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Yorodumi- EMDB-4798: full-length bacterial polysaccharide co-polymerase - C8 symmetry -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4798 | |||||||||
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Title | full-length bacterial polysaccharide co-polymerase - C8 symmetry | |||||||||
Map data | full-length bacterial polysaccharide co-polymerase - C8 symmetry | |||||||||
Sample |
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Function / homology | Polysaccharide chain length determinant N-terminal domain / Chain length determinant protein / lipopolysaccharide biosynthetic process / protein tyrosine kinase activity / membrane => GO:0016020 / plasma membrane / Chain length determinant protein Function and homology information | |||||||||
Biological species | Escherichia coli K-12 (bacteria) / Escherichia coli (strain K12) (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
Authors | Wiseman B / Nitharwal RG / Hogbom M | |||||||||
Funding support | Sweden, 2 items
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Citation | Journal: Nat Commun / Year: 2021 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 |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4798.map.gz | 6.1 MB | EMDB map data format | |
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Header (meta data) | emd-4798-v30.xml emd-4798.xml | 13.1 KB 13.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_4798_fsc.xml | 14.4 KB | Display | FSC data file |
Images | emd_4798.png | 64.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4798 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4798 | HTTPS FTP |
-Related structure data
Related structure data | 6rbgMC 4791C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_4798.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | full-length bacterial polysaccharide co-polymerase - C8 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
-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: Escherichia coli K-12 (bacteria) |
Recombinant expression | Organism: Escherichia coli DH5[alpha] (bacteria) |
Molecular weight | Theoretical: 300 KDa |
-Macromolecule #1: Chain length determinant protein
Macromolecule | Name: Chain length determinant protein / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12 |
Molecular weight | Theoretical: 38.370621 KDa |
Recombinant expression | Organism: Escherichia coli DH5[alpha] (bacteria) |
Sequence | String: MRVENNNVSG QNHDPEQIDL IDLLVQLWRG KMTIIISVIV AIALAIGYLA VAKEKWTSTA IITQPDVGQI AGYNNAMNVI YGQAAPKVS DLQETLIGRF SSAFSALAET LDNQEEREKL TIEPSVKNQQ LPLTVSYVGQ TAEGAQMKLA QYIQQVDDKV N QELEKDLK ...String: MRVENNNVSG QNHDPEQIDL IDLLVQLWRG KMTIIISVIV AIALAIGYLA VAKEKWTSTA IITQPDVGQI AGYNNAMNVI YGQAAPKVS DLQETLIGRF SSAFSALAET LDNQEEREKL TIEPSVKNQQ LPLTVSYVGQ TAEGAQMKLA QYIQQVDDKV N QELEKDLK DNIALGRKNL QDSLRTQEVV AQEQKDLRIR QIQEALQYAN QAQVTKPQIQ QTGEDITQDT LFLLGSEALE SM IKHEATR PLVFSPNYYQ TRQNLLDIES LKVDDLDIHA YRYVMKPMLP IRRDSPKKAI TLILAVLLGG MVGAGIVLGR NAL RNYNAK EFRVPGSHHH HHHHH |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-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 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
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 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Overall B value: 87 |
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Output model | PDB-6rbg: |