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- PDB-3u8x: Crystal Structure of a chimera containing the N-terminal domain (... -

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Basic information

Entry
Database: PDB / ID: 3u8x
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
Components
  • Actin, alpha skeletal muscle
  • Thymosin beta-4
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 / sequestering of actin monomers / cellular response to glucocorticoid stimulus / cytoskeletal motor activator activity / positive regulation of wound healing / tropomyosin binding / mesenchyme migration / troponin I binding ...larval central nervous system remodeling / positive regulation of neutrophil migration / negative regulation of neutrophil chemotaxis / sequestering of actin monomers / cellular response to glucocorticoid stimulus / cytoskeletal motor activator activity / positive regulation of wound healing / 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 / regulation of cell migration / protein sequestering activity / 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 / 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. / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / Actins signature 1. / Actin, conserved site ...Thymosin beta-4 family signature. / 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'-TRIPHOSPHATE / Ciboulot, isoform A / Thymosin beta-4 / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Bos taurus (cattle)
Oryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 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
DepositionOct 17, 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 / 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 / _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

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Assembly

Deposited unit
A: Actin, alpha skeletal muscle
B: Thymosin beta-4
C: Actin, alpha skeletal muscle
D: Thymosin beta-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,7668
Polymers95,7034
Non-polymers1,0634
Water00
1
A: Actin, alpha skeletal muscle
B: Thymosin beta-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3834
Polymers47,8512
Non-polymers5312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-23 kcal/mol
Surface area17350 Å2
MethodPISA
2
C: Actin, alpha skeletal muscle
D: Thymosin beta-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3834
Polymers47,8512
Non-polymers5312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-23 kcal/mol
Surface area17230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.011, 75.326, 128.866
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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) Oryctolagus cuniculus (rabbit) / References: UniProt: P68135
#2: Protein Thymosin beta-4 / T beta-4 / Hematopoietic system regulatory peptide / Seraspenide


Mass: 5988.682 Da / Num. of mol.: 2
Fragment: UNP O97428 residues 8-29, UNP P62326 residues 18-44
Source method: isolated from a genetically manipulated source
Details: chimeric protein containing the N-terminal domain (residues 8-29) of drosophila Ciboulot and the C-terminal domain (residues 17-44) of bovine Thymosin-beta4
Source: (gene. exp.) Drosophila melanogaster (fruit fly), (gene. exp.) Bos taurus (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: 47.29 %
Crystal growTemperature: 298 K / Method: hanging drop / pH: 6.5
Details: 20% 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: ID29 / Wavelength: 0.97903 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 6, 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, L10.5
11-h,-k,l20.5
ReflectionResolution: 2→20 Å / Num. obs: 59601 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 25.299 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 17.06
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2-2.010.4454.23478179088.1
2.01-2.020.4026.79742383697.5
2.02-2.030.3687.53726479698.8
2.03-2.040.3487.6747083198.5
2.04-2.050.3437.59741483698
2.05-2.060.337.83690677696.9
2.06-2.080.3128.1913549152098.6
2.08-2.10.2968.5113333151998.3
2.1-2.150.2569.7431268342298.5
2.15-2.20.2399.9428636319898.7
2.2-2.30.19811.7151119559699.4
2.3-2.40.16713.3943191467299.4
2.4-40.09320.352574302722899.9
4-60.06727.8448506534599.8
6-80.05528.2812257131999.9
8-100.05627.88397747599.4
10-120.05525.951556213100
12-150.05524.998214698.6
150.05520.514218353.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å19.63 Å
Translation2.5 Å19.63 Å

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Processing

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

1sqk


Resolution: 2→19.7 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.89 / WRfactor Rfree: 0.2432 / WRfactor Rwork: 0.1909 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8078 / SU B: 4.244 / SU ML: 0.097 / SU R Cruickshank DPI: 0.0361 / SU Rfree: 0.0344 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2382 4162 7.2 %RANDOM
Rwork0.1861 ---
obs0.19 58181 98.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 50.17 Å2 / Biso mean: 24.38 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å20 Å21.78 Å2
2---14.4 Å20 Å2
3---13.63 Å2
Refinement stepCycle: LAST / Resolution: 2→19.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5926 0 64 0 5990
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0226118
X-RAY DIFFRACTIONr_angle_refined_deg2.2761.9788298
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6865750
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.1824.361266
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.418151058
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.331534
X-RAY DIFFRACTIONr_chiral_restr0.1470.2922
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214564
X-RAY DIFFRACTIONr_mcbond_it1.1311.53764
X-RAY DIFFRACTIONr_mcangle_it1.83926088
X-RAY DIFFRACTIONr_scbond_it3.26732354
X-RAY DIFFRACTIONr_scangle_it4.6234.52210
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1428TIGHT POSITIONAL0.210.05
1A1398MEDIUM POSITIONAL0.410.5
1A1428TIGHT THERMAL1.670.5
1A1398MEDIUM THERMAL2.012
2B84TIGHT POSITIONAL0.360.05
2B86MEDIUM POSITIONAL1.010.5
2B84TIGHT THERMAL1.970.5
2B86MEDIUM THERMAL2.972
LS refinement shellResolution: 2.003→2.054 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 270 -
Rwork0.184 3772 -
all-4042 -
obs--94.22 %
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)
10.6075-0.2332-0.11440.92230.53940.36620.04880.0933-0.0061-0.1078-0.0134-0.0633-0.0675-0.0136-0.03540.04050.0087-0.00180.10520.00230.008210.83714.631352.969
21.3406-1.15030.95581.80250.69233.4883-0.382-0.23010.30530.20410.3187-0.3565-0.52450.04850.06330.13820.0447-0.06360.0816-0.05290.192430.4724-4.874760.1723
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 371
2X-RAY DIFFRACTION1A501 - 502
3X-RAY DIFFRACTION2B12 - 32

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