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- PDB-9u4t: Cryo-EM map of MSMEG_3496 in complex with AcpM, size exclusion ch... -

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Basic information

Entry
Database: PDB / ID: 9u4t
TitleCryo-EM map of MSMEG_3496 in complex with AcpM, size exclusion chromatography peak1
Components
  • Meromycolate extension acyl carrier protein
  • MmpL4 protein
KeywordsMEMBRANE PROTEIN / Efflux pump MSMEG_3496-AcpM 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
MmpL4 protein / Meromycolate extension acyl carrier protein
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.11 Å
AuthorsGao, F. / Zhang, X. / Li, D. / Ma, X.
Funding support China, 2items
OrganizationGrant numberCountry
Other government202403021211192 China
National Natural Science Foundation of China (NSFC)32161133022 China
CitationJournal: Sci China Life Sci / Year: 2025
Title: Cryo-EM structures of mycobacteria MmpL5-AcpM complex.
Authors: Delin Li / Xiaokang Zhang / Kai Yuan / Xiaomin Ma / Yucheng Wang / Pu Han / Junqing Sun / Tianling Guo / Xuefei Pang / Kefang Liu / Yan Wu / Yingxia Liu / Shuguang Tan / Xu Zhang / Haixia ...Authors: Delin Li / Xiaokang Zhang / Kai Yuan / Xiaomin Ma / Yucheng Wang / Pu Han / Junqing Sun / Tianling Guo / Xuefei Pang / Kefang Liu / Yan Wu / Yingxia Liu / Shuguang Tan / Xu Zhang / Haixia Xiao / George Fu Gao / Feng Gao /
History
DepositionMar 20, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MmpL4 protein
B: Meromycolate extension acyl carrier protein


Theoretical massNumber of molelcules
Total (without water)121,4422
Polymers121,4422
Non-polymers00
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 MmpL4 protein / MmpL family efflux pump


Mass: 110357.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria)
Gene: MSMEG_3496
Production host: Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QY12
#2: Protein Meromycolate extension acyl carrier protein / ACP


Mass: 11084.209 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria)
Gene: acpM, MSMEG_4326, MSMEI_4226
Production host: Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0R0B3
Has ligand of interestY
Has protein modificationY

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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: Cryo-EM structure of MSMEG_3496 in complex with AcpM,size exclusion chromatography peak1
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Source (recombinant)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Buffer solutionpH: 8
SpecimenConc.: 5.28 mg/ml / Embedding 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 defocus max: 2000 nm / Nominal defocus min: 900 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.11 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 4926409 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 135.12 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00416428
ELECTRON MICROSCOPYf_angle_d0.65318755
ELECTRON MICROSCOPYf_chiral_restr0.0441043
ELECTRON MICROSCOPYf_plane_restr0.00381109
ELECTRON MICROSCOPYf_dihedral_angle_d4.2709889

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