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- PDB-5uvn: Structure of E. coli MCE protein PqiB, periplasmic domain -

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Basic information

Entry
Database: PDB / ID: 5uvn
TitleStructure of E. coli MCE protein PqiB, periplasmic domain
ComponentsParaquat-inducible protein B
KeywordsTRANSPORT PROTEIN / MCE protein / bacterial lipid transport
Function/homologyMce/MlaD / MlaD protein / outer membrane-bounded periplasmic space / integral component of membrane / plasma membrane / Paraquat-inducible protein B
Function and homology information
Specimen sourceEscherichia coli / bacteria / /
MethodElectron microscopy (3.96 Å resolution / Particle / Single particle) / Transmission electron microscopy
AuthorsBhabha, G. / Ekiert, D.C.
CitationJournal: Cell / Year: 2017
Title: Architectures of Lipid Transport Systems for the Bacterial Outer Membrane.
Authors: Damian C Ekiert / Gira Bhabha / Georgia L Isom / Garrett Greenan / Sergey Ovchinnikov / Ian R Henderson / Jeffery S Cox / Ronald D Vale
Abstract: How phospholipids are trafficked between the bacterial inner and outer membranes through the hydrophilic space of the periplasm is not known. We report that members of the mammalian cell entry (MCE) ...How phospholipids are trafficked between the bacterial inner and outer membranes through the hydrophilic space of the periplasm is not known. We report that members of the mammalian cell entry (MCE) protein family form hexameric assemblies with a central channel capable of mediating lipid transport. The E. coli MCE protein, MlaD, forms a ring associated with an ABC transporter complex in the inner membrane. A soluble lipid-binding protein, MlaC, ferries lipids between MlaD and an outer membrane protein complex. In contrast, EM structures of two other E. coli MCE proteins show that YebT forms an elongated tube consisting of seven stacked MCE rings, and PqiB adopts a syringe-like architecture. Both YebT and PqiB create channels of sufficient length to span the periplasmic space. This work reveals diverse architectures of highly conserved protein-based channels implicated in the transport of lipids between the membranes of bacteria and some eukaryotic organelles.
Copyright: 2017 Elsevier Inc. All rights reserved.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Feb 20, 2017 / Release: Apr 12, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Apr 12, 2017Structure modelrepositoryInitial release
1.1Apr 19, 2017Structure modelDatabase references
1.2Sep 27, 2017Structure modelAuthor supporting evidence / Data collectionem_image_scans / em_software / pdbx_audit_support_em_software.name / _pdbx_audit_support.funding_organization

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Structure visualization

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Assembly

Deposited unit
A: Paraquat-inducible protein B
B: Paraquat-inducible protein B
C: Paraquat-inducible protein B
D: Paraquat-inducible protein B
E: Paraquat-inducible protein B
F: Paraquat-inducible protein B


Theoretical massNumber of molelcules
Total (without water)293,1426
Polyers293,1426
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)24640
ΔGint (kcal/M)-166
Surface area (Å2)119970
MethodPISA

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Components

#1: Protein/peptide
Paraquat-inducible protein B


Mass: 48857.043 Da / Num. of mol.: 6 / Source: (gene. exp.) Escherichia coli / bacteria / / / Strain: K12 / Gene: pqiB, pqi5B, b0951, JW0934 / Production host: Escherichia coli / References: UniProt:P43671
Sequence detailsThe actual sample sequence is MHHHHHHENLYFQSHQGPEVTLITANAEGIEGGKTTIKSRSVDVGVVESATLADD ...The actual sample sequence is MHHHHHHENLYFQSHQGPEVTLITANAEGIEGGKTTIKSRSVDVGVVESATLADD LTHVEIKARLNSGMEKLLHKDTVFWVVKPQIGREGISGLGTLLSGVYIELQPGAK GSKMDKYDLLDSPPLAPPDAKGIRVILDSKKAGQLSPGDPVLFRGYRVGSVETST FDTQKRNISYQLFINAPYDRLVTNNVRFWKDSGIAVDLTSAGMRVEMGSLTTLLS GGVSFDVPEGLDLGQPVAPKTAFVLYDDQKSIQDSLYTDHIDYLMFFKDSVRGLQ PGAPVEFRGIRLGTVSKVPFFAPNMRQTFNDDYRIPVLIRIEPERLKMQLGENAD VVEHLGELLKRGLRGSLKTGNLVTGALYVDLDFYPNTPAITGIREFNGYQIIPTV SGGLAQIQQRLMEALDKINKLPLNPMIEQATSTLSESQRTMKNLQTTLDSMNKIL ASQSMQQLPTDMQSTLRELNRSMQGFQPGSAAYNKMVADMQRLDQVLRELQPVLK TLNEKSNALVFEAKDKKDPEPKRAKQ

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: homo hexamer of PqiB / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Molecular weightValue: 0.347 deg. / Units: MEGADALTONS
Source (natural)Organism: Escherichia coli / Strain: K12
Source (recombinant)Organism: Escherichia coli
Buffer solutionDetails: 20 mM Tris pH 8.0 and 150 mM NaCl / pH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 / Grid type: Quantifoil 1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 80 e/Å2 / Details: 80 e/A2 is total dose for 50 frames / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.10.1_2155: / Classification: refinement
EM software
IDNameVersionCategory
4Gctf0.5CTF CORRECTION
7Coot0.8.1MODEL FITTING
9RELION1.4INITIAL EULER ASSIGNMENT
10RELION1.4FINAL EULER ASSIGNMENT
11RELION1.4CLASSIFICATION
12RELION1.4RECONSTRUCTION
13PHENIX1.9MODEL REFINEMENT
CTF correctionType: NONE
SymmetryPoint symmetry: C6
3D reconstructionResolution: 3.96 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 36591 / Symmetry type: POINT
Atomic model buildingRef protocol: OTHER / Ref space: REAL
Least-squares processHighest resolution: 3.96 Å

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