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- PDB-3u9d: Crystal Structure of a chimera containing the N-terminal domain (... -

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Basic information

Entry
Database: PDB / ID: 3u9d
TitleCrystal Structure of a chimera containing the N-terminal domain (residues 8-24) of drosophila Ciboulot and the C-terminal domain (residues 13-44) of bovine Thymosin-beta4, bound to G-actin-ATP
Components
  • Actin, alpha skeletal muscle
  • Thymosin beta-4, Chimeric protein
KeywordsCONTRACTILE PROTEIN / PROTEIN BINDING
Function / homology
Function and homology information


Formation of the dystrophin-glycoprotein complex (DGC) / skeletal muscle fiber adaptation / Striated Muscle Contraction / larval central nervous system remodeling / positive regulation of neutrophil migration / negative regulation of neutrophil chemotaxis / negative regulation of actin filament polymerization / cellular response to potassium ion / response to steroid hormone / cellular response to glucocorticoid stimulus ...Formation of the dystrophin-glycoprotein complex (DGC) / skeletal muscle fiber adaptation / Striated Muscle Contraction / larval central nervous system remodeling / positive regulation of neutrophil migration / negative regulation of neutrophil chemotaxis / negative regulation of actin filament polymerization / cellular response to potassium ion / response to steroid hormone / cellular response to glucocorticoid stimulus / positive regulation of wound healing / mesenchyme migration / striated muscle thin filament / skeletal muscle thin filament assembly / actin monomer binding / response to mechanical stimulus / skeletal muscle fiber development / stress fiber / protein sequestering activity / regulation of cell migration / actin filament organization / sarcomere / 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 / lamellipodium / actin cytoskeleton / cell body / cytoskeleton / hydrolase activity / positive regulation of gene expression / extracellular space / ATP 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 / Ciboulot, isoform A / Thymosin beta-4 / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Bos taurus (domestic cattle)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 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 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 28, 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_ncs_dom_lim / 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_asym_id / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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
B: Thymosin beta-4, Chimeric protein
C: Actin, alpha skeletal muscle
D: Thymosin beta-4, Chimeric protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,7148
Polymers95,6514
Non-polymers1,0634
Water00
1
A: Actin, alpha skeletal muscle
B: Thymosin beta-4, Chimeric protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3574
Polymers47,8252
Non-polymers5312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-26 kcal/mol
Surface area17090 Å2
MethodPISA
2
C: Actin, alpha skeletal muscle
D: Thymosin beta-4, Chimeric protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3574
Polymers47,8252
Non-polymers5312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-23 kcal/mol
Surface area17070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.698, 75.738, 128.518
Angle α, β, γ (deg.)90.00, 90.03, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111THRTHRHISHIS2AA6 - 3716 - 371
211THRTHRHISHIS2CC6 - 3716 - 371
121ATPATPMGMG4AE - F501 - 502
221ATPATPMGMG4CG - H501 - 502
112PROPROLYSLYS2BB12 - 3210 - 30
212PROPROLYSLYS2DD12 - 3210 - 30

NCS ensembles :
ID
1
2

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Components

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


Mass: 41862.613 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: organ: alpha Skeletal Muscle / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P68136
#2: Protein Thymosin beta-4, Chimeric protein / T beta-4 / Hematopoietic system regulatory peptide / Seraspenide


Mass: 5962.708 Da / Num. of mol.: 2
Fragment: UNP O97428 residues 8-24, UNP P62326 residues 13-44
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly), (gene. exp.) Bos taurus (domestic cattle)
Gene: TMSB4, THYB4 / Plasmid: pGEX-6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62326, UniProt: O97428
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: Mg

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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: 2.33 Å3/Da / Density % sol: 47.1 %
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: 0.97903 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 5, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97903 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.521
11-h,-k,l20.479
ReflectionResolution: 2.5→20 Å / Num. obs: 29916 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.061 / Net I/σ(I): 17.25
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.5-2.550.2944.31196.8
2.55-2.60.2635.03199.3
2.6-2.650.2525.21199.2
2.65-2.70.2196.08198.8
2.7-2.750.2056.65198.5
2.75-2.80.1867.14197.8
2.8-2.850.1698.07198.3
2.85-2.90.1618.14198.1
2.9-2.950.1449.17198.6
2.95-30.1439.49198.6
3-3.10.11711.14197.8
3.1-3.20.09313.56197.8
3.2-3.30.07715.39198.1
3.3-40.04922.41198.2
4-80.03432.56197.6
8-100.01944.59198.3
10-150.01845.57193.7
15-170.01643.89193.2
170.01540.34132.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å19.64 Å
Translation2.5 Å19.64 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: 1SQK

1sqk


Resolution: 2.5→19.64 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.888 / Occupancy max: 1 / Occupancy min: 1 / SU B: 19.18 / SU ML: 0.194 / SU R Cruickshank DPI: 0.1256 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23974 1521 5.1 %RANDOM
Rwork0.20403 ---
obs0.20598 28380 97.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.722 Å2
Baniso -1Baniso -2Baniso -3
1--2.28 Å20 Å2-1.05 Å2
2---17.24 Å20 Å2
3---19.52 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5922 0 64 0 5986
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0226112
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4211.9798286
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1325750
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.65924.275262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.898151062
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2471534
X-RAY DIFFRACTIONr_chiral_restr0.0870.2922
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214540
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6891.53762
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.29226084
X-RAY DIFFRACTIONr_scbond_it1.76432350
X-RAY DIFFRACTIONr_scangle_it2.8674.52202
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1428tight positional0.270.05
22B84tight positional0.080.05
11A1398medium positional0.480.5
22B83medium positional0.210.5
11A1428tight thermal0.850.5
22B84tight thermal0.10.5
11A1398medium thermal1.242
22B83medium thermal0.12
LS refinement shellResolution: 2.498→2.562 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 84 -
Rwork0.207 2007 -
obs--94.32 %
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)
10.3971-0.2321-0.00810.69640.40430.46720.04040.08060.0325-0.0477-0.0105-0.00870.0258-0.015-0.02990.0690.0009-0.05460.0270.01420.0448-10.90533.661-10.9582
20.34670.2433-0.02060.73730.16320.39230.0669-0.0585-0.0190.0572-0.0183-0.0364-0.02090.0078-0.04860.0595-0.0127-0.03820.01090.00380.0317-10.8977-33.6113-53.2896
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 371
2X-RAY DIFFRACTION1A501 - 502
3X-RAY DIFFRACTION1B12 - 32
4X-RAY DIFFRACTION2C6 - 371
5X-RAY DIFFRACTION2C501 - 502
6X-RAY DIFFRACTION2D12 - 32

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