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- EMDB-48706: Cluster of bipartite complex of MmpL5-AcpM from Mycolicibacterium... -

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Basic information

Entry
Database: EMDB / ID: EMD-48706
TitleCluster of bipartite complex of MmpL5-AcpM from Mycolicibacterium smegmatis
Map data
Sample
  • Complex: MmpL5-AcpM
    • Protein or peptide: Meromycolate extension acyl carrier protein
    • Protein or peptide: MmpL5 protein
  • Ligand: 4'-PHOSPHOPANTETHEINE
KeywordsMycolicibacterium smegmatis / MmpL5 / AcpM / membrane protein / bipartite complex
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: 3.35 Å
AuthorsZhang Z / Maharjan R / Gregor W
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Sci Adv / Year: 2025
Title: Structures of MmpL complexes reveal the assembly and mechanism of this family of transporters.
Authors: Zhemin Zhang / Rakesh Maharjan / William D Gregor / Philip A Klenotic / Edward W Yu /
Abstract: We coexpressed the mycobacterial membrane protein large 5 (MmpL5) transporter and MmpS5 adaptor proteins in and defined their structures from detergent-solubilized crude membranes. We observed that ...We coexpressed the mycobacterial membrane protein large 5 (MmpL5) transporter and MmpS5 adaptor proteins in and defined their structures from detergent-solubilized crude membranes. We observed that MmpL5 presents as a monomer in complex with the cytosolic meromycolate extension acyl carrier protein M (AcpM), where these AcpM-MmpL5 complexes generate regular two-dimensional arrays. We also provide structural information to show that MmpL5 assembles as a trimer that interacts with MmpS5 and AcpM to form the tripartite complex AcpM-MmpL5-MmpS5 that spans both the inner and outer membranes of the mycobacterium. In addition, we found that MmpL5 and AcpM are able to form the trimeric AcpM-MmpL5 complex. The structural data reveal that the full-length MmpL5 trimer is capable of spanning the entire mycobacterial cell envelope to transport substrates. However, this assembly requires the presence of MmpS5 to stabilize secondary structural features of the MmpL5 periplasmic subdomains.
History
DepositionJan 17, 2025-
Header (metadata) releaseJul 30, 2025-
Map releaseJul 30, 2025-
UpdateFeb 18, 2026-
Current statusFeb 18, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48706.png

Downloads & links

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Map

FileDownload / File: emd_48706.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 400 pix.
= 428. Å		1.07 Å/pix.
x 400 pix.
= 428. Å		1.07 Å/pix.
x 400 pix.
= 428. 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: 0.08
Minimum - Maximum-0.08033951 - 0.619749
Average (Standard dev.)0.0049597053 (±0.017932262)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 428.00003 Å
α=β=γ: 90.0 °

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Supplemental data

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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: 12 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria)
Molecular weightTheoretical: 10.743876 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis (bacteria)
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: 12 / 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: 8 / 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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 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 / Nominal magnification: 81000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 96036
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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