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- PDB-7wr4: Crystal structure of OspC3-calmodulin-caspase-4 complex -

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Basic information

Entry
Database: PDB / ID: 7wr4
TitleCrystal structure of OspC3-calmodulin-caspase-4 complex
Components
  • Calmodulin-1
  • Caspase-4
  • OspC3
KeywordsTRANSFERASE / ADP-riboxanase / effector
Function / homology
Function and homology information


symbiont-mediated suppression of host signal transduction pathway / symbiont-mediated suppression of host calcium-mediated signal transduction / caspase-4 / Lyases; Carbon-nitrogen lyases; Other carbon-nitrogen lyases / ADP-riboxanase activity / non-canonical inflammasome complex / positive regulation of interleukin-18-mediated signaling pathway / symbiont-mediated suppression of host programmed cell death / non-canonical inflammasome complex assembly / symbiont-mediated perturbation of host programmed cell death ...symbiont-mediated suppression of host signal transduction pathway / symbiont-mediated suppression of host calcium-mediated signal transduction / caspase-4 / Lyases; Carbon-nitrogen lyases; Other carbon-nitrogen lyases / ADP-riboxanase activity / non-canonical inflammasome complex / positive regulation of interleukin-18-mediated signaling pathway / symbiont-mediated suppression of host programmed cell death / non-canonical inflammasome complex assembly / symbiont-mediated perturbation of host programmed cell death / NLRP1 inflammasome complex / CARD domain binding / positive regulation of tumor necrosis factor-mediated signaling pathway / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / CaMK IV-mediated phosphorylation of CREB / PKA activation / negative regulation of high voltage-gated calcium channel activity / 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 / 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 / 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 / RHO GTPases activate PAKs / protein autoprocessing / 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 / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / DARPP-32 events / catalytic complex / Smooth Muscle Contraction / Pyroptosis / detection of calcium ion / regulation of cardiac muscle contraction / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / cellular response to interferon-beta / Protein methylation / calcium channel inhibitor activity / Activation of AMPK downstream of NMDARs / presynaptic cytosol / Ion homeostasis / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / eNOS activation / titin binding / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / sperm midpiece / regulation of calcium-mediated signaling / voltage-gated potassium channel complex / calcium channel complex / FCERI mediated Ca+2 mobilization / substantia nigra development / intrinsic apoptotic signaling pathway / Ras activation upon Ca2+ influx through NMDA receptor / regulation of heart rate / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / calyx of Held / adenylate cyclase activator activity / protein maturation / sarcomere / VEGFR2 mediated cell proliferation / protein serine/threonine kinase activator activity / VEGFR2 mediated vascular permeability / regulation of cytokinesis / spindle microtubule / calcium channel regulator activity / Translocation of SLC2A4 (GLUT4) to the plasma membrane / positive regulation of receptor signaling pathway via JAK-STAT / lipopolysaccharide binding / RAF activation / Transcriptional activation of mitochondrial biogenesis / NOD1/2 Signaling Pathway / response to calcium ion / cellular response to type II interferon / Stimuli-sensing channels
Similarity search - Function
Arginine ADP-riboxanase OspC1-3 / Shigella flexneri OspC protein / Caspase recruitment domain / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Rossmann fold - #1460 / Peptidase C14 family / Peptidase family C14A, His active site / Caspase family histidine active site. ...Arginine ADP-riboxanase OspC1-3 / Shigella flexneri OspC protein / Caspase recruitment domain / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Rossmann fold - #1460 / 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 / : / Death-like domain superfamily / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Calmodulin-1 / Caspase-4 / Arginine ADP-riboxanase OspC3
Similarity search - Component
Biological speciesShigella flexneri (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsHou, Y.J. / Zeng, H. / Shao, F. / Ding, J.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2023
Title: Structural mechanisms of calmodulin activation of Shigella effector OspC3 to ADP-riboxanate caspase-4/11 and block pyroptosis.
Authors: Hou, Y. / Zeng, H. / Li, Z. / Feng, N. / Meng, F. / Xu, Y. / Li, L. / Shao, F. / Ding, J.
History
DepositionJan 26, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2023Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 29, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: OspC3
B: Calmodulin-1
C: Caspase-4


Theoretical massNumber of molelcules
Total (without water)98,6533
Polymers98,6533
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5390 Å2
ΔGint-29 kcal/mol
Surface area38150 Å2
Unit cell
Length a, b, c (Å)61.041, 118.473, 146.450
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

#1: Protein OspC3


Mass: 49705.074 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: ospC3 / Plasmid: pGEX-6p-2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: R4X5L7
#2: Protein Calmodulin-1


Mass: 16852.545 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CALM1, CALM, CAM, CAM1 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0DP23
#3: Protein Caspase-4 / CASP-4


Mass: 32095.428 Da / Num. of mol.: 1 / Mutation: C258A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP4 / Plasmid: pET28a-SUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P49662, caspase-4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 25% PEG3350, 0.1 M HEPES pH 7.4, 0.2 M Ammonium sulfate, 0.3 M NDSB-195
PH range: 6.8-7.8

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2.75→43.6 Å / Num. obs: 28191 / % possible obs: 99.4 % / Redundancy: 13.06 % / Biso Wilson estimate: 84.44 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.061 / Rrim(I) all: 0.063 / Net I/σ(I): 28.12
Reflection shellResolution: 2.75→2.82 Å / Rmerge(I) obs: 1.246 / Mean I/σ(I) obs: 2.28 / Num. unique obs: 2043 / CC1/2: 0.825

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7WR3, 7WR0

7wr3

7wr0


Resolution: 2.75→43.6 Å / SU ML: 0.4299 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.5538
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2698 1999 7.11 %
Rwork0.2321 26122 -
obs0.2349 28121 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 93.86 Å2
Refinement stepCycle: LAST / Resolution: 2.75→43.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6565 0 0 0 6565
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00316691
X-RAY DIFFRACTIONf_angle_d0.54149009
X-RAY DIFFRACTIONf_chiral_restr0.0415983
X-RAY DIFFRACTIONf_plane_restr0.00341180
X-RAY DIFFRACTIONf_dihedral_angle_d21.37252521
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.820.39151390.3221821X-RAY DIFFRACTION98.39
2.82-2.90.38841420.30221836X-RAY DIFFRACTION99.4
2.9-2.980.38161380.28261816X-RAY DIFFRACTION99.74
2.98-3.080.33831430.29011852X-RAY DIFFRACTION99.75
3.08-3.190.37161420.29421847X-RAY DIFFRACTION99.85
3.19-3.320.40881410.30941847X-RAY DIFFRACTION99.85
3.32-3.470.36841400.29511840X-RAY DIFFRACTION98.51
3.47-3.650.37211420.27431858X-RAY DIFFRACTION99.85
3.65-3.880.2891430.25031877X-RAY DIFFRACTION99.85
3.88-4.180.2831430.22811866X-RAY DIFFRACTION99.75
4.18-4.60.23931430.20261871X-RAY DIFFRACTION98.53
4.6-5.260.24741440.19341877X-RAY DIFFRACTION99.95
5.26-6.620.24721460.24141926X-RAY DIFFRACTION99
6.63-43.60.18951530.19311988X-RAY DIFFRACTION98.35

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