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- EMDB-4791: full-length bacterial polysaccharide co-polymerase - C1 symmetry -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-4791 | |||||||||
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Title | full-length bacterial polysaccharide co-polymerase - C1 symmetry | |||||||||
![]() | Full-length bacterial polysaccharide co-polymerase - C1 symmetry | |||||||||
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Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
![]() | Wiseman B / Nitharwal RG / Hogbom M | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of a full-length bacterial polysaccharide co-polymerase. Authors: Benjamin Wiseman / Ram Gopal Nitharwal / Göran Widmalm / Martin Högbom / ![]() ![]() Abstract: Lipopolysaccharides are important components of the bacterial cell envelope that among other things act as a protective barrier against the environment and toxic molecules such as antibiotics. One of ...Lipopolysaccharides are important components of the bacterial cell envelope that among other things act as a protective barrier against the environment and toxic molecules such as antibiotics. One of the most widely disseminated pathways of polysaccharide biosynthesis is the inner membrane bound Wzy-dependent pathway. Here we present the 3.0 Å structure of the co-polymerase component of this pathway, WzzB from E. coli solved by single-particle cryo-electron microscopy. The overall architecture is octameric and resembles a box jellyfish containing a large bell-shaped periplasmic domain with the 2-helix transmembrane domain from each protomer, positioned 32 Å apart, encircling a large empty transmembrane chamber. This structure also reveals the architecture of the transmembrane domain, including the location of key residues for the Wzz-family of proteins and the Wzy-dependent pathway present in many Gram-negative bacteria, explaining several of the previous biochemical and mutational studies and lays the foundation for future investigations. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 8.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 12.3 KB 12.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 14.4 KB | Display | ![]() |
Images | ![]() | 58.2 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Full-length bacterial polysaccharide co-polymerase - C1 symmetry | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Octameric bacterial polysaccharide co-polymerase complex
Entire | Name: Octameric bacterial polysaccharide co-polymerase complex |
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Components |
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-Supramolecule #1: Octameric bacterial polysaccharide co-polymerase complex
Supramolecule | Name: Octameric bacterial polysaccharide co-polymerase complex type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() |
Molecular weight | Theoretical: 300 KDa |
-Macromolecule #1: Bacterial polysaccharide co-polymerase
Macromolecule | Name: Bacterial polysaccharide co-polymerase / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MRVENNNVSG QNHDPEQIDL IDLLVQLWRG KMTIIISVIV AIALAIGYLA VAKEKWTSTA IITQPDVGQI AGYNNAMNVI YGQAAPKVSD LQETLIGRFS SAFSALAETL DNQEEREKLT IEPSVKNQQL PLTVSYVGQT AEGAQMKLAQ YIQQVDDKVN QELEKDLKDN ...String: MRVENNNVSG QNHDPEQIDL IDLLVQLWRG KMTIIISVIV AIALAIGYLA VAKEKWTSTA IITQPDVGQI AGYNNAMNVI YGQAAPKVSD LQETLIGRFS SAFSALAETL DNQEEREKLT IEPSVKNQQL PLTVSYVGQT AEGAQMKLAQ YIQQVDDKVN QELEKDLKDN IALGRKNLQD SLRTQEVVAQ EQKDLRIRQI QEALQYANQA QVTKPQIQQT GEDITQDTLF LLGSEALESM IKHEATRPLV FSPNYYQTRQ NLLDIESLKV DDLDIHAYRY VMKPMLPIRR DSPKKAITLI LAVLLGGMVG AGIVLGRNAL RNYNAKEFRV PGSHHHHHHH H |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 3.5 mg/mL |
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Buffer | pH: 8 |
Grid | Model: Quantifoil R2/2 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE / Details: 40 seconds at 20 mA |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Number real images: 2347 / Average electron dose: 52.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |