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- EMDB-77071: Cryo-EM structure of Pseudomonas aeruginosa soluble lipoprotein PA3214 -

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Basic information

Entry
Database: EMDB / ID: EMD-77071
TitleCryo-EM structure of Pseudomonas aeruginosa soluble lipoprotein PA3214
Map datastructure of Pseudomonas aeruginosa soluble lipoprotein
Sample
  • Complex: PA3214
    • Protein or peptide: ABC-type transport auxiliary lipoprotein component domain-containing protein
Keywordslipoprotein / Pseudomonas aeruginosa / MCE system / LIPID TRANSPORT
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 (bacteria) / Pseudomonas aeruginosa PAO1 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.67 Å
AuthorsRedler R / Giacometti SI / Coudray N / Bhabha G / Ekiert DC
Funding support United States, 5 items
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 Institute of General Medical Sciences (NIH/NIGMS)R24GM154185 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, 2026-
Header (metadata) releaseMay 20, 2026-
Map releaseMay 20, 2026-
UpdateJun 3, 2026-
Current statusJun 3, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_77071.png

Downloads & links

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Map

FileDownload / File: emd_77071.map.gz / Format: CCP4 / Size: 12.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationstructure of Pseudomonas aeruginosa soluble lipoprotein
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 150 pix.
= 154.327 Å		1.03 Å/pix.
x 150 pix.
= 154.327 Å		1.03 Å/pix.
x 150 pix.
= 154.327 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.02885 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.302
Minimum - Maximum-0.2767127 - 0.6890159
Average (Standard dev.)0.009279345 (±0.05894444)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions150150150
Spacing150150150
CellA=B=C: 154.3275 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: sharpened map

Fileemd_77071_additional_1.map
Annotationsharpened map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

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Half map: #1

Fileemd_77071_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_77071_half_map_2.map
Projections & Slices
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Sample components

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Entire : PA3214

EntireName: PA3214
Components
  • Complex: PA3214
    • Protein or peptide: ABC-type transport auxiliary lipoprotein component domain-containing protein

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Supramolecule #1: PA3214

SupramoleculeName: PA3214 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Pseudomonas aeruginosa (bacteria) / Strain: PAO1
Molecular weightTheoretical: 0.1644 kDa/nm

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Macromolecule #1: ABC-type transport auxiliary lipoprotein component domain-contain...

MacromoleculeName: ABC-type transport auxiliary lipoprotein component domain-containing protein
type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 22.922693 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MHHHHHHQHQ HENLYFQGSI LPEAQVLQVY LLPVHNPPAS AAARPVDWSL RIARPRTSLV LESPRIAVRP HGDEISVYQG ARWSDPAPS LLRDRLMQAF QADGRVRGLS SDDSNLQADF ELGGDLRAFQ TEYPNGQASA LIRYDARLVR TDDKRVVASR R FEVSQPVD ...String:
MHHHHHHQHQ HENLYFQGSI LPEAQVLQVY LLPVHNPPAS AAARPVDWSL RIARPRTSLV LESPRIAVRP HGDEISVYQG ARWSDPAPS LLRDRLMQAF QADGRVRGLS SDDSNLQADF ELGGDLRAFQ TEYPNGQASA LIRYDARLVR TDDKRVVASR R FEVSQPVD GKKVAAVVSA FGKAGDTLSA QVLDWTLRQA SAQPAVQP

UniProtKB: ABC-type transport auxiliary lipoprotein component domain-containing protein

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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

Concentration0.3 mg/mL
BufferpH: 8
Component:
ConcentrationNameFormula
20.0 mMHEPES
150.0 mMSodium chlorideNaCl
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 5 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
SoftwareName: SerialEM
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Number grids imaged: 1 / Number real images: 6463 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 22500
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3638701
CTF correctionSoftware - Name: cryoSPARC / Software - details: CTFFIND4 / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C8 (8 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.67 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 654956
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: in silico model / Details: Phyre2
SoftwareName: Coot
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-13hq:
Cryo-EM structure of Pseudomonas aeruginosa soluble lipoprotein PA3214

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