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- PDB-6ic4: Cryo-EM structure of the A. baumannii MLA complex at 8.7 A resolution -

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Basic information

Entry
Database: PDB / ID: 6ic4
TitleCryo-EM structure of the A. baumannii MLA complex at 8.7 A resolution
Components
  • ABC transporter ATP-binding protein
  • ABC transporter permease
  • Toluene tolerance efflux transporter (ABC superfamily, PerI-bind)
  • Ttg2E
KeywordsPROTEIN TRANSPORT / Membrane protein Antibiotic resistance ABC transporter
Function / homology
Function and homology information


membrane => GO:0016020 / ATP-binding cassette (ABC) transporter complex / ATP hydrolysis activity / ATP binding
Similarity search - Function
: / ABC transport permease subunit MlaE, Proteobacteria / ABC transporter permease MalE / Permease MlaE / STAS domain / Mce/MlaD / MlaD protein / STAS domain / STAS domain superfamily / ABC transporter ...: / ABC transport permease subunit MlaE, Proteobacteria / ABC transporter permease MalE / Permease MlaE / STAS domain / Mce/MlaD / MlaD protein / STAS domain / STAS domain superfamily / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ABC transporter ATP-binding protein / Ttg2E / Toluene tolerance efflux transporter (ABC superfamily, PerI-bind) / Intermembrane phospholipid transport system permease protein MlaE
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.7 Å
AuthorsBergeron, J.R. / Kollman, J.M.
CitationJournal: Elife / Year: 2019
Title: The Mla system and glycerophospholipid transport to the outer membrane.
Authors: Cassandra Kamischke / Junping Fan / Julien Bergeron / Hemantha D Kulasekara / Zachary D Dalebroux / Anika Burrell / Justin M Kollman / Samuel I Miller /
Abstract: The outer membrane (OM) of Gram-negative bacteria serves as a selective permeability barrier that allows entry of essential nutrients while excluding toxic compounds, including antibiotics. The OM is ...The outer membrane (OM) of Gram-negative bacteria serves as a selective permeability barrier that allows entry of essential nutrients while excluding toxic compounds, including antibiotics. The OM is asymmetric and contains an outer leaflet of lipopolysaccharides (LPS) or lipooligosaccharides (LOS) and an inner leaflet of glycerophospholipids (GPL). We screened transposon mutants and identified a number of mutants with OM defects, including an ABC transporter system homologous to the Mla system in We further show that this opportunistic, antibiotic-resistant pathogen uses this multicomponent protein complex and ATP hydrolysis at the inner membrane to promote GPL export to the OM. The broad conservation of the Mla system in Gram-negative bacteria suggests the system may play a conserved role in OM biogenesis. The importance of the Mla system to OM integrity and antibiotic sensitivity suggests that its components may serve as new antimicrobial therapeutic targets.
History
DepositionDec 2, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: Database references / Category: citation / Item: _citation.title
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: Toluene tolerance efflux transporter (ABC superfamily, PerI-bind)
B: Toluene tolerance efflux transporter (ABC superfamily, PerI-bind)
C: Toluene tolerance efflux transporter (ABC superfamily, PerI-bind)
D: Toluene tolerance efflux transporter (ABC superfamily, PerI-bind)
E: Toluene tolerance efflux transporter (ABC superfamily, PerI-bind)
F: Toluene tolerance efflux transporter (ABC superfamily, PerI-bind)
G: ABC transporter permease
H: ABC transporter permease
I: ABC transporter ATP-binding protein
J: ABC transporter ATP-binding protein
K: Ttg2E
L: Ttg2E


Theoretical massNumber of molelcules
Total (without water)246,31712
Polymers246,31712
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
MethodPISA

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Components

#1: Protein
Toluene tolerance efflux transporter (ABC superfamily, PerI-bind)


Mass: 19916.736 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: ttg2C, SAMEA104305283_00402 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A334XBW3
#2: Protein ABC transporter permease / Putative phospholipid ABC transporter permease protein MlaE / Toluene tolerance efflux ABC transporter


Mass: 27209.285 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: ttg2B, mlaE, A7M79_03105, A7M90_14775, A7N09_05510, Aba7804_03380, Aba810CP_02080, APD06_03860, AZE33_17930, B4R90_07005, B9X95_19830, BGC29_10505, C2U32_12245, C3415_18770, CAS83_02490, CHQ89_ ...Gene: ttg2B, mlaE, A7M79_03105, A7M90_14775, A7N09_05510, Aba7804_03380, Aba810CP_02080, APD06_03860, AZE33_17930, B4R90_07005, B9X95_19830, BGC29_10505, C2U32_12245, C3415_18770, CAS83_02490, CHQ89_09020, CPI82_03200, DCD77_11945, IX87_12245, LV38_01098, SAMEA104305242_00211, SAMEA104305261_03368, SAMEA104305271_02119, SAMEA104305341_02652, SAMEA104305343_00596, SAMEA104305351_00191, SAMEA104305385_01589
Production host: Escherichia coli (E. coli) / References: UniProt: V5V9F4
#3: Protein ABC transporter ATP-binding protein / Phospholipid ABC transporter ATP-binding protein MlaF / Toluene tolerance efflux transporter (ABC ...Phospholipid ABC transporter ATP-binding protein MlaF / Toluene tolerance efflux transporter (ABC superfamily / ATP-bind)


Mass: 25554.471 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: ttg2A, A7M79_03110, A7M90_14770, A7N09_05505, AB719_19875, Aba810CP_02075, B4R90_07000, B9X91_22285, BGC29_10510, BWP00_03605, C3415_18775, C7G90_12995, CBE85_06065, CEJ63_09375, CPI82_03205, ...Gene: ttg2A, A7M79_03110, A7M90_14770, A7N09_05505, AB719_19875, Aba810CP_02075, B4R90_07000, B9X91_22285, BGC29_10510, BWP00_03605, C3415_18775, C7G90_12995, CBE85_06065, CEJ63_09375, CPI82_03205, CSB70_3297, IX87_12250, NCTC13305_02842, SAMEA104305208_00091, SAMEA104305242_00212, SAMEA104305271_02118, SAMEA104305318_02181, SAMEA104305341_02651, SAMEA104305343_00597, SAMEA104305351_00192, SAMEA104305385_01588
Production host: Escherichia coli (E. coli) / References: UniProt: A0A086HZU3
#4: Protein Ttg2E


Mass: 10644.346 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: SAMEA104305318_02185 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A333U4T6

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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: MlaBDEF / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Acinetobacter baumannii (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7
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: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 100 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 8.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 14000 / Symmetry type: POINT

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