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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: To Be Published
Title: Interactions of outer membrane lipoproteins P. aeruginosa PA3214 and E. coli PqiC with their MCE protein binding partners, PA3213 and PqiB
Authors: Giacometti SI / Coudray N / Redler R / Bhabha G / Ekiert DC
History
DepositionMay 6, 2026-
Header (metadata) releaseMay 20, 2026-
Map releaseMay 20, 2026-
UpdateMay 20, 2026-
Current statusMay 20, 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

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_77071_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_77071_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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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