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- PDB-1sqk: CRYSTAL STRUCTURE OF CIBOULOT IN COMPLEX WITH SKELETAL ACTIN -

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Basic information

Entry
Database: PDB / ID: 1sqk
TitleCRYSTAL STRUCTURE OF CIBOULOT IN COMPLEX WITH SKELETAL ACTIN
Components
  • ACTIN, ALPHA SKELETAL MUSCLE
  • CIBOULOT
KeywordsSTRUCTURAL PROTEIN/PROTEIN BINDING / CIBOULOT / WH2 DOMAIN / ACTIN / ACTIN-BINDING PROTEIN / STRUCTURAL PROTEIN-PROTEIN BINDING COMPLEX
Function / homology
Function and homology information


larval central nervous system remodeling / 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 ...larval central nervous system remodeling / 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 organization / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / brain development / calcium-dependent protein binding / lamellipodium / cell body / cytoskeleton / hydrolase activity / protein domain specific binding / calcium ion binding / positive regulation of gene expression / magnesium ion binding / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Beta-thymosin / Beta-thymosin superfamily / Thymosin beta-4 family / Thymosin beta actin-binding motif. / Actin; Chain A, domain 2 / Actin; Chain A, domain 2 / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / Actins signature 1. ...Beta-thymosin / Beta-thymosin superfamily / Thymosin beta-4 family / Thymosin beta actin-binding motif. / Actin; Chain A, domain 2 / Actin; Chain A, domain 2 / 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 / Roll / Alpha-Beta Complex / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / LATRUNCULIN A / Ciboulot, isoform A / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Oryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHertzog, M. / Van Heijenoort, C. / Didry, D. / Gaudier, M. / Gigant, B. / Coutant, J. / Didelot, G. / Preat, T. / Knossow, M. / Guittet, E. / Carlier, M.F.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2004
Title: The beta-Thymosin/WH2 Domain; Structural Basis for the Switch from Inhibition to Promotion of Actin Assembly
Authors: Hertzog, M. / Van Heijenoort, C. / Didry, D. / Gaudier, M. / Coutant, J. / Gigant, B. / Didelot, G. / Knossow, M. / Guittet, E. / Carlier, M.F.
History
DepositionMar 19, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: ACTIN, ALPHA SKELETAL MUSCLE
B: CIBOULOT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7615
Polymers44,8882
Non-polymers8733
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-31 kcal/mol
Surface area16760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.494, 75.198, 85.314
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein ACTIN, ALPHA SKELETAL MUSCLE / / ALPHA-ACTIN 1


Mass: 42096.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ACTA1, ACTA / Source: (natural) Oryctolagus cuniculus (rabbit) / Organ: MUSCLESkeletal muscle / References: UniProt: P68135
#2: Protein/peptide CIBOULOT / CG4944-PC


Mass: 2791.117 Da / Num. of mol.: 1 / Fragment: residues 10-34
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Production host: Escherichia coli (E. coli) / References: UniProt: O97428

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Non-polymers , 4 types, 95 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: 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
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.41 Å3/Da / Density % sol: 48.97 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000 20%, MAGNESIUM ACETATE 200MM, SODIUM CACODYLATE 100 MM, pH 6.50, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9763
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 12, 2002 / Details: TOROIDAL MIRROR
RadiationMonochromator: YES / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 15490 / Num. obs: 15413 / % possible obs: 99.9 % / Observed criterion σ(F): 2.5 / Observed criterion σ(I): 1.25 / Redundancy: 5.9 % / Biso Wilson estimate: 25.7 Å2 / Rsym value: 0.09 / Net I/σ(I): 20.8
Reflection shellResolution: 2.5→2.54 Å / Mean I/σ(I) obs: 4.9 / Num. unique all: 1565 / Rsym value: 0.311

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ACTIN-LATRUNCULINA 1IJJ

1ijj


Resolution: 2.5→20 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1626978.82 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.278 1565 10.2 %RANDOM
Rwork0.219 ---
all-15490 --
obs-15413 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.825 Å2 / ksol: 0.384917 e/Å3
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3011 0 57 92 3160
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d1.06
X-RAY DIFFRACTIONc_mcbond_it1.031.5
X-RAY DIFFRACTIONc_mcangle_it1.652
X-RAY DIFFRACTIONc_scbond_it1.722
X-RAY DIFFRACTIONc_scangle_it2.532.5
LS refinement shellResolution: 2.5→2.54 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.379 1565 10.1 %
Rwork0.306 2183 -
obs-15413 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ADP-LAR.PARADP-LAR.TOP
X-RAY DIFFRACTION3ION.PARAMWATER.TOP
X-RAY DIFFRACTION4WATER.PARAMION.TOP

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