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- PDB-6z5u: Cryo-EM structure of the A. baumannii MlaBDEF complex bound to APPNHP -

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Basic information

Entry
Database: PDB / ID: 6z5u
TitleCryo-EM structure of the A. baumannii MlaBDEF complex bound to APPNHP
Components
  • (ABC transporter ...ATP-binding cassette transporter) x 2
  • Anti-sigma factor antagonist
  • MCE family protein
KeywordsMEMBRANE PROTEIN / lipid transport / antibiotic resistance / ABC transporter
Function / homology
Function and homology information


ATP-binding cassette (ABC) transporter complex / ATP binding / membrane
Similarity search - Function
Probable ABC transporter ATP-binding protein MlaF/Mkl / 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 ...Probable ABC transporter ATP-binding protein MlaF/Mkl / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / ABC transporter ATP-binding protein / ABC transporter periplasmic substrate-binding protein / Intermembrane phospholipid transport system permease protein MlaE / Anti-sigma factor antagonist
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsMann, D. / Bergeron, J.R.C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R019061/1 United Kingdom
Citation
Journal: Commun Biol / Year: 2021
Title: Structure and lipid dynamics in the maintenance of lipid asymmetry inner membrane complex of A. baumannii.
Authors: Daniel Mann / Junping Fan / Kamolrat Somboon / Daniel P Farrell / Andrew Muenks / Svetomir B Tzokov / Frank DiMaio / Syma Khalid / Samuel I Miller / Julien R C Bergeron /
Abstract: Multi-resistant bacteria are a major threat in modern medicine. The gram-negative coccobacillus Acinetobacter baumannii currently leads the WHO list of pathogens in critical need for new therapeutic ...Multi-resistant bacteria are a major threat in modern medicine. The gram-negative coccobacillus Acinetobacter baumannii currently leads the WHO list of pathogens in critical need for new therapeutic development. The maintenance of lipid asymmetry (MLA) protein complex is one of the core machineries that transport lipids from/to the outer membrane in gram-negative bacteria. It also contributes to broad-range antibiotic resistance in several pathogens, most prominently in A. baumannii. Nonetheless, the molecular details of its role in lipid transport has remained largely elusive. Here, we report the cryo-EM maps of the core MLA complex, MlaBDEF, from the pathogen A. baumannii, in the apo-, ATP- and ADP-bound states, revealing multiple lipid binding sites in the cytosolic and periplasmic side of the complex. Molecular dynamics simulations suggest their potential trajectory across the membrane. Collectively with the recently-reported structures of the E. coli orthologue, this data also allows us to propose a molecular mechanism of lipid transport by the MLA system.
#1: Journal: Biorxiv / Year: 2020
Title: Structure and lipid dynamics in the A. baumannii maintenance of lipid asymmetry (MLA) inner membrane complex
Authors: Mann, D. / Fan, J. / Farrell, D.P. / Somboon, K. / Muenks, A. / Tzokov, S.B. / Khalid, S. / Dimaio, F. / Miller, S.I. / Bergeron, J.R.C.
History
DepositionMay 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 14, 2021Group: Database references / Category: citation / citation_author

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Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
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  • Superimposition on EM map
  • EMDB-11082
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
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Assembly

Deposited unit
A: ABC transporter permease
B: ABC transporter permease
C: Anti-sigma factor antagonist
D: Anti-sigma factor antagonist
E: MCE family protein
G: MCE family protein
H: MCE family protein
I: MCE family protein
J: MCE family protein
K: ABC transporter ATP-binding protein
L: ABC transporter ATP-binding protein
F: MCE family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)283,00316
Polymers281,94212
Non-polymers1,0614
Water0
1


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

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Components

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ABC transporter ... , 2 types, 4 molecules ABKL

#1: Protein ABC transporter permease / Lipid asymmetry maintenance ABC transporter permease subunit MlaE / Phospholipid/cholesterol/gamma- ...Lipid asymmetry maintenance ABC transporter permease subunit MlaE / Phospholipid/cholesterol/gamma-HCH transport system permease protein / Putative phospholipid ABC transporter permease protein MlaE / Toluene tolerance efflux ABC transporter


