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

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Basic information

Entry
Database: PDB / ID: 13hr
TitleCryo-EM structure of Pseudomonas aeruginosa outer-membrane lipoprotein PA3214 bound to MCE protein PA3213 C-terminal peptide
Components
  • ABC-type transport auxiliary lipoprotein component domain-containing protein
  • Mce/MlaD 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 / 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 PAO1 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsGiacometti, S.I. / Coudray, N. / Bhabha, G. / Ekiert, D.C.
Funding support United States, 5items
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, S.I. / Coudray, N. / Redler, R. / Bhabha, G. / Ekiert, D.C.
History
DepositionMay 6, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2026Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Additional map / Part number: 2 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Additional map / Part number: 3 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Primary map / Data content type: Primary map / Provider: 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
I: Mce/MlaD domain-containing protein
J: Mce/MlaD domain-containing protein
K: Mce/MlaD domain-containing protein
L: Mce/MlaD domain-containing protein
M: Mce/MlaD domain-containing protein
N: Mce/MlaD domain-containing protein
O: Mce/MlaD domain-containing protein
P: Mce/MlaD 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)453,23516
Polymers453,23516
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
#2: Protein
Mce/MlaD domain-containing protein


Mass: 33410.922 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: PA3213 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9HZ27
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 in complex with PA3213 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.165 MDa / Experimental value: NO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria) / Strain: PAO1
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21(DE3)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTris(hydroxymethyl)aminomethane hydrochloride1
2150 mMSodium chlorideNaCl1
30.5 mMN-Dodecyl-B-D-maltosideDDM1
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 BIOQUANTUM (6k x 4k)16057
2151.43GATAN K3 BIOQUANTUM (6k x 4k)13929collected 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
9cryoSPARCinitial Euler assignment
10cryoSPARCfinal Euler assignment
11cryoSPARCclassification
12cryoSPARC3D reconstruction
13PHENIX1.21.2_5419model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 4242449
SymmetryPoint symmetry: C8 (8 fold cyclic)
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 378252 / Num. of class averages: 5 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model building
ID 3D fitting-IDSource nameTypeDetails (eV)
11AlphaFoldin silico model
21Otherin silico modelModelAngelo
RefinementHighest resolution: 2.7 Å / Cross valid method: NONE
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00311752
ELECTRON MICROSCOPYf_angle_d0.59115968
ELECTRON MICROSCOPYf_dihedral_angle_d11.7474424
ELECTRON MICROSCOPYf_chiral_restr0.0431768
ELECTRON MICROSCOPYf_plane_restr0.012136

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