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- EMDB-77072: Cryo-EM structure of Pseudomonas aeruginosa outer-membrane lipopr... -

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Basic information

Entry
Database: EMDB / ID: EMD-77072
TitleCryo-EM structure of Pseudomonas aeruginosa outer-membrane lipoprotein PA3214 bound to MCE protein PA3213 C-terminal peptide (CASP target)
Map dataC8 symmetry - Structure of Pseudomonas aeruginosa outer-membrane lipoprotein PA3214 bound to MCE protein PA3213 C-terminal peptide
Sample
  • Complex: PA3214 in complex with PA3213
    • Protein or peptide: ABC-type transport auxiliary lipoprotein component domain-containing protein
    • Protein or peptide: Mce/MlaD domain-containing protein
Keywordsouter membrane lipoprotein / Pseudomonas aeruginosa / MCE system / LIPID TRANSPORT
Function / homologyABC-type transport auxiliary lipoprotein component / ABC-type transport auxiliary lipoprotein component / Mce/MlaD / MlaD protein / Prokaryotic membrane lipoprotein lipid attachment site profile. / ABC-type transport auxiliary lipoprotein component domain-containing protein / Mce/MlaD domain-containing protein
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria) / Pseudomonas aeruginosa PAO1 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsGiacometti 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
Simons FoundationSF349247 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_77072.png

Downloads & links

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Map

FileDownload / File: emd_77072.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationC8 symmetry - Structure of Pseudomonas aeruginosa outer-membrane lipoprotein PA3214 bound to MCE protein PA3213 C-terminal peptide
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 256 pix.
= 277.248 Å		1.08 Å/pix.
x 256 pix.
= 277.248 Å		1.08 Å/pix.
x 256 pix.
= 277.248 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.083 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.249
Minimum - Maximum-0.40911523 - 1.3017411
Average (Standard dev.)0.00028768778 (±0.049562998)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 277.248 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: C8 symmetry (sharpened map)

Fileemd_77072_additional_1.map
AnnotationC8 symmetry (sharpened map)
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AxesZYX

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Additional map: C1 symmetry (sharpened map)

Fileemd_77072_additional_2.map
AnnotationC1 symmetry (sharpened map)
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Additional map: C1 symmetry

Fileemd_77072_additional_3.map
AnnotationC1 symmetry
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AxesZYX

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Half map: C8 symmetry - Half Map B

Fileemd_77072_half_map_1.map
AnnotationC8 symmetry - Half Map B
Projections & Slices
AxesZYX

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Histogram

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Half map: C8 symmetry - Half Map A

Fileemd_77072_half_map_2.map
AnnotationC8 symmetry - Half Map A
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AxesZYX

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Sample components

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Entire : PA3214 in complex with PA3213

EntireName: PA3214 in complex with PA3213
Components
  • Complex: PA3214 in complex with PA3213
    • Protein or peptide: ABC-type transport auxiliary lipoprotein component domain-containing protein
    • Protein or peptide: Mce/MlaD domain-containing protein

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Supramolecule #1: PA3214 in complex with PA3213

SupramoleculeName: PA3214 in complex with PA3213 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Pseudomonas aeruginosa (bacteria) / Strain: PAO1
Molecular weightTheoretical: 165 KDa

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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: 23.243482 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MRLALRPLRR LSLAAGLAAL ATLGACSILP EAQVLQVYLL PVHNPPASAA ARPVDWSLRI ARPRTSLVLE SPRIAVRPHG DEISVYQGA RWSDPAPSLL RDRLMQAFQA DGRVRGLSSD DSNLQADFEL GGDLRAFQTE YPNGQASALI RYDARLVRTD D KRVVASRR ...String:
MRLALRPLRR LSLAAGLAAL ATLGACSILP EAQVLQVYLL PVHNPPASAA ARPVDWSLRI ARPRTSLVLE SPRIAVRPHG DEISVYQGA RWSDPAPSLL RDRLMQAFQA DGRVRGLSSD DSNLQADFEL GGDLRAFQTE YPNGQASALI RYDARLVRTD D KRVVASRR FEVSQPVDGK KVAAVVSAFG KAGDTLSAQV LDWTLRQASA QPAVQP

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

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Macromolecule #2: Mce/MlaD domain-containing protein

MacromoleculeName: Mce/MlaD domain-containing protein / type: protein_or_peptide / ID: 2 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 33.410922 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: METRAHHVLI GLFSVIVIGA ALLFGLWLAK SGSEGKFNYY DIVFNEAVSG LSQGSSVQYS GIKVGDVAFL RLDPKDPRKV WARIRVVAS APIKQDTTAK LALTGITGTS IIQLSSGTPA SPMLEGKDGK IPVIVATPSP LTQLLSNGED LMGNINQLIA R FSNLLSEE ...String:
METRAHHVLI GLFSVIVIGA ALLFGLWLAK SGSEGKFNYY DIVFNEAVSG LSQGSSVQYS GIKVGDVAFL RLDPKDPRKV WARIRVVAS APIKQDTTAK LALTGITGTS IIQLSSGTPA SPMLEGKDGK IPVIVATPSP LTQLLSNGED LMGNINQLIA R FSNLLSEE NTARISRTLD HLDQATGALS AERENVSAVM QQLAQASRQA NAALAQASEL MRSANGLLNE QGKGMLENAN KT MASLERT SATLDQLISE NRHSLDGGIQ GLAELGPAVS ELRDTLAALR GISRRLEENP ANYLLGREKT KEFTP

UniProtKB: Mce/MlaD 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

Concentration0.23 mg/mL
BufferpH: 8
Component:
ConcentrationNameFormula
20.0 mMTris(hydroxymethyl)aminomethane hydrochloride
150.0 mMSodium chlorideNaCl
0.5 mMN-Dodecyl-B-D-maltosideDDM
10.0 %Glycerol
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / 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: Leginon
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / #0 - Number grids imaged: 1 / #0 - Number real images: 6057 / #0 - Average electron dose: 51.51 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / #1 - Number grids imaged: 1 / #1 - Number real images: 3929 / #1 - Average electron dose: 51.43 e/Å2 / #1 - Details: collected at 30 degree tilt
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: 3.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 81000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Image recording ID1
Particle selectionNumber selected: 4242449
CTF correctionSoftware - Name: cryoSPARC / Software - details: Patch CTF / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 5 / Applied symmetry - Point group: C8 (8 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 378252
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 25 / Avg.num./class: 63561 / Software - Name: cryoSPARC

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Atomic model buiding 1

Initial model
ChainDetails
source_name: AlphaFold, initial_model_type: in silico model
source_name: Other, initial_model_type: in silico modelModelAngelo
SoftwareName: Coot
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-13hr:
Cryo-EM structure of Pseudomonas aeruginosa outer-membrane lipoprotein PA3214 bound to MCE protein PA3213 C-terminal peptide

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