+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33310 | |||||||||
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Title | Cryo-EM structure of CopC-CaM-caspase-3 with NAD+ | |||||||||
Map data | ||||||||||
Sample |
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Keywords | type III secretion system / Chromobacterium violaceum / caspase-3 / new PTM / programmed cell deathA / DP-ribosylation / ADPR-deacylization / TOXIN | |||||||||
Function / homology | Function and homology information Lyases; Carbon-nitrogen lyases; Other carbon-nitrogen lyases / ADP-riboxanase activity / symbiont-mediated perturbation of host programmed cell death / caspase-3 / Stimulation of the cell death response by PAK-2p34 / phospholipase A2 activator activity / anterior neural tube closure / intrinsic apoptotic signaling pathway in response to osmotic stress / leukocyte apoptotic process / positive regulation of pyroptotic inflammatory response ...Lyases; Carbon-nitrogen lyases; Other carbon-nitrogen lyases / ADP-riboxanase activity / symbiont-mediated perturbation of host programmed cell death / caspase-3 / Stimulation of the cell death response by PAK-2p34 / phospholipase A2 activator activity / anterior neural tube closure / intrinsic apoptotic signaling pathway in response to osmotic stress / leukocyte apoptotic process / positive regulation of pyroptotic inflammatory response / glial cell apoptotic process / NADE modulates death signalling / luteolysis / response to cobalt ion / cysteine-type endopeptidase activity involved in apoptotic signaling pathway / death-inducing signaling complex / cyclin-dependent protein serine/threonine kinase inhibitor activity / cellular response to staurosporine / Apoptosis induced DNA fragmentation / cysteine-type endopeptidase activity involved in execution phase of apoptosis / Caspase activation via Dependence Receptors in the absence of ligand / Apoptotic cleavage of cell adhesion proteins / death receptor binding / SMAC, XIAP-regulated apoptotic response / Activation of caspases through apoptosome-mediated cleavage / axonal fasciculation / Signaling by Hippo / cysteine-type endopeptidase activity involved in apoptotic process / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / fibroblast apoptotic process / execution phase of apoptosis / Reduction of cytosolic Ca++ levels / negative regulation of cytokine production / epithelial cell apoptotic process / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Activation of Ca-permeable Kainate Receptor / Loss of phosphorylation of MECP2 at T308 / platelet formation / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / negative regulation of high voltage-gated calcium channel activity / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / positive regulation of cyclic-nucleotide phosphodiesterase activity / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / CLEC7A (Dectin-1) induces NFAT activation / Other interleukin signaling / regulation of cardiac muscle cell action potential / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / positive regulation of amyloid-beta formation / Activation of RAC1 downstream of NMDARs / positive regulation of ryanodine-sensitive calcium-release channel activity / regulation of cell communication by electrical coupling involved in cardiac conduction / Negative regulation of NMDA receptor-mediated neuronal transmission / negative regulation of peptidyl-threonine phosphorylation / Synthesis of IP3 and IP4 in the cytosol / Apoptotic cleavage of cellular proteins / Unblocking of NMDA receptors, glutamate binding and activation / pyroptotic inflammatory response / negative regulation of B cell proliferation / Phase 0 - rapid depolarisation / T cell homeostasis / protein phosphatase activator activity / negative regulation of activated T cell proliferation / RHO GTPases activate PAKs / positive regulation of phosphoprotein phosphatase activity / Ion transport by P-type ATPases / B cell homeostasis / Long-term potentiation / neurotrophin TRK receptor signaling pathway / Uptake and function of anthrax toxins / protein maturation / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / negative regulation of cell cycle / catalytic complex / DARPP-32 events / response to X-ray / detection of calcium ion / regulation of cardiac muscle contraction / negative regulation of ryanodine-sensitive calcium-release channel activity / Smooth Muscle Contraction / calcium channel inhibitor activity / Caspase-mediated cleavage of cytoskeletal proteins / RHO GTPases activate IQGAPs / cellular response to interferon-beta / response to amino acid / cell fate commitment / regulation of macroautophagy / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / response to tumor necrosis factor / Pyroptosis / Protein methylation Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Chromobacterium violaceum (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.35 Å | |||||||||
Authors | Zhang K / Peng T / Tao XY / Tian M / Li YX / Wang Z / Ma SF / Hu SF / Pan X / Xue J ...Zhang K / Peng T / Tao XY / Tian M / Li YX / Wang Z / Ma SF / Hu SF / Pan X / Xue J / Luo JW / Wu QL / Fu Y / Li S | |||||||||
Funding support | 1 items
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Citation | Journal: Mol Cell / Year: 2022 Title: Structural insights into caspase ADPR deacylization catalyzed by a bacterial effector and host calmodulin. Authors: Kuo Zhang / Ting Peng / Xinyuan Tao / Miao Tian / Yanxin Li / Zhao Wang / Shuaifei Ma / Shufan Hu / Xing Pan / Juan Xue / Jiwei Luo / Qiulan Wu / Yang Fu / Shan Li / Abstract: Programmed cell death and caspase proteins play a pivotal role in host innate immune response combating pathogen infections. Blocking cell death is employed by many bacterial pathogens as a universal ...Programmed cell death and caspase proteins play a pivotal role in host innate immune response combating pathogen infections. Blocking cell death is employed by many bacterial pathogens as a universal virulence strategy. CopC family type III effectors, including CopC from an environmental pathogen Chromobacterium violaceum, utilize calmodulin (CaM) as a co-factor to inactivate caspases by arginine ADPR deacylization. However, the molecular basis of the catalytic and substrate/co-factor binding mechanism is unknown. Here, we determine successive cryo-EM structures of CaM-CopC-caspase-3 ternary complex in pre-reaction, transition, and post-reaction states, which elucidate a multistep enzymatic mechanism of CopC-catalyzed ADPR deacylization. Moreover, we capture a snapshot of the detachment of modified caspase-3 from CopC. These structural insights are validated by mutagenesis analyses of CopC-mediated ADPR deacylization in vitro and animal infection in vivo. Our study offers a structural framework for understanding the molecular basis of arginine ADPR deacylization catalyzed by the CopC family. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33310.map.gz | 167.6 MB | EMDB map data format | |
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Header (meta data) | emd-33310-v30.xml emd-33310.xml | 17.1 KB 17.1 KB | Display Display | EMDB header |
Images | emd_33310.png | 173.7 KB | ||
Filedesc metadata | emd-33310.cif.gz | 6.1 KB | ||
Others | emd_33310_half_map_1.map.gz emd_33310_half_map_2.map.gz | 165.1 MB 165.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33310 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33310 | HTTPS FTP |
-Validation report
Summary document | emd_33310_validation.pdf.gz | 918 KB | Display | EMDB validaton report |
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Full document | emd_33310_full_validation.pdf.gz | 917.6 KB | Display | |
Data in XML | emd_33310_validation.xml.gz | 15.4 KB | Display | |
Data in CIF | emd_33310_validation.cif.gz | 18.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33310 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33310 | HTTPS FTP |
-Related structure data
