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- PDB-8zkq: Cryo-EM structure of the efflux transporter MmpL5/MmpS5 from Myco... -

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Basic information

Entry
Database: PDB / ID: 8zkq
TitleCryo-EM structure of the efflux transporter MmpL5/MmpS5 from Mycobacterium tuberculosis, C1 symmetry
Components
  • Meromycolate extension acyl carrier protein
  • Siderophore export accessory protein MmpS5
  • Siderophore exporter MmpL5
KeywordsMEMBRANE PROTEIN / membrane transporter
Function / homology
Function and homology information


lipid A biosynthetic process / acyl binding / acyl carrier activity / extracellular region / membrane / plasma membrane / cytosol
Similarity search - Function
Transport accessory protein MmpS / Transport accessory protein MmpS, C-terminal / Mycobacterium membrane protein / Membrane transport protein MmpL family / : / : / Membrane transport protein MMPL domain / MMPL family / Acyl carrier protein (ACP) / Phosphopantetheine attachment site ...Transport accessory protein MmpS / Transport accessory protein MmpS, C-terminal / Mycobacterium membrane protein / 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
CARDIOLIPIN / Chem-PEV / Chem-PN7 / Meromycolate extension acyl carrier protein / Siderophore export accessory protein MmpS5 / Siderophore exporter MmpL5
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
Mycolicibacterium smegmatis MC2 155 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.84 Å
AuthorsZhang, B. / Xiong, Z. / Rao, Z.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171217 China
National Natural Science Foundation of China (NSFC)32394010 China
CitationJournal: To Be Published
Title: Membrane transporter
Authors: Zhang, B. / Xiong, Z. / Rao, Z.
History
DepositionMay 17, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 21, 2025Provider: repository / Type: Initial release
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Revision 1.1May 28, 2025Group: Data collection / Database references / Structure summary
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Revision 2.0May 28, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / pdbx_database_related / Data content type: EM metadata / EM metadata / EM metadata
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Siderophore exporter MmpL5
F: Siderophore export accessory protein MmpS5
H: Meromycolate extension acyl carrier protein
B: Siderophore exporter MmpL5
C: Siderophore export accessory protein MmpS5
D: Meromycolate extension acyl carrier protein
E: Siderophore exporter MmpL5
G: Siderophore export accessory protein MmpS5
I: Meromycolate extension acyl carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)406,81924
Polymers392,6409
Non-polymers14,17915
Water00
1


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

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Components

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Protein , 3 types, 9 molecules ABEFCGHDI

#1: Protein Siderophore exporter MmpL5


Mass: 104874.656 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: mmpL5, Rv0676c, MTV040.04c
Production host: Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: P9WJV1
#2: Protein Siderophore export accessory protein MmpS5


Mass: 15261.456 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: mmpS5, Rv0677c, MTV040.05c
Production host: Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: P9WJS7
#3: Protein Meromycolate extension acyl carrier protein / ACP


Mass: 10743.876 Da / Num. of mol.: 3
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

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Non-polymers , 3 types, 15 molecules

#4: Chemical
ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL


Mass: 1464.043 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C81H156O17P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#5: Chemical
ChemComp-PEV / (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / PHOSPHATIDYLETHANOLAMINE / 1-PALMITOYL-2-OLEOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE


Mass: 720.012 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C39H78NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: POPE, phospholipid*YM
#6: Chemical ChemComp-PN7 / N~3~-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-(2-sulfanylethyl)-beta-alaninamide


Mass: 358.348 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H23N2O7PS / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
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: membrane complex / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Mycobacterium tuberculosis H37Rv (bacteria)83332
31Mycolicibacterium smegmatis MC2 155 (bacteria)246196
Source (recombinant)Organism: Mycolicibacterium smegmatis MC2 155 (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: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 83178 / Symmetry type: POINT
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00921465
ELECTRON MICROSCOPYf_angle_d0.70528986
ELECTRON MICROSCOPYf_dihedral_angle_d14.12912894
ELECTRON MICROSCOPYf_chiral_restr0.0483372
ELECTRON MICROSCOPYf_plane_restr0.0043582

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