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- PDB-7wr3: Crystal structure of MBP-fused OspC3 in complex with calmodulin -

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Basic information

Entry
Database: PDB / ID: 7wr3
TitleCrystal structure of MBP-fused OspC3 in complex with calmodulin
Components
  • Calmodulin-1
  • MBP-fused 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 / symbiont-mediated suppression of host programmed cell death / Lyases; Carbon-nitrogen lyases; Other carbon-nitrogen lyases / ADP-riboxanase activity / symbiont-mediated perturbation of host programmed cell death / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers ...symbiont-mediated suppression of host signal transduction pathway / : / symbiont-mediated suppression of host calcium-mediated signal transduction / symbiont-mediated suppression of host programmed cell death / Lyases; Carbon-nitrogen lyases; Other carbon-nitrogen lyases / ADP-riboxanase activity / symbiont-mediated perturbation of host programmed cell death / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Activation of Ca-permeable Kainate Receptor / Loss of phosphorylation of MECP2 at T308 / 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 / autophagosome membrane docking / mitochondrion-endoplasmic reticulum membrane tethering / CLEC7A (Dectin-1) induces NFAT activation / Activation of RAC1 downstream of NMDARs / regulation of cardiac muscle cell action potential / positive regulation of ryanodine-sensitive calcium-release channel activity / detection of maltose stimulus / regulation of cell communication by electrical coupling involved in cardiac conduction / maltose transport complex / Synthesis of IP3 and IP4 in the cytosol / negative regulation of peptidyl-threonine phosphorylation / Negative regulation of NMDA receptor-mediated neuronal transmission / Phase 0 - rapid depolarisation / Unblocking of NMDA receptors, glutamate binding and activation / negative regulation of ryanodine-sensitive calcium-release channel activity / protein phosphatase activator activity / RHO GTPases activate PAKs / maltose binding / carbohydrate transport / maltose transport / maltodextrin transmembrane transport / Ion transport by P-type ATPases / : / Uptake and function of anthrax toxins / Long-term potentiation / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / catalytic complex / carbohydrate transmembrane transporter activity / DARPP-32 events / detection of calcium ion / regulation of cardiac muscle contraction / Smooth Muscle Contraction / regulation of ryanodine-sensitive calcium-release channel activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium channel inhibitor activity / cellular response to interferon-beta / eNOS activation / Protein methylation / voltage-gated potassium channel complex / Activation of AMPK downstream of NMDARs / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Ion homeostasis / : / titin binding / positive regulation of protein autophosphorylation / regulation of calcium-mediated signaling / sperm midpiece / calcium channel complex / substantia nigra development / adenylate cyclase activator activity / Ras activation upon Ca2+ influx through NMDA receptor / regulation of heart rate / sarcomere / FCERI mediated Ca+2 mobilization / ATP-binding cassette (ABC) transporter complex / protein serine/threonine kinase activator activity / FCGR3A-mediated IL10 synthesis / cell chemotaxis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / VEGFR2 mediated vascular permeability / regulation of cytokinesis / VEGFR2 mediated cell proliferation / positive regulation of peptidyl-threonine phosphorylation / spindle microtubule / Translocation of SLC2A4 (GLUT4) to the plasma membrane / positive regulation of receptor signaling pathway via JAK-STAT / RAF activation / Transcriptional activation of mitochondrial biogenesis / positive regulation of protein serine/threonine kinase activity / Stimuli-sensing channels / cellular response to type II interferon / spindle pole / response to calcium ion
Similarity search - Function
Arginine ADP-riboxanase OspC1-3 / Shigella flexneri OspC protein / : / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / EF-hand domain pair / EF-hand, calcium binding motif ...Arginine ADP-riboxanase OspC1-3 / Shigella flexneri OspC protein / : / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / 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
Similarity search - Domain/homology
NICOTINAMIDE / Maltose/maltodextrin-binding periplasmic protein / Calmodulin-1 / Arginine ADP-riboxanase OspC3
Similarity search - Component
Biological speciesBolitoglossa (mushroomtongue salamanders)
Shigella flexneri (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 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

