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- PDB-7d06: Cryo EM structure of the nucleotide free Acinetobacter MlaFEDB complex -

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Basic information

Entry
Database: PDB / ID: 7d06
TitleCryo EM structure of the nucleotide free Acinetobacter MlaFEDB complex
Components
  • ABC transporter ATP-binding protein
  • Anti-sigma factor antagonist
  • Intermembrane phospholipid transport system permease protein MlaE
  • MCE family protein
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


phospholipid transporter activity / ATP-binding cassette (ABC) transporter complex / phospholipid binding / ATP hydrolysis activity / ATP binding / membrane
Similarity search - Function
: / ABC transport permease subunit MlaE, Proteobacteria / : / ABC transporter permease MalE / Permease MlaE / STAS domain / STAS domain / Mce/MlaD / MlaD protein / Transcription Regulator spoIIAA ...: / ABC transport permease subunit MlaE, Proteobacteria / : / ABC transporter permease MalE / Permease MlaE / STAS domain / STAS domain / Mce/MlaD / MlaD protein / Transcription Regulator spoIIAA / STAS domain / STAS domain superfamily / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-PGV / 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: 3.1 Å
AuthorsZhang, Y.Y. / Fan, Q.X. / Chi, X.M. / Zhou, Q. / Li, Y.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31930059 China
CitationJournal: Cell Discov / Year: 2020
Title: Cryo-EM structures of Acinetobacter baumannii glycerophospholipid transporter.
Authors: Yuanyuan Zhang / Qiongxuan Fan / Ximin Chi / Qiang Zhou / Yanyan Li /
History
DepositionSep 9, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Mar 27, 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: Intermembrane phospholipid transport system permease protein MlaE
B: ABC transporter ATP-binding protein
C: Anti-sigma factor antagonist
D: Intermembrane phospholipid transport system permease protein MlaE
E: ABC transporter ATP-binding protein
F: Anti-sigma factor antagonist
G: MCE family protein
H: MCE family protein
I: MCE family protein
J: MCE family protein
K: MCE family protein
L: MCE family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)292,41324
Polymers283,42512
Non-polymers8,98812
Water00
1


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

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Components

#1: Protein Intermembrane phospholipid transport system permease protein MlaE


Mass: 27322.443 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: V5V9F4
#2: Protein ABC transporter ATP-binding protein / ATP-binding cassette domain-containing protein / Iron(III) ABC transporter / ATP-binding protein / ...ATP-binding cassette domain-containing protein / Iron(III) ABC transporter / ATP-binding protein / Phospholipid ABC transporter ATP-binding protein MlaF / Toluene tolerance efflux transporter


Mass: 30070.455 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: A0A086HZU3
#3: 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: 11913.760 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: V5V9K5
#4: 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


Mass: 24135.322 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: V5V921
#5: Chemical
ChemComp-PGV / (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE / PHOSPHATIDYLGLYCEROL / 2-VACCENOYL-1-PALMITOYL-SN-GLYCEROL-3-PHOSPHOGLYCEROL


Mass: 749.007 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C40H77O10P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
Has ligand of interestY

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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: nucleotide free Acinetobacter MlaFEDB complex / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Source (natural)Organism: Acinetobacter baumannii (bacteria)
Source (recombinant)Organism: Escherichia coli K-12 (bacteria)
Buffer solutionpH: 8
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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: RELION / Version: 3.0.6 / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 314199 / Symmetry type: POINT

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