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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: To Be Published
Title: Cluster of bipartite complex of MmpL5-AcpM from Mycolicibacterium smegmatis
Authors: Zhang, Z. / Maharjan, R. / Gregor, W.
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

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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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