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- EMDB-33310: Cryo-EM structure of CopC-CaM-caspase-3 with NAD+ -

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Basic information

Entry
Database: EMDB / ID: EMD-33310
TitleCryo-EM structure of CopC-CaM-caspase-3 with NAD+
Map data
Sample
  • Complex: Cryo-EM structure of CopC-CaM-caspase-3 with NAD+
    • Protein or peptide: Caspase-3
    • Protein or peptide: Arginine ADP-riboxanase CopC
    • Protein or peptide: Calmodulin-1
  • Ligand: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
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 / phospholipase A2 activator activity / Stimulation of the cell death response by PAK-2p34 / 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 / phospholipase A2 activator activity / Stimulation of the cell death response by PAK-2p34 / 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 / cyclin-dependent protein serine/threonine kinase inhibitor activity / death-inducing signaling complex / 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 / Signaling by Hippo / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / axonal fasciculation / regulation of synaptic vesicle cycle / death receptor binding / fibroblast apoptotic process / CaM pathway / epithelial cell apoptotic process / Cam-PDE 1 activation / Sodium/Calcium exchangers / platelet formation / Calmodulin induced events / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Other interleukin signaling / response to anesthetic / Loss of phosphorylation of MECP2 at T308 / execution phase of apoptosis / CREB1 phosphorylation through the activation of Adenylate Cyclase / negative regulation of cytokine production / CaMK IV-mediated phosphorylation of CREB / PKA activation / negative regulation of high voltage-gated calcium channel activity / positive regulation of amyloid-beta formation / Glycogen breakdown (glycogenolysis) / CLEC7A (Dectin-1) induces NFAT activation / Activation of RAC1 downstream of NMDARs / negative regulation of ryanodine-sensitive calcium-release channel activity / organelle localization by membrane tethering / Apoptotic cleavage of cellular proteins / negative regulation of B cell proliferation / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / negative regulation of calcium ion export across plasma membrane / regulation of cardiac muscle cell action potential / pyroptotic inflammatory response / presynaptic endocytosis / neurotrophin TRK receptor signaling pathway / negative regulation of activated T cell proliferation / Synthesis of IP3 and IP4 in the cytosol / regulation of cell communication by electrical coupling involved in cardiac conduction / Phase 0 - rapid depolarisation / calcineurin-mediated signaling / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / response to tumor necrosis factor / negative regulation of cell cycle / RHO GTPases activate PAKs / T cell homeostasis / B cell homeostasis / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / regulation of ryanodine-sensitive calcium-release channel activity / protein phosphatase activator activity / Long-term potentiation / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / DARPP-32 events / catalytic complex / Smooth Muscle Contraction / cell fate commitment / detection of calcium ion / Pyroptosis / regulation of macroautophagy / Caspase-mediated cleavage of cytoskeletal proteins / response to X-ray / regulation of cardiac muscle contraction / response to amino acid / response to glucose / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / response to UV / cellular response to interferon-beta / Protein methylation / calcium channel inhibitor activity / Activation of AMPK downstream of NMDARs
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: 3.35 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-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33310.png

Downloads & links

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Map

FileDownload / File: emd_33310.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
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 9.0
Minimum - Maximum-37.665190000000003 - 58.040819999999997
Average (Standard dev.)0.000000000002802 (±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_33310_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_33310_half_map_2.map
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Sample components

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Entire : Cryo-EM structure of CopC-CaM-caspase-3 with NAD+

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

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Supramolecule #1: Cryo-EM structure of CopC-CaM-caspase-3 with NAD+

SupramoleculeName: Cryo-EM structure of CopC-CaM-caspase-3 with NAD+ / 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: 31.651938 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 TAPGYYSWRN SKDGSWFIQS LCAMLKQYAD KLEFMHILTR VN RKVATEF 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)
Strain: ATCC 12472 / DSM 30191 / JCM 1249 / NBRC 12614 / NCIMB 9131 / NCTC 9757
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-ADENINE-DINUCLEOTIDE

MacromoleculeName: NICOTINAMIDE-ADENINE-DINUCLEOTIDE / type: ligand / ID: 4 / Number of copies: 1 / Formula: NAD
Molecular weightTheoretical: 663.425 Da
Chemical component information

ChemComp-NAD:
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD*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: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 102210
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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