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- EMDB-33312: Cryo-EM structure of CopC-CaM-caspase-3 with ADPR-deacylization -

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Basic information

Entry
Database: EMDB / ID: EMD-33312
TitleCryo-EM structure of CopC-CaM-caspase-3 with ADPR-deacylization
Map data
Sample
  • Complex: Cryo-EM structure of CopC-CaM-caspase-3 with ADPR-deacylization
    • Protein or peptide: Caspase-3
    • Protein or peptide: Arginine ADP-riboxanase CopC
    • Protein or peptide: Calmodulin-1
  • Ligand: NICOTINAMIDE
Keywordstype 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 / cellular response to staurosporine / death-inducing signaling complex / cyclin-dependent protein serine/threonine kinase inhibitor activity / response to anesthetic / Apoptosis induced DNA fragmentation / Apoptotic cleavage of cell adhesion proteins / Caspase activation via Dependence Receptors in the absence of ligand / SMAC, XIAP-regulated apoptotic response / Activation of caspases through apoptosome-mediated cleavage / death receptor binding / Signaling by Hippo / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / axonal fasciculation / regulation of synaptic vesicle cycle / CaM pathway / Cam-PDE 1 activation / fibroblast apoptotic process / Sodium/Calcium exchangers / Calmodulin induced events / epithelial cell apoptotic process / Other interleukin signaling / Reduction of cytosolic Ca++ levels / platelet formation / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / negative regulation of cytokine production / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / CaMK IV-mediated phosphorylation of CREB / negative regulation of high voltage-gated calcium channel activity / positive regulation of amyloid-beta formation / Glycogen breakdown (glycogenolysis) / execution phase of apoptosis / CLEC7A (Dectin-1) induces NFAT activation / Activation of RAC1 downstream of NMDARs / negative regulation of calcium ion export across plasma membrane / organelle localization by membrane tethering / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / negative regulation of B cell proliferation / presynaptic endocytosis / Apoptotic cleavage of cellular proteins / regulation of cardiac muscle cell action potential / positive regulation of ryanodine-sensitive calcium-release channel activity / pyroptotic inflammatory response / Synthesis of IP3 and IP4 in the cytosol / regulation of cell communication by electrical coupling involved in cardiac conduction / Phase 0 - rapid depolarisation / negative regulation of activated T cell proliferation / Negative regulation of NMDA receptor-mediated neuronal transmission / negative regulation of ryanodine-sensitive calcium-release channel activity / Unblocking of NMDA receptors, glutamate binding and activation / RHO GTPases activate PAKs / calcineurin-mediated signaling / T cell homeostasis / neurotrophin TRK receptor signaling pathway / Ion transport by P-type ATPases / B cell homeostasis / Uptake and function of anthrax toxins / Long-term potentiation / negative regulation of cell cycle / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / protein phosphatase activator activity / response to tumor necrosis factor / regulation of ryanodine-sensitive calcium-release channel activity / DARPP-32 events / Smooth Muscle Contraction / catalytic complex / cell fate commitment / response to amino acid / response to X-ray / detection of calcium ion / Pyroptosis / regulation of macroautophagy / regulation of cardiac muscle contraction / Caspase-mediated cleavage of cytoskeletal proteins / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / presynaptic cytosol / calcium channel inhibitor activity / response to glucose / cellular response to interferon-beta / Protein methylation
Similarity search - Function
Arginine ADP-riboxanase OspC1-3 / Shigella flexneri OspC protein / Ankyrin repeat / Peptidase C14 family / Peptidase family C14A, His active site / Caspase family histidine active site. / Peptidase C14, caspase non-catalytic subunit p10 / Peptidase family C14A, cysteine active site / Caspase family cysteine active site. / Caspase family p10 domain profile. ...Arginine ADP-riboxanase OspC1-3 / Shigella flexneri OspC protein / Ankyrin repeat / Peptidase C14 family / Peptidase family C14A, His active site / Caspase family histidine active site. / Peptidase C14, caspase non-catalytic subunit p10 / Peptidase family C14A, cysteine active site / Caspase family cysteine active site. / Caspase family p10 domain profile. / Peptidase C14A, caspase catalytic domain / Caspase, interleukin-1 beta converting enzyme (ICE) homologues / Peptidase C14, p20 domain / Caspase family p20 domain profile. / : / Caspase domain / Caspase-like domain superfamily / : / EF-hand domain pair / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / Ankyrin repeat / EF-hand, calcium binding motif / Ankyrin repeat-containing domain superfamily / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
Calmodulin-1 / Caspase-3 / Arginine ADP-riboxanase CopC
Similarity search - Component
Biological speciesHomo sapiens (human) / Chromobacterium violaceum (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.45 Å
AuthorsZhang 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 support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: 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
DepositionApr 28, 2022-
Header (metadata) releaseDec 14, 2022-
Map releaseDec 14, 2022-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33312.png

