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- PDB-9doh: Cryo-EM structure of LptB2FG apo-1 -

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Basic information

Entry
Database: PDB / ID: 9doh
TitleCryo-EM structure of LptB2FG apo-1
Components
  • Lipopolysaccharide export system ATP-binding protein LptB
  • Lipopolysaccharide export system permease protein LptF
  • Permease
KeywordsLIPID TRANSPORT / LPS transporter
Function / homology
Function and homology information


lipopolysaccharide transport / ATP-binding cassette (ABC) transporter complex / transmembrane transport / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
Permease LptG/LptF-related / LPS export ABC transporter permease LptF / LPS export ABC transporter permease LptG / Lipopolysaccharide export system permease LptF/LptG / Branched-chain amino acid ATP-binding cassette transporter, C-terminal / Branched-chain amino acid ATP-binding cassette transporter / LPS export ABC transporter, ATP-binding protein LptB / : / ABC transporter-like, conserved site / ABC transporters family signature. ...Permease LptG/LptF-related / LPS export ABC transporter permease LptF / LPS export ABC transporter permease LptG / Lipopolysaccharide export system permease LptF/LptG / Branched-chain amino acid ATP-binding cassette transporter, C-terminal / Branched-chain amino acid ATP-binding cassette transporter / LPS export ABC transporter, ATP-binding protein LptB / : / ABC transporter-like, conserved site / ABC transporters family signature. / 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
1,2-Distearoyl-sn-glycerophosphoethanolamine / Lipopolysaccharide export system permease protein LptF / Lipopolysaccharide export system ATP-binding protein LptB / LPS export ABC transporter permease LptG
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.34 Å
AuthorsSu, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Structural snapshots of Pseudomonas aeruginosa LptB2FG and LptB2FGC reveal insights into lipopolysaccharide recognition and transport
Authors: Su, C.
History
DepositionSep 19, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release
Revision 1.0Nov 19, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Nov 19, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Nov 19, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Nov 19, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 19, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 19, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 19, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

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MolmilJmol/JSmol

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Assembly

Deposited unit
B: Lipopolysaccharide export system ATP-binding protein LptB
A: Lipopolysaccharide export system ATP-binding protein LptB
G: Permease
F: Lipopolysaccharide export system permease protein LptF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,0677
Polymers136,8234
Non-polymers2,2443
Water00
1


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

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Components

#1: Protein Lipopolysaccharide export system ATP-binding protein LptB


Mass: 27833.975 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: lptB_3, lptB, lptB_2, CAZ10_21010, GNQ48_11505, GUL26_13595, IPC1295_15315, IPC737_20870, NCTC13621_04169, PAERUG_P19_London_7_VIM_2_05_10_06438
Production host: Escherichia coli (E. coli) / References: UniProt: A0A071L2Z5
#2: Protein Permease


Mass: 39511.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: lptG, CAZ10_29115, GNQ48_26920, IPC737_18645, NCTC13621_00519
Production host: Escherichia coli (E. coli) / References: UniProt: A0A071LDY1
#3: Protein Lipopolysaccharide export system permease protein LptF


Mass: 41643.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: lptF, CAZ10_29120, DT376_04500, GNQ48_26915, GUL26_00985, IPC1295_13765, IPC737_18640, PAERUG_P19_London_7_VIM_2_05_10_06506
Production host: Escherichia coli (E. coli) / References: UniProt: A0A071L107
#4: Chemical ChemComp-3PE / 1,2-Distearoyl-sn-glycerophosphoethanolamine / 3-SN-PHOSPHATIDYLETHANOLAMINE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE


Mass: 748.065 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM
Has ligand of interestN
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: LptB2FG / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: This is from a heterogeneous and impure protein sample.
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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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 FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 29 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: 3.34 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 66740 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0039516
ELECTRON MICROSCOPYf_angle_d0.51612869
ELECTRON MICROSCOPYf_dihedral_angle_d6.21388
ELECTRON MICROSCOPYf_chiral_restr0.041484
ELECTRON MICROSCOPYf_plane_restr0.0031631

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