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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: 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_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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

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)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: C1 symmetry (sharpened map)

Fileemd_77072_additional_2.map
AnnotationC1 symmetry (sharpened map)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: C1 symmetry

Fileemd_77072_additional_3.map
AnnotationC1 symmetry
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: C8 symmetry - Half Map A

Fileemd_77072_half_map_2.map
AnnotationC8 symmetry - Half Map A
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 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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