Downloads & links

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Assembly

Deposited unit
A: MBP-fused OspC3
B: MBP-fused OspC3
C: Calmodulin-1
D: Calmodulin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,03212
Polymers215,7194
Non-polymers1,3138
Water24,0861337
1
A: MBP-fused OspC3
C: Calmodulin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,5166
Polymers107,8602
Non-polymers6574
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5540 Å2
ΔGint-31 kcal/mol
Surface area41350 Å2
MethodPISA
2
B: MBP-fused OspC3
D: Calmodulin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,5166
Polymers107,8602
Non-polymers6574
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5870 Å2
ΔGint-40 kcal/mol
Surface area41370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.846, 201.866, 101.515
Angle α, β, γ (deg.)90.000, 102.105, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein MBP-fused OspC3 / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP


Mass: 90608.555 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bolitoglossa (mushroomtongue salamanders), (gene. exp.) Shigella flexneri (bacteria)
Gene: malE, ospC3 / Plasmid: pGEX-6P-2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0AEX9, UniProt: R4X5L7
#2: Protein Calmodulin-1


Mass: 17250.984 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CALM1, CALM, CAM, CAM1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0DP23

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Sugars , 1 types, 2 molecules

#3: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 3 types, 1343 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-NCA / NICOTINAMIDE


Mass: 122.125 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H6N2O / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1337 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.72 Å3/Da / Density % sol: 54.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% PEG3350, 0.1 M Tris pH 8.2-8.4, 0.2 M Lithium Sulfate, 0.7% 1-Butanol
PH range: 8.2 - 8.4

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.87→49.99 Å / Num. obs: 187465 / % possible obs: 99.2 % / Redundancy: 6.86 % / Biso Wilson estimate: 29.61 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.088 / Rrim(I) all: 0.096 / Net I/σ(I): 12.49
Reflection shellResolution: 1.87→1.92 Å / Rmerge(I) obs: 0.865 / Mean I/σ(I) obs: 2.29 / Num. unique obs: 13706 / CC1/2: 0.736 / Rrim(I) all: 0.939 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7WR2, 5WQ6

7wr2

5wq6


Resolution: 1.87→49.99 Å / SU ML: 0.2321 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 23.8264
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2284 1989 1.06 %
Rwork0.196 185456 -
obs0.1963 187445 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.31 Å2
Refinement stepCycle: LAST / Resolution: 1.87→49.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14804 0 84 1337 16225
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005515191
X-RAY DIFFRACTIONf_angle_d0.741620513
X-RAY DIFFRACTIONf_chiral_restr0.0482237
X-RAY DIFFRACTIONf_plane_restr0.0052669
X-RAY DIFFRACTIONf_dihedral_angle_d16.25695597
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.87-1.920.34711330.286312958X-RAY DIFFRACTION97.5
1.92-1.970.27921410.244113200X-RAY DIFFRACTION98.87
1.97-2.030.26891480.223113263X-RAY DIFFRACTION98.78
2.03-2.10.23511430.212813028X-RAY DIFFRACTION98.12
2.1-2.170.26651370.205113234X-RAY DIFFRACTION99.24
2.17-2.260.22621550.196513273X-RAY DIFFRACTION99.38
2.26-2.360.23781250.193413297X-RAY DIFFRACTION99.44
2.36-2.480.24951570.191813174X-RAY DIFFRACTION99.26
2.49-2.640.23661380.197813208X-RAY DIFFRACTION99.25
2.64-2.840.22981460.196613367X-RAY DIFFRACTION99.73
2.84-3.130.26341360.200913349X-RAY DIFFRACTION99.85
3.13-3.580.2131440.188613284X-RAY DIFFRACTION99.5
3.58-4.510.17321420.17313419X-RAY DIFFRACTION99.95
4.51-49.990.2381440.19813402X-RAY DIFFRACTION99.37

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