[English] 日本語
Yorodumi
- PDB-8bjj: ExoY Nucleotidyl Cyclase domain from Vibrio nigripulchritudo MART... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8bjj
TitleExoY Nucleotidyl Cyclase domain from Vibrio nigripulchritudo MARTX toxin, bound to ATP-Mg-actin, human profilin 1 and a sulfate ion
Components
  • Actin, alpha skeletal muscle, intermediate form
  • Profilin-1
  • Putative Adenylate cyclase
KeywordsTOXIN / bacterial nucleotidyl cyclase toxin / activated complex
Function / homology
Function and homology information


calcium- and calmodulin-responsive adenylate cyclase activity / synapse maturation / modification of postsynaptic actin cytoskeleton / negative regulation of actin filament bundle assembly / adenyl-nucleotide exchange factor activity / negative regulation of actin filament polymerization / positive regulation of actin filament bundle assembly / adenylate cyclase / regulation of actin filament polymerization / Signaling by ROBO receptors ...calcium- and calmodulin-responsive adenylate cyclase activity / synapse maturation / modification of postsynaptic actin cytoskeleton / negative regulation of actin filament bundle assembly / adenyl-nucleotide exchange factor activity / negative regulation of actin filament polymerization / positive regulation of actin filament bundle assembly / adenylate cyclase / regulation of actin filament polymerization / Signaling by ROBO receptors / positive regulation of ATP-dependent activity / proline-rich region binding / positive regulation of ruffle assembly / PCP/CE pathway / negative regulation of stress fiber assembly / host cell cytosol / cytoskeletal motor activator activity / positive regulation of actin filament polymerization / tropomyosin binding / myosin heavy chain binding / troponin I binding / mesenchyme migration / filamentous actin / actin filament bundle / striated muscle thin filament / actin filament bundle assembly / skeletal muscle thin filament assembly / skeletal muscle myofibril / actin monomer binding / positive regulation of epithelial cell migration / stress fiber / skeletal muscle fiber development / titin binding / phosphatidylinositol-4,5-bisphosphate binding / actin filament polymerization / phosphotyrosine residue binding / filopodium / actin filament / RHO GTPases Activate Formins / neural tube closure / modulation of chemical synaptic transmission / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / small GTPase binding / calcium-dependent protein binding / Platelet degranulation / lamellipodium / actin binding / transferase activity / cell body / toxin activity / cell cortex / actin cytoskeleton organization / blood microparticle / cytoskeleton / hydrolase activity / protein stabilization / cadherin binding / protein domain specific binding / cysteine-type endopeptidase activity / focal adhesion / calcium ion binding / positive regulation of gene expression / regulation of transcription by RNA polymerase II / host cell plasma membrane / glutamatergic synapse / magnesium ion binding / proteolysis / RNA binding / extracellular exosome / extracellular region / ATP binding / identical protein binding / nucleus / membrane / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Yersinia/Haemophilus virulence surface antigen / RtxA toxin / RtxA repeat / Peptidase C58, YopT-type domain / Profilin1/2/3, vertebrate / Dermonecrotic/RTX toxin, membrane localization domain / Anthrax toxin, edema factor, central / Anthrax toxin, edema factor, C-terminal / Anthrax toxin, edema factor, central domain superfamily / Anthrax toxin LF subunit ...Yersinia/Haemophilus virulence surface antigen / RtxA toxin / RtxA repeat / Peptidase C58, YopT-type domain / Profilin1/2/3, vertebrate / Dermonecrotic/RTX toxin, membrane localization domain / Anthrax toxin, edema factor, central / Anthrax toxin, edema factor, C-terminal / Anthrax toxin, edema factor, central domain superfamily / Anthrax toxin LF subunit / Membrane Localization Domain / Profilin conserved site / Profilin signature. / Profilin / Profilin / : / Profilin / Profilin superfamily / CGT/MARTX, cysteine protease (CPD) domain / CGT/MARTX, cysteine protease (CPD) domain superfamily / Peptidase C80 family / CGT/MARTX cysteine protease (CPD) domain profile. / Serralysin-like metalloprotease, C-terminal / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / LATRUNCULIN B / HYDROGEN PEROXIDE / Putative Adenylate cyclase / Profilin-1 / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesHomo sapiens (human)
Vibrio nigripulchritudo (bacteria)
Oryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.699 Å
AuthorsTeixeira-Nunes, M. / Renault, L. / Retailleau, P.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-18-CE44-0001 France
CitationJournal: Plos Pathog. / Year: 2023
Title: Functional and structural insights into the multi-step activation and catalytic mechanism of bacterial ExoY nucleotidyl cyclase toxins bound to actin-profilin.
Authors: Teixeira-Nunes, M. / Retailleau, P. / Raoux-Barbot, D. / Comisso, M. / Missinou, A.A. / Velours, C. / Plancqueel, S. / Ladant, D. / Mechold, U. / Renault, L.
History
DepositionNov 4, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Actin, alpha skeletal muscle, intermediate form
C: Profilin-1
B: Putative Adenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,96016
Polymers103,0503
Non-polymers1,91013
Water13,007722
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.186, 63.202, 93.455
Angle α, β, γ (deg.)90.000, 91.040, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 3 types, 3 molecules ACB

