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- PDB-4h03: Crystal structure of NAD+-Ia-actin complex -

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Basic information

Entry
Database: PDB / ID: 4h03
TitleCrystal structure of NAD+-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 / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / actin filament bundle / filamentous actin / actin filament bundle assembly / skeletal muscle thin filament assembly / striated muscle thin filament ...cytoskeletal motor activator activity / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / actin filament bundle / filamentous actin / actin filament bundle assembly / skeletal muscle thin filament assembly / striated muscle thin filament / skeletal muscle myofibril / actin monomer binding / skeletal muscle fiber development / stress fiber / titin binding / actin filament polymerization / filopodium / actin filament / 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 / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 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: 1.75 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 7, 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_conn / 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_conn.pdbx_leaving_atom_flag / _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

Downloads & links

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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)94,80155
Polymers90,0952
Non-polymers4,70653
Water4,900272
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.862, 135.037, 154.510
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: 41875.633 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 , 7 types, 325 molecules

#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 48 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#8: 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 / Latrunculin


Mass: 421.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H31NO5S / Comment: toxin*YM
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 272 / 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: 3.12 Å3/Da / Density % sol: 60.62 %
Crystal growTemperature: 277.13 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 18% PEG1500, 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: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: May 29, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. all: 114683 / Num. obs: 110554 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 19.9
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.416 / Mean I/σ(I) obs: 3.2 / Num. unique all: 5154 / % possible all: 90.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREP11phasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BUZ

3buz


Resolution: 1.75→26.29 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.187 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23329 5535 5 %RANDOM
Rwork0.21598 ---
all0.21683 109001 --
obs0.21683 104936 96.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.68 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å2-0 Å2-0 Å2
2--0.02 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.75→26.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6171 0 302 272 6745
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.026612
X-RAY DIFFRACTIONr_bond_other_d0.0070.026380
X-RAY DIFFRACTIONr_angle_refined_deg1.422.0088837
X-RAY DIFFRACTIONr_angle_other_deg0.83314733
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1265771
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.59225.204294
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.961151144
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1451529
X-RAY DIFFRACTIONr_chiral_restr0.1410.2954
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217157
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021397
LS refinement shellResolution: 1.748→1.794 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 386 -
Rwork0.29 7166 -
obs-7166 90.09 %
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)
10.0877-0.0733-0.02830.10980.06510.08670.00230.00250.00160.00850.00890.0021-0.00230.0134-0.01130.02610.00170.00320.0158-0.01790.0268-14.1018-3.578651.3574
20.0801-0.0290.00550.0493-0.01150.0913-0.0049-0.00440.0137-0.00310.0017-0.005-0.00050.00530.00320.0242-0.001700.0160.00050.0075-2.4279-34.447624.8806
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 413
2X-RAY DIFFRACTION1A501 - 502
3X-RAY DIFFRACTION2B5 - 374
4X-RAY DIFFRACTION2B401 - 403

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