Downloads & links

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Map

FileDownload / File: emd_33312.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesX (Sec.)Y (Row.)Z (Col.)
0.84 Å/pix.
x 360 pix.
= 303.12 Å		0.84 Å/pix.
x 360 pix.
= 303.12 Å		0.84 Å/pix.
x 360 pix.
= 303.12 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.842 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 9.0
Minimum - Maximum-35.045765000000003 - 62.418640000000003
Average (Standard dev.)-0.000000000005149 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 303.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_33312_half_map_1.map
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Half map: #1

Fileemd_33312_half_map_2.map
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Sample components

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Entire : Cryo-EM structure of CopC-CaM-caspase-3 with ADPR-deacylization

EntireName: Cryo-EM structure of CopC-CaM-caspase-3 with ADPR-deacylization
Components
  • Complex: Cryo-EM structure of CopC-CaM-caspase-3 with ADPR-deacylization
    • Protein or peptide: Caspase-3
    • Protein or peptide: Arginine ADP-riboxanase CopC
    • Protein or peptide: Calmodulin-1
  • Ligand: NICOTINAMIDE

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Supramolecule #1: Cryo-EM structure of CopC-CaM-caspase-3 with ADPR-deacylization

SupramoleculeName: Cryo-EM structure of CopC-CaM-caspase-3 with ADPR-deacylization
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Caspase-3

MacromoleculeName: Caspase-3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: caspase-3
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 32.175195 KDa
Recombinant expressionOrganism: Bacteria Latreille et al. 1825 (Bacteria stick insect)
SequenceString: 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 TAPGYYSW(A1LTQ)N SKDGSWFIQS LCAMLKQYAD KLEFMH ILT RVNRKVATEF ESFSFDATFH AKKQIPCIVS MLTKELYFYH

UniProtKB: Caspase-3

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Macromolecule #2: Arginine ADP-riboxanase CopC

MacromoleculeName: 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
Source (natural)Organism: Chromobacterium violaceum (bacteria)
Molecular weightTheoretical: 52.985516 KDa
Recombinant expressionOrganism: Bacteria Latreille et al. 1825 (Bacteria stick insect)
SequenceString: 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

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Macromolecule #3: Calmodulin-1

MacromoleculeName: Calmodulin-1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.852545 KDa
Recombinant expressionOrganism: Bacteria Latreille et al. 1825 (Bacteria stick insect)
SequenceString:
MADQLTEEQI AEFKEAFSLF DKDGDGTITT KELGTVMRSL GQNPTEAELQ DMINEVDADG NGTIDFPEFL TMMARKMKDT DSEEEIREA FRVFDKDGNG YISAAELRHV MTNLGEKLTD EEVDEMIREA DIDGDGQVNY EEFVQMMTAK

UniProtKB: Calmodulin-1

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Macromolecule #4: NICOTINAMIDE

MacromoleculeName: NICOTINAMIDE / type: ligand / ID: 4 / Number of copies: 1 / Formula: NCA
Molecular weightTheoretical: 122.125 Da
Chemical component information

ChemComp-NCA:
NICOTINAMIDE / medication*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 82876
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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