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- PDB-3u9z: Crystal structure between actin and a protein construct containin... -

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Basic information

Entry
Database: PDB / ID: 3u9z
TitleCrystal structure between actin and a protein construct containing the first beta-thymosin domain of drosophila ciboulot (residues 2-58) with the three mutations N26D/Q27K/D28S
Components
  • Actin, alpha skeletal muscle
  • Ciboulot, isoform A
KeywordsCONTRACTILE PROTEIN / PROTEIN BINDING
Function / homology
Function and homology information


larval central nervous system remodeling / cytoskeletal motor activator activity / tropomyosin binding / mesenchyme migration / troponin I binding / myosin heavy chain binding / filamentous actin / actin filament bundle / skeletal muscle thin filament assembly / striated muscle thin filament ...larval central nervous system remodeling / cytoskeletal motor activator activity / tropomyosin binding / mesenchyme migration / troponin I binding / myosin heavy chain binding / filamentous actin / actin filament bundle / skeletal muscle thin filament assembly / striated muscle thin filament / actin filament bundle assembly / skeletal muscle myofibril / actin monomer binding / skeletal muscle fiber development / stress fiber / titin binding / actin filament polymerization / filopodium / actin filament / actin filament organization / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / brain development / calcium-dependent protein binding / lamellipodium / cell body / hydrolase activity / protein domain specific binding / calcium ion binding / positive regulation of gene expression / magnesium ion binding / ATP binding / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Beta-thymosin / Beta-thymosin superfamily / Thymosin beta-4 family / Thymosin beta actin-binding motif. / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / Actins signature 1. / Actin, conserved site / Actins signature 2. ...Beta-thymosin / Beta-thymosin superfamily / Thymosin beta-4 family / Thymosin beta actin-binding motif. / 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'-DIPHOSPHATE / Ciboulot, isoform A / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Oryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.09 Å
AuthorsRenault, L. / Husson, C. / Carlier, M.F. / Didry, D.
Citation
Journal: Embo J. / Year: 2012
Title: How a single residue in individual beta-thymosin/WH2 domains controls their functions in actin assembly
Authors: Didry, D. / Cantrelle, F.X. / Husson, C. / Roblin, P. / Moorthy, A.M. / Perez, J. / Le Clainche, C. / Hertzog, M. / Guittet, E. / Carlier, M.F. / van Heijenoort, C. / Renault, L.
#1: Journal: 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. / Preat, T. / Knossow, M. / Guittet, E. / Carlier, M.F.
History
DepositionOct 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Sep 13, 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_ref_seq_dif / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _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: Actin, alpha skeletal muscle
C: Ciboulot, isoform A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5734
Polymers48,1222
Non-polymers4522
Water6,630368
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-27 kcal/mol
Surface area16680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.795, 75.181, 117.708
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Actin, alpha skeletal muscle / Alpha-actin-1


Mass: 41862.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: organ: alpha Skeletal Muscle / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P68135
#2: Protein Ciboulot, isoform A / Ciboulot / isoform B / EG:EG0007.11 protein / RE50273p


Mass: 6259.113 Da / Num. of mol.: 1 / Fragment: UNP residues 2-58 / Mutation: N26D, Q27K, D28S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: cib, EG:EG0007.11, CG4944, Dmel_CG4944 / Plasmid: pGEX-6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O97428
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 368 / 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: 2.11 Å3/Da / Density % sol: 41.58 %
Crystal growTemperature: 298 K / Method: hanging drop / pH: 6.5
Details: 18% PEG3350, 0.05M NaAcetate pH4.7, 0.1M MgAcetate pH6.5, 0.32M Guanidine HCl, 0.8% Dioxane, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.93 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 16, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2.09→46 Å / Num. all: 24792 / Num. obs: 24772 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 30.764 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 26.84
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.09-2.10.4757.045826346100
2.1-2.110.4557.555728331100
2.11-2.120.4637.38545732199.7
2.12-2.20.4297.9421862472100
2.2-2.220.3838.889222542100
2.22-2.230.33710.23468227099.6
2.23-2.240.33810.124446262100
2.24-2.250.3479.864645272100
2.25-2.260.30510.484546266100
2.26-2.270.3659.394034237100
2.27-2.280.31710.27447326099.6
2.28-2.290.349.674371257100
2.29-30.16318.831757151032899.9
3-40.06841.9797024877100
4-50.04856.5328175177399.9
5-60.0457.3812807796100
6-100.0361.8814110890100
10-12.50.02664.941860129100
12.50.02747.13153414397.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.8 Å46.27 Å
Translation2.8 Å46.27 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER1.3.2phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SQK

1sqk


Resolution: 2.09→46 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.921 / WRfactor Rfree: 0.2194 / WRfactor Rwork: 0.1542 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8747 / SU B: 9.155 / SU ML: 0.112 / SU R Cruickshank DPI: 0.2054 / SU Rfree: 0.1868 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2266 1851 7.5 %RANDOM
Rwork0.1598 ---
obs0.1647 24652 99.93 %-
all-24672 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 70.35 Å2 / Biso mean: 30.093 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-1.04 Å20 Å20 Å2
2---1.22 Å20 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 2.09→46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2949 0 28 368 3345
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0223041
X-RAY DIFFRACTIONr_angle_refined_deg1.4521.9784123
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2415374
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.71224.275131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.68515527
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1081517
X-RAY DIFFRACTIONr_chiral_restr0.1230.2459
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212274
X-RAY DIFFRACTIONr_mcbond_it1.1511.51876
X-RAY DIFFRACTIONr_mcangle_it2.00923033
X-RAY DIFFRACTIONr_scbond_it3.54731165
X-RAY DIFFRACTIONr_scangle_it5.4614.51090
LS refinement shellResolution: 2.093→2.147 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 144 -
Rwork0.171 1629 -
all-1773 -
obs--99.94 %
Refinement TLS params.Method: refined / Origin x: 11.4475 Å / Origin y: 4.2091 Å / Origin z: 18.8459 Å
111213212223313233
T0.0263 Å20.0261 Å20.0046 Å2-0.0277 Å20.0079 Å2--0.026 Å2
L0.6067 °2-0.3264 °2-0.0628 °2-1.0365 °20.0553 °2--0.6464 °2
S0.0803 Å °0.093 Å °0.0156 Å °-0.1146 Å °-0.1047 Å °-0.0862 Å °0.0575 Å °0.0668 Å °0.0244 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 371
2X-RAY DIFFRACTION1A376 - 377
3X-RAY DIFFRACTION1C13 - 32

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