Related structure data | 7xn4MC 7xn5C 7xn6C 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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Related items in Molecule of the Month |
-Map
File | Download / File: emd_33310.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.842 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_33310_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_33310_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Cryo-EM structure of CopC-CaM-caspase-3 with NAD+
Entire | Name: Cryo-EM structure of CopC-CaM-caspase-3 with NAD+ |
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Components |
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-Supramolecule #1: Cryo-EM structure of CopC-CaM-caspase-3 with NAD+
Supramolecule | Name: Cryo-EM structure of CopC-CaM-caspase-3 with NAD+ / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Caspase-3
Macromolecule | Name: Caspase-3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: caspase-3 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 31.651938 KDa |
Recombinant expression | Organism: Bacteria Latreille et al. 1825 (Bacteria stick insect) |
Sequence | String: MENTENSVDS KSIKNLEPKI IHGSESMDSG ISLDNSYKMD YPEMGLCIII NNKNFHKSTG MTSRSGTDVD AANLRETFRN LKYEVRNKN DLTREEIVEL MRDVSKEDHS KRSSFVCVLL SHGEEGIIFG TNGPVDLKKI TNFFRGDRCR SLTGKPKLFI I QACRGTEL ...String: MENTENSVDS KSIKNLEPKI IHGSESMDSG ISLDNSYKMD YPEMGLCIII NNKNFHKSTG MTSRSGTDVD AANLRETFRN LKYEVRNKN DLTREEIVEL MRDVSKEDHS KRSSFVCVLL SHGEEGIIFG TNGPVDLKKI TNFFRGDRCR SLTGKPKLFI I QACRGTEL DCGIETDSGV DDDMACHKIP VEADFLYAYS TAPGYYSWRN SKDGSWFIQS LCAMLKQYAD KLEFMHILTR VN RKVATEF ESFSFDATFH AKKQIPCIVS MLTKELYFYH UniProtKB: Caspase-3 |
-Macromolecule #2: Arginine ADP-riboxanase CopC
Macromolecule | Name: Arginine ADP-riboxanase CopC / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO EC number: Lyases; Carbon-nitrogen lyases; Other carbon-nitrogen lyases |
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Source (natural) | Organism: Chromobacterium violaceum (bacteria) Strain: ATCC 12472 / DSM 30191 / JCM 1249 / NBRC 12614 / NCIMB 9131 / NCTC 9757 |
Molecular weight | Theoretical: 52.985516 KDa |
Recombinant expression | Organism: Bacteria Latreille et al. 1825 (Bacteria stick insect) |
Sequence | String: MRVENHSPSL SKLNPPEAGS GDPTAIGRRL SGIRRAPLPH VSAGSDGEAA AAGKIGAFLR KAVAAQSYGL MFANGKLFEA TGDALEKRG QYGFSALQRL DGLSRRNLAA VEARLGALDS AERGLKERIM TGAWHFRHQS NAALDDGKTA AIASNHLLAR E SRSSGGNT ...String: MRVENHSPSL SKLNPPEAGS GDPTAIGRRL SGIRRAPLPH VSAGSDGEAA AAGKIGAFLR KAVAAQSYGL MFANGKLFEA TGDALEKRG QYGFSALQRL DGLSRRNLAA VEARLGALDS AERGLKERIM TGAWHFRHQS NAALDDGKTA AIASNHLLAR E SRSSGGNT FAGDKALLSN HDFVFFGVEF SGRGKQDKPL NHKHSTMDFG ANAYVVPDTL PACRHGYLTL TDHFFNRVPG GR EAEHQDF VGSFPQMGAE TGRWIHEGKY RQNAPIFNYR DMKAAVALHL IEFLRDSKDA AFKAYVFDQA MQSGQALDRV LNS VFQAEF HIPRLMATTD YAKHPLRPML LKEAVDSVNL PALSGLVSSK GDAVTAMWHA IDKGKDAVAA HLLGNWRFEA GDFA SAPPG FYHELNYALS EHGASVYILD QFLSRGWAAV NAPFEHVNSG ETMLDNAVKY GNREMAAALI KHGADRNLLS EWNGG KLDA LLA UniProtKB: Arginine ADP-riboxanase CopC |
-Macromolecule #3: Calmodulin-1
Macromolecule | Name: Calmodulin-1 / type: protein_or_peptide / ID: 3 / 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: Bacteria Latreille et al. 1825 (Bacteria stick insect) |
Sequence | String: MADQLTEEQI AEFKEAFSLF DKDGDGTITT KELGTVMRSL GQNPTEAELQ DMINEVDADG NGTIDFPEFL TMMARKMKDT DSEEEIREA FRVFDKDGNG YISAAELRHV MTNLGEKLTD EEVDEMIREA DIDGDGQVNY EEFVQMMTAK UniProtKB: Calmodulin-1 |
-Macromolecule #4: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Macromolecule | Name: NICOTINAMIDE-ADENINE-DINUCLEOTIDE / type: ligand / ID: 4 / Number of copies: 1 / Formula: NAD |
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Molecular weight | Theoretical: 663.425 Da |
Chemical component information | ChemComp-NAD: |
-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 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 102210 |
Initial angle assignment | Type: OTHER |
Final angle assignment | Type: OTHER |