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- PDB-9mx0: Cluster of bipartite complex of MmpL5-AcpM from Mycolicibacterium... -

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Basic information

Entry
Database: PDB / ID: 9mx0
TitleCluster of bipartite complex of MmpL5-AcpM from Mycolicibacterium smegmatis
Components
  • Meromycolate extension acyl carrier protein
  • MmpL5 protein
KeywordsMEMBRANE PROTEIN / Mycolicibacterium smegmatis / MmpL5 / AcpM / 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
4'-PHOSPHOPANTETHEINE / MmpL5 protein / Meromycolate extension acyl carrier protein
Similarity search - Component
Biological speciesMycolicibacterium smegmatis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.35 Å
AuthorsZhang, Z. / Maharjan, R. / Gregor, W.
Funding support United States, 1items
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, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Feb 18, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Revision 1.1Feb 18, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Meromycolate extension acyl carrier protein
A: MmpL5 protein
C: Meromycolate extension acyl carrier protein
D: MmpL5 protein
E: Meromycolate extension acyl carrier protein
F: MmpL5 protein
G: Meromycolate extension acyl carrier protein
H: MmpL5 protein
I: Meromycolate extension acyl carrier protein
J: MmpL5 protein
K: Meromycolate extension acyl carrier protein
L: MmpL5 protein
M: Meromycolate extension acyl carrier protein
N: Meromycolate extension acyl carrier protein
O: Meromycolate extension acyl carrier protein
P: MmpL5 protein
Q: MmpL5 protein
R: MmpL5 protein
S: Meromycolate extension acyl carrier protein
T: Meromycolate extension acyl carrier protein
U: Meromycolate extension acyl carrier protein
V: MmpL5 protein
W: MmpL5 protein
X: MmpL5 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,398,97232
Polymers1,396,10524
Non-polymers2,8678
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Meromycolate extension acyl carrier protein / ACP


Mass: 10743.876 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis (bacteria) / Gene: acpM, MSMEG_4326, MSMEI_4226 / Production host: Mycolicibacterium smegmatis (bacteria) / References: UniProt: A0R0B3
#2: Protein
MmpL5 protein


Mass: 105598.219 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis (bacteria) / Gene: MSMEG_1382 / Production host: Mycolicibacterium smegmatis (bacteria) / References: UniProt: A0QS80
#3: Chemical
ChemComp-PNS / 4'-PHOSPHOPANTETHEINE


Mass: 358.348 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C11H23N2O7PS
Has ligand of interestN
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: MmpL5-AcpM / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria)
Source (recombinant)Organism: Mycolicibacterium smegmatis (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding 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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 96036 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00174886
ELECTRON MICROSCOPYf_angle_d0.351102104
ELECTRON MICROSCOPYf_dihedral_angle_d8.41126488
ELECTRON MICROSCOPYf_chiral_restr0.03612320
ELECTRON MICROSCOPYf_plane_restr0.00312878

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