+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10100 | ||||||||||||
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Title | Legionella pneumophila SidJ-Human calmodulin complex | ||||||||||||
Map data | SidJ_Cam map | ||||||||||||
Sample |
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Function / homology | Function and homology information Ligases / negative regulation of calcium ion transmembrane transporter activity / negative regulation of calcium ion export across plasma membrane / positive regulation of ryanodine-sensitive calcium-release channel activity / regulation of cell communication by electrical coupling involved in cardiac conduction / negative regulation of peptidyl-threonine phosphorylation / protein phosphatase activator activity / positive regulation of cyclic-nucleotide phosphodiesterase activity / positive regulation of phosphoprotein phosphatase activity / ligase activity ...Ligases / negative regulation of calcium ion transmembrane transporter activity / negative regulation of calcium ion export across plasma membrane / positive regulation of ryanodine-sensitive calcium-release channel activity / regulation of cell communication by electrical coupling involved in cardiac conduction / negative regulation of peptidyl-threonine phosphorylation / protein phosphatase activator activity / positive regulation of cyclic-nucleotide phosphodiesterase activity / positive regulation of phosphoprotein phosphatase activity / ligase activity / adenylate cyclase binding / catalytic complex / detection of calcium ion / negative regulation of ryanodine-sensitive calcium-release channel activity / regulation of cardiac muscle contraction / calcium channel inhibitor activity / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / voltage-gated potassium channel complex / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / cysteine-type peptidase activity / regulation of calcium-mediated signaling / positive regulation of protein dephosphorylation / titin binding / positive regulation of protein autophosphorylation / sperm midpiece / calcium channel complex / substantia nigra development / adenylate cyclase activator activity / regulation of heart rate / protein serine/threonine kinase activator activity / sarcomere / positive regulation of peptidyl-threonine phosphorylation / regulation of cytokinesis / spindle microtubule / positive regulation of protein serine/threonine kinase activity / spindle pole / response to calcium ion / calcium-dependent protein binding / G2/M transition of mitotic cell cycle / myelin sheath / transferase activity / vesicle / transmembrane transporter binding / G protein-coupled receptor signaling pathway / nucleotide binding / centrosome / calcium ion binding / protein kinase binding / protein-containing complex / proteolysis / membrane / metal ion binding / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Legionella pneumophila (bacteria) / Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.15 Å | ||||||||||||
Authors | Pfleiderer MM / Galej WP / Adams M / Bhogaraju S | ||||||||||||
Funding support | Germany, 3 items
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Citation | Journal: Nature / Year: 2019 Title: Inhibition of bacterial ubiquitin ligases by SidJ-calmodulin catalysed glutamylation. Authors: Sagar Bhogaraju / Florian Bonn / Rukmini Mukherjee / Michael Adams / Moritz M Pfleiderer / Wojciech P Galej / Vigor Matkovic / Jaime Lopez-Mosqueda / Sissy Kalayil / Donghyuk Shin / Ivan Dikic / Abstract: The family of bacterial SidE enzymes catalyses phosphoribosyl-linked serine ubiquitination and promotes infectivity of Legionella pneumophila, a pathogenic bacteria that causes Legionnaires' disease. ...The family of bacterial SidE enzymes catalyses phosphoribosyl-linked serine ubiquitination and promotes infectivity of Legionella pneumophila, a pathogenic bacteria that causes Legionnaires' disease. SidE enzymes share the genetic locus with the Legionella effector SidJ that spatiotemporally opposes the toxicity of these enzymes in yeast and mammalian cells, through a mechanism that is currently unknown. Deletion of SidJ leads to a substantial defect in the growth of Legionella in both its natural hosts (amoebae) and in mouse macrophages. Here we demonstrate that SidJ is a glutamylase that modifies the catalytic glutamate in the mono-ADP ribosyl transferase domain of the SdeA, thus blocking the ubiquitin ligase activity of SdeA. The glutamylation activity of SidJ requires interaction with the eukaryotic-specific co-factor calmodulin, and can be regulated by intracellular changes in Ca concentrations. The cryo-electron microscopy structure of SidJ in complex with human apo-calmodulin revealed the architecture of this heterodimeric glutamylase. We show that, in cells infected with L. pneumophila, SidJ mediates the glutamylation of SidE enzymes on the surface of vacuoles that contain Legionella. We used quantitative proteomics to uncover multiple host proteins as putative targets of SidJ-mediated glutamylation. Our study reveals the mechanism by which SidE ligases are inhibited by a SidJ-calmodulin glutamylase, and opens avenues for exploring an understudied protein modification (glutamylation) in eukaryotes. | ||||||||||||
