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- PDB-13hs: Cryo-EM structure of Pseudomonas aeruginosa outer-membrane lipopr... -

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Basic information

Entry
Database: PDB / ID: 13hs
TitleCryo-EM structure of Pseudomonas aeruginosa outer-membrane lipoprotein PA3214 in the open conformation
ComponentsABC-type transport auxiliary lipoprotein component domain-containing protein
KeywordsLIPID TRANSPORT / outer membrane lipoprotein / Pseudomonas aeruginosa / MCE system
Function / homologyABC-type transport auxiliary lipoprotein component / ABC-type transport auxiliary lipoprotein component / Prokaryotic membrane lipoprotein lipid attachment site profile. / ABC-type transport auxiliary lipoprotein component domain-containing protein
Function and homology information
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsGiacometti, S.I. / Coudray, N. / Bhabha, G. / Ekiert, D.C.
Funding support United States, 8items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)2021318502 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM128777 United States
The Pew Charitable Trusts00033055 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P30CA016087 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01NS108151-07 United States
Simons FoundationSF349247 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)NIGMS R24 GM154192 United States
Other governmentU24 GM129539 United States
CitationJournal: bioRxiv / Year: 2026
Title: Interactions of outer membrane lipoproteins PA3214 and PqiC with their MCE protein binding partners, PA3213 and PqiB.
Authors: Sabrina I Giacometti / Nicolas Coudray / Rachel L Redler / Gira Bhabha / Damian C Ekiert
Abstract: Members of the Mammalian Cell Entry (MCE) superfamily interact with other proteins to form diverse architectures for the transport of hydrophobic molecules across the cell envelope in Gram-negative ...Members of the Mammalian Cell Entry (MCE) superfamily interact with other proteins to form diverse architectures for the transport of hydrophobic molecules across the cell envelope in Gram-negative bacteria. Some of these trans-envelope MCE protein complexes include a PqiC-like outer membrane (OM) lipoprotein component. The best-studied member of this group of OM lipoproteins is PqiC, from the PqiABC system, which can form an octameric ring. How PqiC-like lipoproteins interact with their MCE protein binding partners to facilitate transport is not well understood. Here we report the cryo-electron microscopy structures of PA3214, a homolog of PqiC, in the context of the full MCE transport PA3211-PA3214 system. Our structure provides insight into the biological assembly of the lipoprotein and interactions with its binding partner, MCE protein PA3213. We utilize deep mutational scanning to identify functionally important sites in PqiC in an unbiased manner. Through phenotypic and biochemical experiments, we characterize the interactions of the lipoproteins PqiC and PA3214 with their associated MCE proteins PqiB and PA3213, thus providing a model for how some MCE proteins employ a C-terminal peptide to mediate key interactions with their cognate lipoproteins at the OM.
History
DepositionMay 6, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ABC-type transport auxiliary lipoprotein component domain-containing protein
B: ABC-type transport auxiliary lipoprotein component domain-containing protein
C: ABC-type transport auxiliary lipoprotein component domain-containing protein
D: ABC-type transport auxiliary lipoprotein component domain-containing protein
E: ABC-type transport auxiliary lipoprotein component domain-containing protein
F: ABC-type transport auxiliary lipoprotein component domain-containing protein
G: ABC-type transport auxiliary lipoprotein component domain-containing protein
H: ABC-type transport auxiliary lipoprotein component domain-containing protein


Theoretical massNumber of molelcules
Total (without water)185,9488
Polymers185,9488
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
ABC-type transport auxiliary lipoprotein component domain-containing protein


Mass: 23243.482 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: PA3214 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9HZ26
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: PA3214 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.165 kDa/nm / Experimental value: NO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria) / Strain: PAO1
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTris(hydroxymethyl)aminomethane hydrochloride1
2150 mMSodium chlorideNaCl1
30.5 mMN-Dodecyl-B-D-maltoside1
410 %Glycerol1
SpecimenConc.: 0.23 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recording
IDImaging-IDElectron dose (e/Å2)Film or detector modelNum. of grids imagedNum. of real imagesDetails (eV)
1151.51GATAN K3 (6k x 4k)16057
2151.43GATAN K3 (6k x 4k)3929collected at 30 degree tilt

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Processing

EM software
IDNameVersionCategoryDetails (eV)
1Warpparticle selectionParticles were selected by WARP
2Leginonimage acquisition
4cryoSPARCCTF correctionPatch CTF
7Cootmodel fitting
8ISOLDEmodel fitting
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
14PHENIX1.21.2_5419model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 4242449
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 187311 / Num. of class averages: 3 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingDetails: complete biological assembly of the closed conformation
Source name: Other / Type: experimental model
RefinementHighest resolution: 3.7 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00411264
ELECTRON MICROSCOPYf_angle_d0.66115320
ELECTRON MICROSCOPYf_dihedral_angle_d12.0514224
ELECTRON MICROSCOPYf_chiral_restr0.0411696
ELECTRON MICROSCOPYf_plane_restr0.012056

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