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- EMDB-0007: MlaBDEF complex from A. baumannii -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-0007
TitleMlaBDEF complex from A. baumannii
Map data
Sample
  • Complex: MlaBDEF
    • Protein or peptide: MlaB
    • Protein or peptide: MlaD
    • Protein or peptide: MlaE
    • Protein or peptide: MlaF
Function / homology
Function and homology information


ATP-binding cassette (ABC) transporter complex / membrane => GO:0016020 / 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 transporter-like, ATP-binding domain ...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)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.7 Å
AuthorsBergeron JRC / Kollman JM
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
DepositionMay 15, 2018-
Header (metadata) releaseFeb 20, 2019-
Map releaseFeb 20, 2019-
UpdateFeb 20, 2019-
Current statusFeb 20, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.043
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.043
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6ic4
  • Surface level: 0.043
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0007.png

Downloads & links

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Map

FileDownload / File: emd_0007.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.26 Å
Density
Contour LevelBy AUTHOR: 0.043 / Movie #1: 0.043
Minimum - Maximum-0.026832027 - 0.103471845
Average (Standard dev.)0.0019379637 (±0.008786473)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 252.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.261.261.26
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z252.000252.000252.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0270.1030.002

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Supplemental data

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Sample components

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Entire : MlaBDEF

EntireName: MlaBDEF
Components
  • Complex: MlaBDEF
    • Protein or peptide: MlaB
    • Protein or peptide: MlaD
    • Protein or peptide: MlaE
    • Protein or peptide: MlaF

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Supramolecule #1: MlaBDEF

SupramoleculeName: MlaBDEF / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Acinetobacter baumannii (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: MlaB

MacromoleculeName: MlaB / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MVQYLNQELV VSGKIDFENA EQQYQAGLAI IKKQTSFPLI VDLKQLEHGN TLALAVLVQW LRQTPQKSGL HFKNVPEKML KIIQACHLQ EDLHLV

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Macromolecule #2: MlaD

MacromoleculeName: MlaD / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKSRTSELAV GIFVIIFGIA LFFLAMKVSG LVGTNLSDGY TMKAQFDNVN GLKPRAKVTM SGVTIGRVDS ITLDPVTRLA TVTFDLDGK LTSFNAEQLK EVQKNALDEL RYSSDYTQAT PAQQKTMEQQ LISNMNSITS IDEDAYIMVA TNGLLGEKYL K IVPGGGLN ...String:
MKSRTSELAV GIFVIIFGIA LFFLAMKVSG LVGTNLSDGY TMKAQFDNVN GLKPRAKVTM SGVTIGRVDS ITLDPVTRLA TVTFDLDGK LTSFNAEQLK EVQKNALDEL RYSSDYTQAT PAQQKTMEQQ LISNMNSITS IDEDAYIMVA TNGLLGEKYL K IVPGGGLN YLKRGDTISN TQGTMDLEDL ISKFITGGGA GKVAAGSSSA EEKAPASTDS SAQPSFVE

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Macromolecule #3: MlaE

MacromoleculeName: MlaE / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNTIAWLGRL VIERIRGIGV AALMLLQIIF SLPSAGGFGR FVYQMHRVGV MSLLIITVSG LFIGLVLGLQ GYSILVNVGS ESMLGTMVS LTLLRELAPV VAALLFAGRA GSALTAEIGS MKQSEQLASM EMIGVDPLKQ IVSPRLWAGI VSLPMLTVIF A AIGIVGGK ...String:
MNTIAWLGRL VIERIRGIGV AALMLLQIIF SLPSAGGFGR FVYQMHRVGV MSLLIITVSG LFIGLVLGLQ GYSILVNVGS ESMLGTMVS LTLLRELAPV VAALLFAGRA GSALTAEIGS MKQSEQLASM EMIGVDPLKQ IVSPRLWAGI VSLPMLTVIF A AIGIVGGK LVGVDFLGVD EGSFWSGMQN NVQFGHDVVN GIIKSIVFAL LCTWIAVFQG YACDPTPEGI ATAMTRTVVY SS LCVLGFD FVLTAVMFGG I

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Macromolecule #4: MlaF

MacromoleculeName: MlaF / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii (bacteria)
SequenceString: MIAIMNNKTP LSTQSLIEVK NLSFNRGERV IYDNISLNIR RGQITAIMGP SGTGKTTLLR LIGGQLVPDQ GEVLLDGKDI AQMSRQELF AARARMGMLF QSGALFTDMS VYENVAFPIR AHTKLSENLI AELVALKLES VGLRGTEQLM PTELSGGMNR R VALARAIA ...String:
MIAIMNNKTP LSTQSLIEVK NLSFNRGERV IYDNISLNIR RGQITAIMGP SGTGKTTLLR LIGGQLVPDQ GEVLLDGKDI AQMSRQELF AARARMGMLF QSGALFTDMS VYENVAFPIR AHTKLSENLI AELVALKLES VGLRGTEQLM PTELSGGMNR R VALARAIA LDPDLIMYDE PFAGQDPIVK GVLTRLIRSL REALDLTTII VSHDVPETLS IADYIYVVAE GKIQGEGTPE EL QAYASPF VKQFLTGSAE GPVEYQFSHQ AYLDNEVRP

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2 mg/mL
BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionResolution.type: BY AUTHOR / Resolution: 8.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 14000

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