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- PDB-3sjh: Crystal Structure of a chimera containing the N-terminal domain (... -

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Basic information

Entry
Database: PDB / ID: 3sjh
TitleCrystal Structure of a chimera containing the N-terminal domain (residues 8-29) of drosophila Ciboulot and the C-terminal domain (residues 18-44) of bovine Thymosin-beta4, bound to G-actin-ATP-Latrunculin A
Components
  • Actin, alpha skeletal muscle
  • Ciboulot/Thymosin beta-4 chimeric protein
KeywordsCONTRACTILE PROTEIN / PROTEIN BINDING / protein-protein complex
Function / homology
Function and homology information


larval central nervous system remodeling / positive regulation of neutrophil migration / negative regulation of neutrophil chemotaxis / negative regulation of actin filament polymerization / cytoskeletal motor activator activity / cellular response to glucocorticoid stimulus / positive regulation of wound healing / myosin heavy chain binding / tropomyosin binding / actin filament bundle ...larval central nervous system remodeling / positive regulation of neutrophil migration / negative regulation of neutrophil chemotaxis / negative regulation of actin filament polymerization / cytoskeletal motor activator activity / cellular response to glucocorticoid stimulus / positive regulation of wound healing / 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 / protein sequestering activity / regulation of cell migration / actin filament organization / filopodium / actin filament / brain development / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / negative regulation of inflammatory response / 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 / extracellular space / ATP binding / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Thymosin beta-4 family signature. / Beta-thymosin / Beta-thymosin superfamily / Thymosin beta-4 family / Thymosin beta actin-binding motif. / WH2 motif / WH2 domain / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain ...Thymosin beta-4 family signature. / Beta-thymosin / Beta-thymosin superfamily / Thymosin beta-4 family / Thymosin beta actin-binding motif. / WH2 motif / WH2 domain / 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 / Ciboulot, isoform A / Thymosin beta-4 / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Bos taurus (domestic cattle)
Oryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsRenault, L. / Husson, C. / Carlier, M.F. / Didry, D.
CitationJournal: 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.
History
DepositionJun 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Sep 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_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.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _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_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
B: Ciboulot/Thymosin beta-4 chimeric protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8045
Polymers47,8512
Non-polymers9533
Water6,467359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-28 kcal/mol
Surface area16540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.644, 74.977, 86.393
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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 Actin, alpha skeletal muscle / Alpha-actin-1


Mass: 41862.613 Da / Num. of mol.: 1 / Fragment: UNP residues 3-377 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Organ: alpha Skeletal Muscle / References: UniProt: P68135
#2: Protein Ciboulot/Thymosin beta-4 chimeric protein / Ciboulot / isoform B / EG:EG0007.11 protein / RE50273p


Mass: 5988.682 Da / Num. of mol.: 1
Fragment: UNP O97428 residues 8-29, UNP P62326 residues 18-44
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly), (gene. exp.) Bos taurus (domestic cattle)
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, UniProt: P62326

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Non-polymers , 4 types, 362 molecules

#3: 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
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#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


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


Mass: 18.015 Da / Num. of mol.: 359 / 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: 2.28 Å3/Da / Density % sol: 46.08 %
Crystal growTemperature: 298 K / Method: hanging drop / pH: 6.5
Details: 22% PEG3350, 0.2M MgAcetate pH6.5, 0.45M Guanidine HCl, 1% Dioxane, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 21, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionHighest resolution: 1.75 Å / Num. obs: 44860 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 24.372 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 26.62
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.75-1.80.228.9827983350397.3
1.8-1.90.15712.23492296076100
1.9-20.10617.2340220496099.9
2-2.20.07323.42602547429100
2.2-2.40.05428.56418855168100
2.4-2.60.04732.3830177372599.9
2.6-2.80.0535.78219882724100
2.8-30.06137.12163582069100
3-3.50.05638.8224136334799.9
3.5-4.50.04743.27227423041100
4.5-60.02345.5212546160099.9
6-100.02144.22719795299.9
10-120.02342.89760114100
12-150.02340.5847681100
15-200.03232.212364890.6
200.0357.95692354.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.9 Å29.04 Å
Translation1.9 Å29.04 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SQK

1sqk


Resolution: 1.75→26.88 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.2092 / WRfactor Rwork: 0.1777 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.8859 / SU B: 4.268 / SU ML: 0.063 / SU R Cruickshank DPI: 0.1055 / SU Rfree: 0.1023 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1994 3229 7.2 %RANDOM
Rwork0.1687 ---
obs0.1709 44851 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 54.65 Å2 / Biso mean: 18.827 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.75→26.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2970 0 61 359 3390
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0223106
X-RAY DIFFRACTIONr_angle_refined_deg1.9461.9874214
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4565376
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.50724.403134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.94415535
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2021517
X-RAY DIFFRACTIONr_chiral_restr0.170.2471
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212303
X-RAY DIFFRACTIONr_mcbond_it1.5011.51889
X-RAY DIFFRACTIONr_mcangle_it2.49623060
X-RAY DIFFRACTIONr_scbond_it4.23431217
X-RAY DIFFRACTIONr_scangle_it6.4154.51154
LS refinement shellResolution: 1.751→1.796 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 213 -
Rwork0.227 3019 -
all-3232 -
obs--99.35 %
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)
10.66330.1944-0.13520.6265-0.01120.4762-0.01770.06120.021-0.00480.01980.02390.0428-0.0371-0.00220.0163-0.00450.00660.01950.00070.005353.054842.498315.3868
25.6777-5.0102-0.9518.69941.41342.7350.27690.57460.0262-0.5186-0.2209-0.1058-0.0563-0.137-0.0560.2046-0.06640.02310.25230.00570.012352.689232.0889-5.8459
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 371
2X-RAY DIFFRACTION1A501 - 503
3X-RAY DIFFRACTION2B12 - 33

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