#1: Protein Actin, alpha skeletal muscle, intermediate form


Mass: 41862.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: skeletal muscle / References: UniProt: P68135
#2: Protein Profilin-1 / Epididymis tissue protein Li 184a / Profilin I


Mass: 14940.021 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PFN1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P07737
#3: Protein Putative Adenylate cyclase / MARTX toxin


Mass: 46247.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio nigripulchritudo (bacteria) / Cell (production host): BL21(DE3) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A6N3LUE9, adenylate cyclase

-
Non-polymers , 9 types, 735 molecules

#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-LAB / LATRUNCULIN B


Mass: 395.513 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H29NO5S / Feature type: SUBJECT OF INVESTIGATION / Comment: toxin*YM
#7: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#8: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-PEO / HYDROGEN PEROXIDE


Mass: 34.015 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2O2
#10: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#11: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 722 / 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: 2.36 Å3/Da / Density % sol: 47.88 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 30% peg3000 0.3M LiSO4 0.1M Tris pH8.5 3% Dioxane

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.699→44.2 Å / Num. obs: 104207 / % possible obs: 99.8 % / Redundancy: 15.2 % / Biso Wilson estimate: 27.04 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 25.3
Reflection shellResolution: 1.7→1.73 Å / Rmerge(I) obs: 1.055 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 5211

-
Processing

Software
NameVersionClassification
BUSTER2.10.3 (20-MAY-2020)refinement
AutoProcess1.0.5 (20200520)data processing
XDSVERSION Jan 31, 2020 BUILT=20200417data reduction
Aimlessversion 0.7.4data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PAV

2pav


Resolution: 1.699→44.2 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.954 / SU R Cruickshank DPI: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.1 / SU Rfree Blow DPI: 0.092 / SU Rfree Cruickshank DPI: 0.09
RfactorNum. reflection% reflectionSelection details
Rfree0.1949 5186 4.98 %RANDOM
Rwork0.1751 ---
obs0.1761 104207 99.8 %-
Displacement parametersBiso max: 110.7 Å2 / Biso mean: 33.36 Å2 / Biso min: 11.21 Å2
Baniso -1Baniso -2Baniso -3
1--0.2029 Å20 Å20.7063 Å2
2--1.0191 Å20 Å2
3----0.8162 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: final / Resolution: 1.699→44.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6718 0 118 723 7559
Biso mean--34.68 40.8 -
Num. residues----861
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2598SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1275HARMONIC5
X-RAY DIFFRACTIONt_it7210HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion947SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7010SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d7210HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg9816HARMONIC20.96
X-RAY DIFFRACTIONt_omega_torsion3.34
X-RAY DIFFRACTIONt_other_torsion15.95
LS refinement shellResolution: 1.7→1.71 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.2376 97 4.65 %
Rwork0.2253 1988 -
all0.2258 2085 -
obs--96.43 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.46980.08490.16420.0561-0.00560.4178-0.02740.0569-0.0372-0.01950.0013-0.05210.0193-0.05350.0262-0.0048-0.01320.0230.0032-0.0221-0.013326.0598-7.563523.1738
20.06310.11370.10260.04820.01571.2473-0.05520.017-0.02770.0299-0.0577-0.05910.0034-0.11060.1130.00710.0338-0.00350.00230.0102-0.035416.93645.9828-14.6297
30.4044-0.3241-0.40310.76720.64731.4256-0.0299-0.09130.09150.0480.1596-0.25240.0270.1343-0.1297-0.01940.0033-0.0338-0.0324-0.04790.078647.99054.992746.8696
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|5 - A|375 }A5 - 375
2X-RAY DIFFRACTION2{ B|466 - B|863 }B466 - 863
3X-RAY DIFFRACTION3{ C|1 - C|139 }C1 - 139

+
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