[English] 日本語
Yorodumi
- PDB-7wr5: Crystal structure of OspC3-calmodulin-caspase-4 complex binding w... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7wr5
TitleCrystal structure of OspC3-calmodulin-caspase-4 complex binding with 2'-aF-NAD+
Components
  • Calmodulin-1
  • Caspase-4Caspase 4
  • OspC3
KeywordsTRANSFERASE / ADP-riboxanase / effector
Function / homology
Function and homology information


symbiont-mediated suppression of host signal transduction pathway / modulation by symbiont of defense-related host calcium ion flux / symbiont-mediated suppression of host calcium or calmodulin-mediated signal transduction / caspase-4 / symbiont-mediated suppression of host programmed cell death / Lyases; Carbon-nitrogen lyases; Other carbon-nitrogen lyases / ADP-riboxanase activity / non-canonical inflammasome complex / positive regulation of interleukin-18-mediated signaling pathway / non-canonical inflammasome complex assembly ...symbiont-mediated suppression of host signal transduction pathway / modulation by symbiont of defense-related host calcium ion flux / symbiont-mediated suppression of host calcium or calmodulin-mediated signal transduction / caspase-4 / symbiont-mediated suppression of host programmed cell death / Lyases; Carbon-nitrogen lyases; Other carbon-nitrogen lyases / ADP-riboxanase activity / non-canonical inflammasome complex / positive regulation of interleukin-18-mediated signaling pathway / non-canonical inflammasome complex assembly / canonical inflammasome complex / CARD domain binding / positive regulation of tumor necrosis factor-mediated signaling pathway / cysteine-type endopeptidase activity involved in execution phase of apoptosis / 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) / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / Activation of RAC1 downstream of NMDARs / mitochondrion-endoplasmic reticulum membrane tethering / CLEC7A (Dectin-1) induces NFAT activation / regulation of cardiac muscle cell action potential / autophagosome membrane docking / positive regulation of ryanodine-sensitive calcium-release channel activity / Negative regulation of NMDA receptor-mediated neuronal transmission / regulation of cell communication by electrical coupling involved in cardiac conduction / negative regulation of peptidyl-threonine phosphorylation / Unblocking of NMDA receptors, glutamate binding and activation / Synthesis of IP3 and IP4 in the cytosol / pyroptotic inflammatory response / Phase 0 - rapid depolarisation / protein phosphatase activator activity / RHO GTPases activate PAKs / positive regulation of cyclic-nucleotide phosphodiesterase activity / positive regulation of phosphoprotein phosphatase activity / Ion transport by P-type ATPases / Long-term potentiation / Uptake and function of anthrax toxins / protein autoprocessing / protein maturation / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / catalytic complex / DARPP-32 events / detection of calcium ion / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / negative regulation of ryanodine-sensitive calcium-release channel activity / Smooth Muscle Contraction / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction / calcium channel inhibitor activity / cellular response to interferon-beta / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / Pyroptosis / Protein methylation / voltage-gated potassium channel complex / eNOS activation / Activation of AMPK downstream of NMDARs / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / positive regulation of protein dephosphorylation / regulation of calcium-mediated signaling / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Ion homeostasis / titin binding / regulation of ryanodine-sensitive calcium-release channel activity / positive regulation of protein autophosphorylation / sperm midpiece / calcium channel complex / substantia nigra development / adenylate cyclase activator activity / Ras activation upon Ca2+ influx through NMDA receptor / regulation of heart rate / protein serine/threonine kinase activator activity / sarcomere / FCERI mediated Ca+2 mobilization / intrinsic apoptotic signaling pathway / FCGR3A-mediated IL10 synthesis / VEGFR2 mediated vascular permeability / regulation of cytokinesis / positive regulation of peptidyl-threonine phosphorylation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / VEGFR2 mediated cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / lipopolysaccharide binding / RAF activation / positive regulation of receptor signaling pathway via JAK-STAT / spindle microtubule / NOD1/2 Signaling Pathway / Transcriptional activation of mitochondrial biogenesis
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 / Peptidase family C14A, His active site / Caspase family histidine active site. / Peptidase C14, caspase non-catalytic subunit p10 / Peptidase family C14A, cysteine active site ...Arginine ADP-riboxanase OspC1-3 / Shigella flexneri OspC protein / Caspase recruitment domain / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / 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
Similarity search - Domain/homology
Chem-5ZV / 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: 3.1 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)99,3194
Polymers98,6533
Non-polymers6661
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6470 Å2
ΔGint-29 kcal/mol
Surface area35310 Å2
Unit cell
Length a, b, c (Å)52.317, 120.074, 141.475
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

-
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 / 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
#4: Chemical ChemComp-5ZV / [[(2~{R},3~{R},4~{S},5~{R})-5-(3-aminocarbonylpyridin-1-yl)-4-fluoranyl-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate


Mass: 666.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27FN7O13P2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350, 0.2 M Potassium acetate

-
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: 3.1→49.07 Å / Num. obs: 16826 / % possible obs: 99.7 % / Redundancy: 12.8 % / Biso Wilson estimate: 82.24 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.16 / Rrim(I) all: 0.167 / Net I/σ(I): 14.98
Reflection shellResolution: 3.1→3.18 Å / Rmerge(I) obs: 1.388 / Mean I/σ(I) obs: 2.25 / Num. unique obs: 1194 / CC1/2: 0.746 / % possible all: 98.6

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7WR4

7wr4


Resolution: 3.1→49.07 Å / SU ML: 0.499 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.5961
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2723 1678 10 %
Rwork0.2257 15105 -
obs0.2304 16783 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 84.54 Å2
Refinement stepCycle: LAST / Resolution: 3.1→49.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6490 0 44 0 6534
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026665
X-RAY DIFFRACTIONf_angle_d0.44318979
X-RAY DIFFRACTIONf_chiral_restr0.0391977
X-RAY DIFFRACTIONf_plane_restr0.00291165
X-RAY DIFFRACTIONf_dihedral_angle_d13.54982497
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.190.40321350.32081213X-RAY DIFFRACTION98.75
3.19-3.30.37151370.27071241X-RAY DIFFRACTION100
3.3-3.410.31871380.26261233X-RAY DIFFRACTION99.93
3.41-3.550.27641370.25191242X-RAY DIFFRACTION99.93
3.55-3.710.30261400.2511250X-RAY DIFFRACTION100
3.71-3.910.2741360.23521224X-RAY DIFFRACTION99.85
3.91-4.150.30611390.22391252X-RAY DIFFRACTION99.93
4.15-4.470.2581390.20411250X-RAY DIFFRACTION99.71
4.47-4.920.27651400.19431267X-RAY DIFFRACTION100
4.92-5.630.24121430.21771276X-RAY DIFFRACTION100
5.63-7.090.2871430.25721294X-RAY DIFFRACTION99.58
7.09-49.070.2211510.19631363X-RAY DIFFRACTION99.08

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more