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_10100.map.gz | 11.9 MB | EMDB map data format | |
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Header (meta data) | emd-10100-v30.xml emd-10100.xml | 18.7 KB 18.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10100_fsc.xml | 5.8 KB | Display | FSC data file |
Images | emd_10100.png | 28.3 KB | ||
Others | emd_10100_half_map_1.map.gz emd_10100_half_map_2.map.gz | 11.9 MB 11.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10100 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10100 | HTTPS FTP |
-Related structure data
Related structure data | 6s5tMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_10100.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | SidJ_Cam map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.96 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: #2
File | emd_10100_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_10100_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Legionella pneumophila SidJ - human calmodulin complex
Entire | Name: Legionella pneumophila SidJ - human calmodulin complex |
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Components |
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-Supramolecule #1: Legionella pneumophila SidJ - human calmodulin complex
Supramolecule | Name: Legionella pneumophila SidJ - human calmodulin complex type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Molecular weight | Theoretical: 120 KDa |
-Supramolecule #2: SidJ
Supramolecule | Name: SidJ / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Legionella pneumophila (bacteria) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Supramolecule #3: calmodulin
Supramolecule | Name: calmodulin / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Macromolecule #1: SidJ
Macromolecule | Name: SidJ / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Legionella pneumophila (bacteria) |
Molecular weight | Theoretical: 100.338469 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MFGFIKKVLD FFGVDQSEDN PSETAVETTD VSTKIKTTDT TQEESSVKTK TVVPTQPGGS VKPETIAPDQ QKKHQIKTET TTSTTKQKG PKVTLMDGHV KQYYFARRGE TSTHDTSLPP PVKVLSGRSI PLKEIPFEAT RNELVQIYLT SIDKLIKSNK L NSIPSQQI ...String: MFGFIKKVLD FFGVDQSEDN PSETAVETTD VSTKIKTTDT TQEESSVKTK TVVPTQPGGS VKPETIAPDQ QKKHQIKTET TTSTTKQKG PKVTLMDGHV KQYYFARRGE TSTHDTSLPP PVKVLSGRSI PLKEIPFEAT RNELVQIYLT SIDKLIKSNK L NSIPSQQI ASHYLFLRSL ANSETDGIKK NQILSLAKPL GTYLASKEPH VWKMINELIE KSEYPIIHYL KNNRAHSNFM LA LIHEYHK EPLTKNQSAF VQKFRDSSVF LFPNPIYTAW LAHSYDEDSS FNPMFRERLS TNFYHSTLTD NLLLRTEPKE VTL SSEHHY KKEKGPIDSS FRYQMSSDRL LRIQGRTLLF STPQNDVVAV KVQKKGEPKS TLEEEFEMAD YLLKHQRRLD VHSK LPQPL GQYSVKKSEI LEISRGSLDF ERFKTLIDDS KDLEVYVYKA PQSYFTYLHD KNQDLEDLTA SVKTNVHDLF VLLRE GIVF PQLADIFHTH FGEDEREDKG RYQALVQLLN VLQFQLGRID KWQKAVEYVN LRSSGLADLG DSLPITSLFT SSDFTK HYF SELLTGGYHP TFFDKSSGTA NSLFTGKRRL FGNYLYLNTI AEYLLVIQLT LGSYGDKVTR DMMDKPKKEA VWRELAN VM FTSCAEAIHI MTGIPQSRAL TLLKQRANIE KHFRQTQFWM TPDYSKLDED TLQMEQYSIY SGEPEYEFTD KLVSGVGL S VDGVHQDLGG YNRESPLREL EKLLYATVTL IEGTMQLDKE FFKQLEQVEK ILSGEIKTDA NSCFEAVAQL LDLARPGCH FQKRLVLSYY EEAKLKYPSA PTDAYDSRFQ VVARTNAAIT IQRFWREARK NLSEKSDIDS EKPESERTTD KRL |
-Macromolecule #2: Calmodulin-2
Macromolecule | Name: Calmodulin-2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 16.852545 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MADQLTEEQI AEFKEAFSLF DKDGDGTITT KELGTVMRSL GQNPTEAELQ DMINEVDADG NGTIDFPEFL TMMARKMKDT DSEEEIREA FRVFDKDGNG YISAAELRHV MTNLGEKLTD EEVDEMIREA DIDGDGQVNY EEFVQMMTAK |
-Macromolecule #3: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Macromolecule | Name: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 3 / Number of copies: 1 / Formula: ANP |
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Molecular weight | Theoretical: 506.196 Da |
Chemical component information | ChemComp-ANP: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
Details | Recombinant Legionella pneumophila SidJ -human calmodulin complex |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 40.0 e/Å2 |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |