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- PDB-6yp9: Rabbit muscle actin in complex with ADF-H and ATP-ATTO-488 -

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Basic information

Entry
Database: PDB / ID: 6yp9
TitleRabbit muscle actin in complex with ADF-H and ATP-ATTO-488
Components
  • Actin, alpha skeletal muscle
  • Twinfilin-1
KeywordsPROTEIN BINDING / actin / ADF-H domain / ATP-ATTO-488
Function / homology
Function and homology information


regulation of actin phosphorylation / RHOBTB2 GTPase cycle / sequestering of actin monomers / negative regulation of actin filament polymerization / actin filament depolymerization / barbed-end actin filament capping / regulation of lamellipodium assembly / cytoskeletal motor activator activity / myofibril / tropomyosin binding ...regulation of actin phosphorylation / RHOBTB2 GTPase cycle / sequestering of actin monomers / negative regulation of actin filament polymerization / actin filament depolymerization / barbed-end actin filament capping / regulation of lamellipodium assembly / cytoskeletal motor activator activity / myofibril / tropomyosin binding / mesenchyme migration / positive regulation of cardiac muscle hypertrophy / 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 / phosphatidylinositol-4,5-bisphosphate binding / actin filament polymerization / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / positive regulation of neuron projection development / calcium-dependent protein binding / cell-cell junction / actin filament binding / actin cytoskeleton / lamellipodium / cell body / protein tyrosine kinase activity / hydrolase activity / protein domain specific binding / calcium ion binding / protein-containing complex binding / positive regulation of gene expression / perinuclear region of cytoplasm / magnesium ion binding / ATP binding / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Twinfilin / Actin-depolymerising factor homology domain / Cofilin/tropomyosin-type actin-binding protein / ADF-H domain profile. / Actin depolymerisation factor/cofilin -like domains / ADF-H/Gelsolin-like domain superfamily / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site ...Twinfilin / Actin-depolymerising factor homology domain / Cofilin/tropomyosin-type actin-binding protein / ADF-H domain profile. / Actin depolymerisation factor/cofilin -like domains / ADF-H/Gelsolin-like domain superfamily / 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
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Actin, alpha skeletal muscle / Twinfilin-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Oryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.564 Å
AuthorsKogan, K. / Kotila, T. / Lappalainen, P.
Funding support Finland, 1items
OrganizationGrant numberCountry
Academy of Finland320161 Finland
CitationJournal: Nat Commun / Year: 2021
Title: A functional family of fluorescent nucleotide analogues to investigate actin dynamics and energetics.
Authors: Colombo, J. / Antkowiak, A. / Kogan, K. / Kotila, T. / Elliott, J. / Guillotin, A. / Lappalainen, P. / Michelot, A.
History
DepositionApr 15, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Actin, alpha skeletal muscle
B: Twinfilin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8634
Polymers58,3152
Non-polymers5472
Water4,414245
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Both proteins elute as a single peak.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-27 kcal/mol
Surface area20830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.552, 69.017, 147.948
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 41875.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P68135
#2: Protein Twinfilin-1 / Protein A6


Mass: 16439.744 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Twf1, Ptk9 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q91YR1
#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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.21 Å3/Da / Density % sol: 38.3 % / Description: Rod-like crystals
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1 M sodium cacodylate (pH 6.0) and 15% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.564→62.546 Å / Num. obs: 17247 / % possible obs: 99.8 % / Redundancy: 6 % / Biso Wilson estimate: 38.87 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.065 / Rrim(I) all: 0.161 / Net I/σ(I): 10.3
Reflection shellResolution: 2.564→2.608 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.885 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 822 / CC1/2: 0.701 / Rpim(I) all: 0.39 / Rrim(I) all: 0.969 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (6-FEB-2020)refinement
XDSBUILT=20200131 (Jan 31, 2020)data reduction
Aimless0.7.4data scaling
PHASER2.5.6phasing
autoPROC1.0.5 (20200206)data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DAW

3daw


Resolution: 2.564→62.55 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.889 / SU R Cruickshank DPI: 2.276 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.299 / SU Rfree Cruickshank DPI: 0.293
RfactorNum. reflection% reflectionSelection details
Rfree0.2299 867 -RANDOM
Rwork0.1739 ---
obs0.1767 17247 99.8 %-
Displacement parametersBiso mean: 41.97 Å2
Baniso -1Baniso -2Baniso -3
1-9.886 Å20 Å20 Å2
2---5.3291 Å20 Å2
3----4.557 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 2.564→62.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3983 0 32 245 4260
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0084112HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.985577HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1445SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes709HARMONIC5
X-RAY DIFFRACTIONt_it4112HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion552SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3672SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.1
X-RAY DIFFRACTIONt_other_torsion18.51
LS refinement shellResolution: 2.564→2.58 Å
RfactorNum. reflection% reflection
Rfree0.2839 20 -
Rwork0.1813 --
obs--99.75 %

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