Mass: 27322.443 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: mlaE, ttg2B, A7M79_03105, A7M90_14775, ABCAM1_3325, APD33_11020, B4R90_07005, B9X95_19830, BGC29_10505, C2U32_12245, CHQ89_09020, CPI82_03200, DLI75_08555, E5294_02070, E5979_07650, EA685_ ...Gene: mlaE, ttg2B, A7M79_03105, A7M90_14775, ABCAM1_3325, APD33_11020, B4R90_07005, B9X95_19830, BGC29_10505, C2U32_12245, CHQ89_09020, CPI82_03200, DLI75_08555, E5294_02070, E5979_07650, EA685_00455, EA706_02625, EA722_02115, EA746_009620, EKS29_03575, EWO92_15675, EWO96_10890, EWP49_16265, FD887_10930, FJU42_03310, FJU87_05505, FJV14_14505, FR761_17360, LV38_01098, SAMEA104305261_03368, SAMEA104305351_00191
Production host: Escherichia coli (E. coli) / References: UniProt: V5V9F4
#4: Protein ABC transporter ATP-binding protein / MlaF


Mass: 30367.848 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: ttg2A, NU60_03710 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4P2WWN2

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Protein , 2 types, 8 molecules CDEGHIJF

#2: Protein Anti-sigma factor antagonist / Phospholipid transport system transporter-binding protein / STAS domain protein / STAS domain- ...Phospholipid transport system transporter-binding protein / STAS domain protein / STAS domain-containing protein / Toluene tolerance protein / Ttg2E


Mass: 10874.672 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: mlaB, A7M79_03090, A7M90_14790, A9843_11720, AA954_03140, ABCAM1_3322, ABUW_0387, APD33_11035, B4R90_07020, B9W69_03450, B9X95_19845, BGC29_10490, C2U32_12230, CEJ64_02055, CHQ89_09005, CPI82_ ...Gene: mlaB, A7M79_03090, A7M90_14790, A9843_11720, AA954_03140, ABCAM1_3322, ABUW_0387, APD33_11035, B4R90_07020, B9W69_03450, B9X95_19845, BGC29_10490, C2U32_12230, CEJ64_02055, CHQ89_09005, CPI82_03185, CSB70_3293, DLI69_20965, DLI75_08570, DOL94_03255, DVA79_09290, E2533_15225, E2536_07480, E5294_02085, E5979_07665, EA685_00440, EA686_18495, EA706_02640, EA722_02130, EA746_009635, EKS29_03590, EWO92_15660, EWO96_10875, EWP49_16250, FD887_10915, FD913_07380, FJU36_09990, FJU42_03325, FJU76_08875, FJU79_12020, FJU87_05520, FJV14_14520, FR761_17345, LV38_01095, NCTC13305_02846, NCTC13420_03382, SAMEA104305261_03371, SAMEA104305351_00188
Production host: Escherichia coli (E. coli) / References: UniProt: V5V9K5
#3: Protein
MCE family protein / Mammalian cell entry protein / Mce related family protein / Outer membrane lipid asymmetry ...Mammalian cell entry protein / Mce related family protein / Outer membrane lipid asymmetry maintenance protein MlaD / Phospholipid/cholesterol/gamma-HCH transport system substrate-binding protein / Putative phospholipid ABC transporter-binding protein MlaD / Toluene tolerance efflux transporter / Toluene tolerance efflux transporter (ABC superfamily / PerI-bind)


Mass: 24135.322 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: mlaD, ttg2C, A7M79_03100, A7M90_14780, A9843_11730, AA954_03130, ABCAM1_3324, ABUW_0385, APD33_11025, B4R90_07010, B9W69_03440, B9X95_19835, BGC29_10500, C2U32_12240, CEJ64_02065, CHQ89_09015, ...Gene: mlaD, ttg2C, A7M79_03100, A7M90_14780, A9843_11730, AA954_03130, ABCAM1_3324, ABUW_0385, APD33_11025, B4R90_07010, B9W69_03440, B9X95_19835, BGC29_10500, C2U32_12240, CEJ64_02065, CHQ89_09015, CPI82_03195, CSB70_3295, DLI69_20975, DLI75_08560, DOL94_03245, DVA79_09280, E2533_15215, E2536_07470, E5294_02075, E5979_07655, EA685_00450, EA706_02630, EA722_02120, EA746_009625, EKS29_03580, EWO92_15670, EWO96_10885, EWP49_16260, FD887_10925, FD913_07390, FJU36_10000, FJU76_08865, FJU79_12010, FJU87_05510, FJV14_14510, FR761_17355, LV38_01097, NCTC13305_02844, NCTC13420_03380, SAMEA104305318_02183, SAMEA104305351_00190
Production host: Escherichia coli (E. coli) / References: UniProt: V5V921

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Non-polymers , 2 types, 4 molecules

#5: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

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Details

Has ligand of interestN

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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 complex / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Molecular weightExperimental value: NO
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: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 47 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 93295 / Symmetry type: POINT

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