[English] 日本語
Yorodumi
- PDB-7wr3: Crystal structure of MBP-fused OspC3 in complex with calmodulin -

+
Open data


ID or keywords:

Loading...

-
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 / Lyases; Carbon-nitrogen lyases; Other carbon-nitrogen lyases / ADP-riboxanase activity / symbiont-mediated suppression of host programmed cell death / symbiont-mediated perturbation of host programmed cell death / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events ...symbiont-mediated suppression of host signal transduction pathway / symbiont-mediated suppression of host calcium-mediated signal transduction / Lyases; Carbon-nitrogen lyases; Other carbon-nitrogen lyases / ADP-riboxanase activity / symbiont-mediated suppression of host programmed cell death / 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 / 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 / detection of maltose stimulus / presynaptic endocytosis / Synthesis of IP3 and IP4 in the cytosol / maltose transport complex / 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 / carbohydrate transport / RHO GTPases activate PAKs / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / regulation of ryanodine-sensitive calcium-release channel activity / Long-term potentiation / protein phosphatase activator activity / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / DARPP-32 events / carbohydrate transmembrane transporter activity / maltose binding / Smooth Muscle Contraction / detection of calcium ion / maltose transport / maltodextrin transmembrane transport / regulation of cardiac muscle contraction / catalytic complex / 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 / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Ion homeostasis / 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 / ATP-binding cassette (ABC) transporter complex / regulation of heart rate / Ras activation upon Ca2+ influx through NMDA receptor / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / calyx of Held / adenylate cyclase activator activity / sarcomere / VEGFR2 mediated cell proliferation / protein serine/threonine kinase activator activity / VEGFR2 mediated vascular permeability / regulation of cytokinesis / cell chemotaxis / spindle microtubule / Translocation of SLC2A4 (GLUT4) to the plasma membrane / positive regulation of receptor signaling pathway via JAK-STAT / calcium channel regulator activity / RAF activation / Transcriptional activation of mitochondrial biogenesis / response to calcium ion / cellular response to type II interferon / Stimuli-sensing channels / G2/M transition of mitotic cell cycle / long-term synaptic potentiation / spindle pole / RAS processing / calcium-dependent protein binding
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 / EF-hand / : / Bacterial extracellular solute-binding protein / Recoverin; domain 1 ...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 / EF-hand / : / Bacterial extracellular solute-binding protein / Recoverin; domain 1 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
NICOTINAMIDE / Maltose/maltodextrin-binding periplasmic protein / Calmodulin-1 / Arginine ADP-riboxanase OspC3
Similarity search - Component
Biological speciesBolitoglossa (mushroom-tongued 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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 (mushroom-tongued 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

-
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

-
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
#6: Water ChemComp-HOH / water


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

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
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