+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8612 | ||||||||||||
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Title | Negative stain reconstruction of E. coli MCE protein PqiB | ||||||||||||
Map data | E. coli MCE protein PqiB, periplasmic domain | ||||||||||||
Sample |
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Function / homology | : / Mce/MlaD / MlaD protein / intermembrane lipid transfer / outer membrane-bounded periplasmic space / identical protein binding / plasma membrane / Intermembrane transport protein PqiB Function and homology information | ||||||||||||
Biological species | Escherichia coli (E. coli) | ||||||||||||
Method | single particle reconstruction / negative staining / Resolution: 25.0 Å | ||||||||||||
Authors | Bhabha G / Ekiert DC | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: 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. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_8612.map.gz | 741.7 KB | EMDB map data format | |
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Header (meta data) | emd-8612-v30.xml emd-8612.xml | 11 KB 11 KB | Display Display | EMDB header |
Images | emd_8612.png | 62.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8612 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8612 | HTTPS FTP |
-Validation report
Summary document | emd_8612_validation.pdf.gz | 340.7 KB | Display | EMDB validaton report |
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Full document | emd_8612_full_validation.pdf.gz | 340.3 KB | Display | |
Data in XML | emd_8612_validation.xml.gz | 4.9 KB | Display | |
Data in CIF | emd_8612_validation.cif.gz | 5.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8612 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8612 | HTTPS FTP |
-Related structure data
Related structure data | 8608C 8610C 8611C 5uvnC 5uw2C 5uw8C 5uwaC 5uwbC C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_8612.map.gz / Format: CCP4 / Size: 1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | E. coli MCE protein PqiB, periplasmic domain | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.42 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : YebT
Entire | Name: YebT |
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Components |
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-Supramolecule #1: YebT
Supramolecule | Name: YebT / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Macromolecule #1: PqiB
Macromolecule | Name: PqiB / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MHHHHHHENL YFQSHQGPEV TLITANAEG IEGGKTTIKS R SVDVGVVE SATLADDLTH VE IKARLNS GMEKLLHKDT VFW VVKPQI GREGISGLGT LLSG VYIEL QPGAKGSKMD KYDLL DSPP LAPPDAKGIR VILDSK KAG QLSPGDPVLF RGYRVGS VE ...String: MHHHHHHENL YFQSHQGPEV TLITANAEG IEGGKTTIKS R SVDVGVVE SATLADDLTH VE IKARLNS GMEKLLHKDT VFW VVKPQI GREGISGLGT LLSG VYIEL QPGAKGSKMD KYDLL DSPP LAPPDAKGIR VILDSK KAG QLSPGDPVLF RGYRVGS VE TSTFDTQKRN ISYQLFIN A PYDRLVTNNV RFWKDSGIA VDLTSAGMRV EMGSLTTLLS GGVSFDVPE GLDLGQPVAP K TAFVLYDD QKSIQDSLYT DH IDYLMFF KDSVRGLQPG APV EFRGIR LGTVSKVPFF APNM RQTFN DDYRIPVLIR IEPER LKMQ LGENADVVEH LGELLK RGL RGSLKTGNLV TGALYVD LD FYPNTPAITG IREFNGYQ I IPTVSGGLAQ IQQRLMEAL DKINKLPLNP MIEQATSTLS ESQRTMKNL QTTLDSMNKI L ASQSMQQL PTDMQSTLRE LN RSMQGFQ PGSAAYNKMV ADM QRLDQV LRELQPVLKT LNEK SNALV FEAKDKKDPE PKRAKQ |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Staining | Type: NEGATIVE / Material: Uranyl Formate |
-Electron microscopy
Microscope | FEI TECNAI 12 |
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Image recording | Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average electron dose: 10.0 e/Å2 |
Electron beam | Acceleration voltage: 120 kV / Electron source: LAB6 |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 4787 |
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Initial angle assignment | Type: RANDOM ASSIGNMENT / Software - Name: RELION (ver. 1.4) |
Final angle assignment | Type: OTHER / Software - Name: RELION (ver. 1.4) |
Final 3D classification | Software - Name: RELION (ver. 1.4) |