siderophore translocation via these 2 transporters, an essential step for iron acquisition that enables the survival and replication of the mycobacterium.
History
DepositionMar 20, 2024-
Header (metadata) releaseOct 2, 2024-
Map releaseOct 2, 2024-
UpdateMar 5, 2025-
Current statusMar 5, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44167.png

Downloads & links

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Map

FileDownload / File: emd_44167.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMycolicibacterium smegmatis MmpL4 structure
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 300 pix.
= 321. Å		1.07 Å/pix.
x 300 pix.
= 321. Å		1.07 Å/pix.
x 300 pix.
= 321. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.5707762 - 1.1697233
Average (Standard dev.)-0.00038110674 (±0.020946821)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 321.00003 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map A

Fileemd_44167_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_44167_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : MmpL4

EntireName: MmpL4
Components
  • Complex: MmpL4
    • Protein or peptide: MmpL4 protein

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Supramolecule #1: MmpL4

SupramoleculeName: MmpL4 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria)
Molecular weightTheoretical: 106.2 kDa/nm

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Macromolecule #1: MmpL4 protein

MacromoleculeName: MmpL4 protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria)
Molecular weightTheoretical: 107.13518 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSNPSHDAPT DAMGVSGPKH ARPGGIAKWI RVLAVPIILV WVAIIAVLNT VVPQLDVVGE MRSVSMSPDD APSVIAMKRV GEVFEEFKS NSSVMIVLEG EQPLGDEAHK YYDEIVDKLE ADPAHVEHVQ DFWGDPLTAS GAQSPDGLAS YVQVYTRGNQ G EALANESV ...String:
MSNPSHDAPT DAMGVSGPKH ARPGGIAKWI RVLAVPIILV WVAIIAVLNT VVPQLDVVGE MRSVSMSPDD APSVIAMKRV GEVFEEFKS NSSVMIVLEG EQPLGDEAHK YYDEIVDKLE ADPAHVEHVQ DFWGDPLTAS GAQSPDGLAS YVQVYTRGNQ G EALANESV EAVQDIVESV PAPPGVKAYV TGPAALSADQ HVASDRSVRV IEALTFAVII TMLLLVYRSI VTVILTLVMV VL SLSAARG MIAFLGYHEI IGLSVFATNL LTTLAIAAAT DYAIFLIGRY QEARSVGEDR EQSYYTMFHS TAHVVLGSGM TIA GATLCL HFTRMPYFQS LGIPLAIGMS VVVLASLTMG AAIISVASRF GKTFEPKRAM RTRGWRKLGA AVVRWPAPIL VTTI ALSVV GLLALPGYQT NYNDRRYLPQ DLPANTGYAA ADRHFSQARM NPELLMIESD HDLRNSADFL VVDRIAKRVF QVPGI SRVQ AITRPQGTPI EHTSIPFQIS MSGTTQMMNM KYMQDRMADM LVMADEMQKS VDTMEEMLKI TREMSDTTHS MVGKMH GMV EDIKELRDHI ADFDDFLRPI RNYFYWEPHC DSIPVCQSIR SIFDTLDGID VMTDDIQRLM PDMDRLDELM PQMLTIM PP MIESMKTMKT MMLTTQATMG GLQDQMEAAM ENQTAMGQAF DASKNDDSFY LPPETFENPD FKRGMKMFLS PDGHAVRF I ISHEGDPMSP EGIKHIDAIK QAAKEAIKGT PLEGSKIYLG GTAATFKDLQ EGANYDLIIA GIAALCLIFI IMLIITRAV VASAVIVGTV VISLGASFGL SVLIWQHIIG LELHWMVLAM AVIVLLAVGA DYNLLLVSRI KEEIHAGLNT GIIRSMGGTG SVVTSAGLV FAFTMMSMAV SELAVIAQVG TTIGLGLLFD TLVIRSFMTP SIAALMGKWF WWPQRVRQRP LPAPWPQPVQ R DPEDALNR VHHHHHH

UniProtKB: MmpL4 protein

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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

Concentration2.0 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4S4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
100.0 mMNaClsodium chloride
0.005 %C47H88O22Lauryl Maltose Neopentyl Glycol
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 4352328
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 78196
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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