+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41042 | ||||||||||||
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Title | S. enterica WbaP in a styrene maleic acid liponanoparticle | ||||||||||||
Map data | |||||||||||||
Sample |
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Keywords | phosphoglycosyl transferase / liponanopaticle / SMALP / O-antigen / Salmonella enterica / TRANSFERASE | ||||||||||||
Function / homology | Function and homology information undecaprenyl-phosphate galactose phosphotransferase / undecaprenyl-phosphate galactose phosphotransferase activity / phosphotransferase activity, for other substituted phosphate groups / O antigen biosynthetic process / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.1 Å | ||||||||||||
Authors | Dodge GJ / Imperiali B | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: Elife / Year: 2024 Title: Mapping the architecture of the initiating phosphoglycosyl transferase from O-antigen biosynthesis in a liponanoparticle. Authors: Greg J Dodge / Alyssa J Anderson / Yi He / Weijing Liu / Rosa Viner / Barbara Imperiali / Abstract: Bacterial cell surface glycoconjugates are critical for cell survival and for interactions between bacteria and their hosts. Consequently, the pathways responsible for their biosynthesis have ...Bacterial cell surface glycoconjugates are critical for cell survival and for interactions between bacteria and their hosts. Consequently, the pathways responsible for their biosynthesis have untapped potential as therapeutic targets. The localization of many glycoconjugate biosynthesis enzymes to the membrane represents a significant challenge for expressing, purifying, and characterizing these enzymes. Here, we leverage cutting-edge detergent-free methods to stabilize, purify, and structurally characterize WbaP, a phosphoglycosyl transferase (PGT) from the (LT2) O-antigen biosynthesis. From a functional perspective, these studies establish WbaP as a homodimer, reveal the structural elements responsible for dimerization, shed light on the regulatory role of a domain of unknown function embedded within WbaP, and identify conserved structural motifs between PGTs and functionally unrelated UDP-sugar dehydratases. From a technological perspective, the strategy developed here is generalizable and provides a toolkit for studying other classes of small membrane proteins embedded in liponanoparticles beyond PGTs. | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_41042.map.gz | 59.7 MB | EMDB map data format | |
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Header (meta data) | emd-41042-v30.xml emd-41042.xml | 16.1 KB 16.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_41042_fsc.xml | 9.6 KB | Display | FSC data file |
Images | emd_41042.png | 78.7 KB | ||
Masks | emd_41042_msk_1.map | 64 MB | Mask map | |
Filedesc metadata | emd-41042.cif.gz | 5.8 KB | ||
Others | emd_41042_half_map_1.map.gz emd_41042_half_map_2.map.gz | 59.3 MB 59.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41042 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41042 | HTTPS FTP |
-Related structure data
Related structure data | 8t53MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_41042.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.3 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_41042_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_41042_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_41042_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : WbaP dimer embedded in a styrene maleic acid liponanoparticle
Entire | Name: WbaP dimer embedded in a styrene maleic acid liponanoparticle |
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Components |
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-Supramolecule #1: WbaP dimer embedded in a styrene maleic acid liponanoparticle
Supramolecule | Name: WbaP dimer embedded in a styrene maleic acid liponanoparticle type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) |
Molecular weight | Theoretical: 250 KDa |
-Macromolecule #1: Undecaprenyl-phosphate galactose phosphotransferase
Macromolecule | Name: Undecaprenyl-phosphate galactose phosphotransferase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO EC number: undecaprenyl-phosphate galactose phosphotransferase |
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Source (natural) | Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) |
Molecular weight | Theoretical: 61.382699 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: GGSGSGGWSH PQFEKGGGSG GGSGGSAWSH PQFEKSSGVD LGTENLYFQS NAMDNIDNKY NPQLCKIFLA ISDLIFFNLA LWFSLGCVY FIFDQVQRFI PQDQLDTRVI THFILSVVCV GWFWIRLRHY TYRKPFWYEL KEIFRTIVIF AIFDLALIAF T KWQFSRYV ...String: GGSGSGGWSH PQFEKGGGSG GGSGGSAWSH PQFEKSSGVD LGTENLYFQS NAMDNIDNKY NPQLCKIFLA ISDLIFFNLA LWFSLGCVY FIFDQVQRFI PQDQLDTRVI THFILSVVCV GWFWIRLRHY TYRKPFWYEL KEIFRTIVIF AIFDLALIAF T KWQFSRYV WVFCWTFALI LVPFFRALTK HLLNKLGIWK KKTIILGSGQ NARGAYSALQ SEEMMGFDVI AFFDTDASDA EI NMLPVIK DTEIIWDLNR TGDVHYILAY EYTELEKTHF WLRELSKHHC RSVTVVPSFR GLPLYNTDMS FIFSHEVMLL RIQ NNLAKR SSRFLKRTFD IVCSIMILII ASPLMIYLWY KVTRDGGPAI YGHQRVGRHG KLFPCYKFRS MVMNSQEVLK ELLA NDPIA RAEWEKDFKL KNDPRITAVG RFIRKTSLDE LPQLFNVLKG DMSLVGPRPI VSDELERYCD DVDYYLMAKP GMTGL WQVS GRNDVDYDTR VYFDSWYVKN WTLWNDIAIL FKTAKVVLRR DGAY UniProtKB: Undecaprenyl-phosphate galactose phosphotransferase |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2 mg/mL | |||||||||
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Buffer | pH: 8 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 | |||||||||
Vitrification | Cryogen name: ETHANE / 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 / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.75 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number real images: 4841 / Average electron dose: 50.13 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |