+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10850 | ||||||||||||
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Title | Inducible lysine decarboxylase LdcI stacks, pH 5.7 | ||||||||||||
Map data | LdcI stack, post-processed map. | ||||||||||||
Sample |
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Function / homology | Function and homology information lysine decarboxylase / lysine catabolic process / lysine decarboxylase activity / guanosine tetraphosphate binding / identical protein binding / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Escherichia coli K-12 (bacteria) / Escherichia coli (strain K12) (bacteria) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.28 Å | ||||||||||||
Authors | Felix J / Jessop M / Desfosses A / Effantin G / Gutsche I | ||||||||||||
Funding support | 3 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2021 Title: Supramolecular assembly of the LdcI upon acid stress. Authors: Matthew Jessop / Clarissa Liesche / Jan Felix / Ambroise Desfosses / Megghane Baulard / Virgile Adam / Angélique Fraudeau / Karine Huard / Grégory Effantin / Jean-Philippe Kleman / Maria ...Authors: Matthew Jessop / Clarissa Liesche / Jan Felix / Ambroise Desfosses / Megghane Baulard / Virgile Adam / Angélique Fraudeau / Karine Huard / Grégory Effantin / Jean-Philippe Kleman / Maria Bacia-Verloop / Dominique Bourgeois / Irina Gutsche / Abstract: Pathogenic and commensal bacteria often have to resist the harsh acidity of the host stomach. The inducible lysine decarboxylase LdcI buffers the cytosol and the local extracellular environment to ...Pathogenic and commensal bacteria often have to resist the harsh acidity of the host stomach. The inducible lysine decarboxylase LdcI buffers the cytosol and the local extracellular environment to ensure enterobacterial survival at low pH. Here, we investigate the acid stress-response regulation of LdcI by combining biochemical and biophysical characterization with negative stain and cryoelectron microscopy (cryo-EM) and wide-field and superresolution fluorescence imaging. Due to deleterious effects of fluorescent protein fusions on native LdcI decamers, we opt for three-dimensional localization of nanobody-labeled endogenous wild-type LdcI in acid-stressed cells and show that it organizes into distinct patches at the cell periphery. Consistent with recent hypotheses that in vivo clustering of metabolic enzymes often reflects their polymerization as a means of stimulus-induced regulation, we show that LdcI assembles into filaments in vitro at physiologically relevant low pH. We solve the structures of these filaments and of the LdcI decamer formed at neutral pH by cryo-EM and reveal the molecular determinants of LdcI polymerization, confirmed by mutational analysis. Finally, we propose a model for LdcI function inside the enterobacterial cell, providing a structural and mechanistic basis for further investigation of the role of its supramolecular organization in the acid stress response. | ||||||||||||
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_10850.map.gz | 118.2 MB | EMDB map data format | |
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Header (meta data) | emd-10850-v30.xml emd-10850.xml | 18.6 KB 18.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10850_fsc.xml | 12.6 KB | Display | FSC data file |
Images | emd_10850.png | 213.7 KB | ||
Masks | emd_10850_msk_1.map | 125 MB | Mask map | |
Others | emd_10850_half_map_1.map.gz emd_10850_half_map_2.map.gz | 116 MB 116 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10850 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10850 | HTTPS FTP |
-Validation report
Summary document | emd_10850_validation.pdf.gz | 609.4 KB | Display | EMDB validaton report |
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Full document | emd_10850_full_validation.pdf.gz | 608.5 KB | Display | |
Data in XML | emd_10850_validation.xml.gz | 17.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10850 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10850 | HTTPS FTP |
-Related structure data
Related structure data | 6yn6MC 6yn5C 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_10850.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | LdcI stack, post-processed map. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.052 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_10850_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: LdcI stack, half map 2.
File | emd_10850_half_map_1.map | ||||||||||||
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Annotation | LdcI stack, half map 2. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: LdcI stack, half map 1.
File | emd_10850_half_map_2.map | ||||||||||||
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Annotation | LdcI stack, half map 1. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : E. coli inducible lysine decarboxylase at pH 5.7
Entire | Name: E. coli inducible lysine decarboxylase at pH 5.7 |
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Components |
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-Supramolecule #1: E. coli inducible lysine decarboxylase at pH 5.7
Supramolecule | Name: E. coli inducible lysine decarboxylase at pH 5.7 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Escherichia coli K-12 (bacteria) |
Recombinant expression | Organism: Escherichia coli str. K-12 substr. MG1655 (bacteria) |
-Macromolecule #1: Inducible lysine decarboxylase
Macromolecule | Name: Inducible lysine decarboxylase / type: protein_or_peptide / ID: 1 / Number of copies: 20 / Enantiomer: LEVO / EC number: lysine decarboxylase |
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Source (natural) | Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12 |
Molecular weight | Theoretical: 81.11057 KDa |
Recombinant expression | Organism: Escherichia coli str. K-12 substr. MG1655 (bacteria) |
Sequence | String: MNVIAILNHM GVYFKEEPIR ELHRALERLN FQIVYPNDRD DLLKLIENNA RLCGVIFDWD KYNLELCEEI SKMNENLPLY AFANTYSTL DVSLNDLRLQ ISFFEYALGA AEDIANKIKQ TTDEYINTIL PPLTKALFKY VREGKYTFCT PGHMGGTAFQ K SPVGSLFY ...String: MNVIAILNHM GVYFKEEPIR ELHRALERLN FQIVYPNDRD DLLKLIENNA RLCGVIFDWD KYNLELCEEI SKMNENLPLY AFANTYSTL DVSLNDLRLQ ISFFEYALGA AEDIANKIKQ TTDEYINTIL PPLTKALFKY VREGKYTFCT PGHMGGTAFQ K SPVGSLFY DFFGPNTMKS DISISVSELG SLLDHSGPHK EAEQYIARVF NADRSYMVTN GTSTANKIVG MYSAPAGSTI LI DRNCHKS LTHLMMMSDV TPIYFRPTRN AYGILGGIPQ SEFQHATIAK RVKETPNATW PVHAVITNST YDGLLYNTDF IKK TLDVKS IHFDSAWVPY TNFSPIYEGK CGMSGGRVEG KVIYETQSTH (LLP)LLAAFSQAS MIHVKGDVNE ETFNEAYMMH TTTSPHYGI VASTETAAAM MKGNAGKRLI NGSIERAIKF RKEIKRLRTE SDGWFFDVWQ PDHIDTTECW PLRSDSTWHG F KNIDNEHM YLDPIKVTLL TPGMEKDGTM SDFGIPASIV AKYLDEHGIV VEKTGPYNLL FLFSIGIDKT KALSLLRALT DF KRAFDLN LRVKNMLPSL YREDPEFYEN MRIQELAQNI HKLIVHHNLP DLMYRAFEVL PTMVMTPYAA FQKELHGMTE EVY LDEMVG RINANMILPY PPGVPLVMPG EMITEESRPV LEFLQMLCEI GAHYPGFETD IHGAYRQADG RYTVKVLKE |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | filament |
-Sample preparation
Concentration | 0.25 mg/mL |
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Buffer | pH: 5.7 |
Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 2564 / Average exposure time: 6.0 sec. / Average electron dose: 29.3 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |