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- EMDB-47097: Mycolicibacterium smegmatis MmpL5-AcpM structure -

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Basic information

Entry
Database: EMDB / ID: EMD-47097
TitleMycolicibacterium smegmatis MmpL5-AcpM structure
Map dataMycolicibacterium smegmatis MmpL5-AcpM structure
Sample
  • Complex: MmpL5-AcpM
    • Protein or peptide: Meromycolate extension acyl carrier protein
    • Protein or peptide: MmpL5 protein
  • Ligand: 4'-PHOSPHOPANTETHEINE
KeywordsMycolicibacterium smegmatis / MmpL5 / AcpM / TRANSPORT PROTEIN
Function / homology
Function and homology information


lipid A biosynthetic process / acyl binding / acyl carrier activity / membrane / plasma membrane / cytosol
Similarity search - Function
Membrane transport protein MmpL family / : / : / Membrane transport protein MMPL domain / MMPL family / Acyl carrier protein (ACP) / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain
Similarity search - Domain/homology
MmpL5 protein / Meromycolate extension acyl carrier protein
Similarity search - Component
Biological speciesMycolicibacterium smegmatis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.81 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
DepositionSep 20, 2024-
Header (metadata) releaseOct 23, 2024-
Map releaseOct 23, 2024-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47097.png

Downloads & links

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Map

FileDownload / File: emd_47097.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMycolicibacterium smegmatis MmpL5-AcpM structure
Projections & slices

Image control

Size
Brightness
Contrast
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-0.47144493 - 1.0293993
Average (Standard dev.)-0.0007106831 (±0.019294182)
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_47097_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_47097_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 : MmpL5-AcpM

EntireName: MmpL5-AcpM
Components
  • Complex: MmpL5-AcpM
    • Protein or peptide: Meromycolate extension acyl carrier protein
    • Protein or peptide: MmpL5 protein
  • Ligand: 4'-PHOSPHOPANTETHEINE

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Supramolecule #1: MmpL5-AcpM

SupramoleculeName: MmpL5-AcpM / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria)

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Macromolecule #1: Meromycolate extension acyl carrier protein

MacromoleculeName: Meromycolate extension acyl carrier protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria)
Molecular weightTheoretical: 10.743876 KDa
SequenceString:
MAATQEEIIA GLAEIIEEVT GIEPSEVTPE KSFVDDLDID SLSMVEIAVQ TEDKYGVKIP DEDLAGLRTV GDVVAYIQKL EEENPEAAA ALREKFAADQ

UniProtKB: Meromycolate extension acyl carrier protein

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Macromolecule #2: MmpL5 protein

MacromoleculeName: MmpL5 protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria)
Molecular weightTheoretical: 105.598219 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis (bacteria)
SequenceString: MSAPTDDTPT DAIAAPRHSA PPRPRLPWFL RTFAVPIILA WVAVVAILNT VVPTLDEVGE MRAVSMAPND APSTLAIKRV GQVFEEYDT SSSVMIVLEG EEPLGIEAHA FYDKMVADLR ADTEHVQHVQ DFWGDTLTAS GAQSVDGKAA YVQVYIAGDQ G ESLANESV ...String:
MSAPTDDTPT DAIAAPRHSA PPRPRLPWFL RTFAVPIILA WVAVVAILNT VVPTLDEVGE MRAVSMAPND APSTLAIKRV GQVFEEYDT SSSVMIVLEG EEPLGIEAHA FYDKMVADLR ADTEHVQHVQ DFWGDTLTAS GAQSVDGKAA YVQVYIAGDQ G ESLANESV EAVRKIATER ETPSGVKAYV TGAAATSADQ RAEGDASMKL IEGVTFAVIT VMLLAVYRSV ITTLIVLAMV VL GLSGARG IVAFLGFYNV FGLTTFATNM VVTLAIAAAT DYAIFLIGRY QEARRAGEDR ESAYYTMFHG TAHVVLASGL TIA GATLCL HFTRLPYFQT MGVPLAIGML IVVAAALTAG PAVISVVSRF GKTLEPKRFS RSPGWHRVGT ATVRWPGAIL VCAV VAALI GLLALPGYYT TYDDRRYLPD DVPANVGYDA AFRHFSQAKM NPDLMMVETD RDLRNPADFL VIDKIAKALK NVHGI AQVQ TITRPDGDPI EHSTIPYTIG QSGTTQIMNN DYMQTNLDNL LKQADDLQTS IDSMTEMMNI QTELAAVSQS MADKMA QTS DDTADVRDHL ADFDDFFRPI RNYLYWEPHC YDIPMCWSMR SIFESIDGIN TMSDDFQELV PEMRRMADLM PRMVAVM PA QIQSMKNQKQ TLLNQYQVQK AQQDQNMAMQ ENATAMSQAF DAAKNDDSFY LPPEAFETDD FQRGMKLFMS PDGHAVRF T IIHQGDPLTE EGTARMDELK VAAADAIKGT PFEGARIYLG GSAATYNDMQ IGADYDLIIV AASALILIFI IMMVLTRAV VAAAVIVGTV VLSLASAFGL SVLLWQHIVG IPLHWMVLPM SVIVLLAVGA DYNLLLVSRM KEEIHAGIRT GIIRAMVGTG AVVTAAGLV FAFTMASMAV SSLITIGQVG TTIGLGLLFD TLVVRSLMTP SIATLLGRWF WWPQRVRERP VPSKWPTPIQ R TPEEALS

UniProtKB: MmpL5 protein

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Macromolecule #3: 4'-PHOSPHOPANTETHEINE

MacromoleculeName: 4'-PHOSPHOPANTETHEINE / type: ligand / ID: 3 / Number of copies: 1 / Formula: PNS
Molecular weightTheoretical: 358.348 Da
Chemical component information

ChemComp-PNS:
4'-PHOSPHOPANTETHEINE

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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
20.0 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: 40.12 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: 3334872
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.81 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 100486
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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