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- PDB-4gy2: Crystal structure of apo-Ia-actin complex -

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Basic information

Entry
Database: PDB / ID: 4gy2
TitleCrystal structure of apo-Ia-actin complex
Components
  • Actin, alpha skeletal muscle
  • Iota toxin component Ia
KeywordsTOXIN/STRUCTURAL PROTEIN / ADP-ribosyltransferase / TOXIN-STRUCTURAL PROTEIN complex
Function / homology
Function and homology information


cytoskeletal motor activator activity / myosin heavy chain binding / tropomyosin binding / actin filament bundle / troponin I binding / filamentous actin / mesenchyme migration / actin filament bundle assembly / skeletal muscle myofibril / striated muscle thin filament ...cytoskeletal motor activator activity / myosin heavy chain binding / tropomyosin binding / actin filament bundle / troponin I binding / filamentous actin / mesenchyme migration / actin filament bundle assembly / skeletal muscle myofibril / striated muscle thin filament / skeletal muscle thin filament assembly / actin monomer binding / skeletal muscle fiber development / stress fiber / titin binding / actin filament polymerization / actin filament / filopodium / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / calcium-dependent protein binding / lamellipodium / cell body / hydrolase activity / protein domain specific binding / nucleotide binding / calcium ion binding / positive regulation of gene expression / magnesium ion binding / extracellular region / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
Binary exotoxin A, clostridial type / Toxin ADP-ribosyltransferase; Chain A, domain 1 / Toxin ADP-ribosyltransferase; Chain A, domain 1 / ADP ribosyltransferase / ADP-ribosyltransferase exoenzyme / Toxin-related mono-ADP-ribosyltransferase (TR mART) core domain profile. / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / Actins signature 1. ...Binary exotoxin A, clostridial type / Toxin ADP-ribosyltransferase; Chain A, domain 1 / Toxin ADP-ribosyltransferase; Chain A, domain 1 / ADP ribosyltransferase / ADP-ribosyltransferase exoenzyme / Toxin-related mono-ADP-ribosyltransferase (TR mART) core domain profile. / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / 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 / Nucleotidyltransferase; domain 5 / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / LATRUNCULIN A / PHOSPHATE ION / Actin, alpha skeletal muscle / Iota toxin component Ia
Similarity search - Component
Biological speciesClostridium perfringens (bacteria)
Oryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å
AuthorsTsurumura, T. / Oda, M. / Nagahama, M. / Tsuge, H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Arginine ADP-ribosylation mechanism based on structural snapshots of iota-toxin and actin complex
Authors: Tsurumura, T. / Tsumori, Y. / Qiu, H. / Oda, M. / Sakurai, J. / Nagahama, M. / Tsuge, H.
History
DepositionSep 5, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 20, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Iota toxin component Ia
B: Actin, alpha skeletal muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,1466
Polymers90,0822
Non-polymers1,0644
Water2,576143
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.442, 135.872, 153.946
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Iota toxin component Ia


Mass: 48219.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: Q46220, NAD+-protein-arginine ADP-ribosyltransferase
#2: Protein Actin, alpha skeletal muscle / Alpha-actin-1


Mass: 41862.613 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: ACTA1 / Production host: Escherichia coli (E. coli) / References: UniProt: P68135

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Non-polymers , 5 types, 147 molecules

#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#6: Chemical ChemComp-LAR / LATRUNCULIN A / 4-(17-HYDROXY-5,12-DIMETHYL-3-OXO-2,16-DIOXABICYCLO[13.3.1]NONADECA-4,8,10-TRIEN-17-YL)-2-THIAZOLIDINONE


Mass: 421.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H31NO5S
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O

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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: 3.16 Å3/Da / Density % sol: 61.08 %
Crystal growTemperature: 277.13 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 18% PEG 1500, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.13K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 7, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.71→37.19 Å / Num. all: 31974 / Num. obs: 31910 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 9.9
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.461 / Mean I/σ(I) obs: 5.1 / Num. unique all: 1539 / % possible all: 99.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREP11phasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BUZ

3buz


Resolution: 2.71→37.19 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.884 / SU B: 11.672 / SU ML: 0.234 / Cross valid method: THROUGHOUT / ESU R: 0.636 / ESU R Free: 0.326 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25733 1605 5 %RANDOM
Rwork0.19862 ---
all0.20159 30369 --
obs0.20159 30220 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.221 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0 Å20 Å2
2--0.04 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.71→37.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6164 0 66 143 6373
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.026360
X-RAY DIFFRACTIONr_angle_refined_deg1.91.9838614
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9965768
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.88125.153295
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.069151143
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.121530
X-RAY DIFFRACTIONr_chiral_restr0.1350.2944
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214776
LS refinement shellResolution: 2.707→2.777 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 90 -
Rwork0.315 1921 -
obs-1921 95.85 %

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